5,377 Matching Annotations
  1. Jun 2025
    1. Author Response:

      The following is the authors’ response to the previous reviews.

      We carefully read through the second-round reviews and the additional reviews. To us, the review process is somewhat unusual and very much dominated by referee 2, who aggressively insists that we mixed up the trigeminal nucleus and inferior olive and that as a consequence our results are meaningless. We think the stance of referee 2 and the focus on one single issue (the alleged mix-up of trigeminal nucleus and inferior olive) is somewhat unfortunate, leaves out much of our findings and we debated at length on how to deal with further revisions. In the end, we decided to again give priority to addressing the criticism of referees 2, because it is hard to go on with a heavily attacked paper without resolving the matter at stake. The following is a summary of, what we did:

      Additional experimental work:

      (1) We checked if the peripherin-antibody indeed reliably identifies climbing fibers.

      To this end, we sectioned the elephant cerebellum and stained sections with the peripherin-antibody. We find: (i) the cerebellar white matter is strongly reactive for peripherin-antibodies, (ii) cerebellar peripherin-antibody staining of has an axonal appearance. (iii) Cerebellar Purkinje cell somata appear to be ensheated by peripherin-antibody staining. (iv) We observed that the peripherin-antibody reactivity gradually decreases from Purkinje cell somata to the pia in the cerebellar molecular layer. This work is shown in our revised Figure 2. All these four features align with the distribution of climbing fibers (which arrive through the white matter, are axons, ensheat Purkinje cell somata, and innervate Purkinje cell proximally not reaching the pia). In line with previous work, which showed similar cerebellar staining patterns in several species (Errante et al. 1998), we conclude that elephant climbing fibers are strongly reactive for peripherin-antibodies.

      (2) We delineated the elephant olivo-cerebellar tract.

      The strong peripherin-antibody reactivity of elephant climbing fibers enabled us to delineate the elephant olivo-cerebellar tract. We find the elephant olivo-cerebellar tract is a strongly peripherin-antibody reactive, well-delineated fiber tract several millimeters wide and about a centimeter in height. The unstained olivo-cerebellar tract has a greyish appearance. In the anterior regions of the olivo-cerebellar tract, we find that peripherin-antibody reactive fibers run in the dorsolateral brainstem and approach the cerebellar peduncle, where the tract gradually diminishes in size, presumably because climbing fibers discharge into the peduncle. Indeed, peripherin-antibody reactive fibers can be seen entering the cerebellar peduncle. Towards the posterior end of the peduncle, the olivo-cerebellar disappears (in the dorsal brainstem directly below the peduncle. We note that the olivo-cerebellar tract was referred to as the spinal trigeminal tract by Maseko et al. 2013. We think the tract in question cannot be the spinal trigeminal tract for two reasons: (i) This tract is the sole brainstem source of peripherin-positive climbing fibers entering the peduncle/ the cerebellum; this is the defining characteristic of the olivo-cerebellar tract. (ii) The tract in question is much smaller than the trigeminal nerve, disappears posterior to where the trigeminal nerve enters the brainstem (see below), and has no continuity with the trigeminal nerve; the continuity with the trigeminal nerve is the defining characteristic of the spinal trigeminal tract, however.

      The anterior regions of the elephant olivo-cerebellar tract are similar to the anterior regions of olivo-cerebellar tract of other mammals in its dorsolateral position and the relation to the cerebellar peduncle. In its more posterior parts, the elephant olivo-cerebellar tract continues for a long distance (~1.5 cm) in roughly the same dorsolateral position and enters the serrated nucleus that we previously identified as the elephant inferior olive. The more posterior parts of the elephant olivo-cerebellar tract therefore differ from the more posterior parts of the olivo-cerebellar tract of other mammals, which follows a ventromedial trajectory towards a ventromedially situated inferior olive. The implication of our delineation of the elephant olivo-cerebellar tract is that we correctly identified the elephant inferior olive.

      (3) An in-depth analysis of peripherin-antibody reactivity also indicates that the trigeminal nucleus receives no climbing fiber input.

      We also studied the peripherin-antibody reactivity in and around the trigeminal nucleus. We had also noted in the previous submission that the trigeminal nucleus is weakly positive for peripherin, but that the staining pattern is uniform and not the type of axon bundle pattern that is seen in the inferior olive of other mammals. To us, this observation already argued against the presence of climbing fibers in the trigeminal nucleus. We also noted that the myelin stripes of the trigeminal nucleus were peripherin-antibody-negative. In the context of our olivo-cerebellar tract tracing we now also scrutinized the surroundings of the trigeminal nucleus for peripherin-antibody reactivity. We find that the ventral brainstem surrounding the trigeminal nucleus is devoid of peripherin-antibody reactivity. Accordingly, no climbing fibers, (which we have shown to be strongly peripherin-antibody-positive, see our point 1) arrive at the trigeminal nucleus. The absence of climbing fiber input indicates that previous work that identified the (trigeminal) nucleus as the inferior olive (Maseko et al 2013) is unlikely to be correct.

      (4) We characterized the entry of the trigeminal nerve into the elephant brain.

      To better understand how trigeminal information enters the elephant’s brain, we characterized the entry of the trigeminal nerve. This analysis indicated to us that the trigeminal nerve is not continuous with the olivo-cerebellar tract (the spinal trigeminal tract of Maseko et al. 2013) as previously claimed by Maseko et al. 2013. We show some of this evidence in Referee-Figure 1 below. The reason we think the trigeminal nerve is discontinuous with the olivo-cerebellar tract is the size discrepancy between the two structures. We first show this for the tracing data of Maseko et al. 2013. In the Maseko et al. 2013 data the trigeminal nerve (Referee-Figure 1A, their plate Y) has 3-4 times the diameter of the olivocerebellar tract (the alleged spinal trigeminal tract, Referee-Figure 1B, their plate Z). Note that most if not all trigeminal fibers are thought to continue from the nerve into the trigeminal tract (see our rat data below). We plotted the diameter of the trigeminal nerve and diameter of the olivo-cerebellar (the spinal trigeminal tract according to Maseko et al. 2013) from the Maseko et al. 2013 data (Referee-Figure 1C) and we found that the olivocerebellar tract has a fairly consistent diameter (46 ± 9 mm2, mean ± SD). Statistical considerations and anatomical evidence suggest that the tracing of the trigeminal nerve into the olivo-cerebellar (the spinal trigeminal tract according to Maseko et al. 2013) is almost certainly wrong. The most anterior point of the alleged spinal trigeminal tract has a diameter of 51 mm2 which is more than 15 standard deviations different from the most posterior diameter (194 mm2) of the trigeminal tract. For this assignment to be correct three-quarters of trigeminal nerve fibers would have to spontaneously disappear, something that does not happen in the brain. We also made similar observations in the African elephant Bibi, where the trigeminal nerve (Referee-Figure 1D) is much larger in diameter than the olivocerebellar tract (Referee-Figure 1E). We could also show that the olivocerebellar tract disappears into the peduncle posterior to where the trigeminal nerve enters (Referee-Figure 1F). Our data are very similar to Maseko et al. indicating that their outlining of structures was done correctly. What appears to have been oversimplified, is the assignment of structures as continuous. We also quantified the diameter of the trigeminal nerve and the spinal trigeminal tract in rats (from the Paxinos & Watson atlas; Referee-Figure 1D); as expected we found the trigeminal nerve and spinal trigeminal tract diameters are essentially continuous.

      In our hands, the trigeminal nerve does not continue into a well-defined tract that could be traced after its entry. In this regard, it differs both from the olivo-cerebellar tract of the elephant or the spinal trigeminal tract of the rodent, both of which are well delineated. We think the absence of a well-delineated spinal trigeminal tract in elephants might have contributed to the putative tracing error highlighted in our Referee-Figure 1A-C.

      We conclude that a size mismatch indicates trigeminal fibers do not run in the olivo-cerebellar tract (the spinal trigeminal tract according to Maseko et al. 2013).

      Author response image 1.

      The trigeminal nerve is discontinuous with the olivo-cerebellar tract (the spinal trigeminal tract according to Maseko et al. 2013). A, Trigeminal nerve (orange) in the brain of African elephant LAX as delineated by Maseko et al. 2013 (coronal section; their plate Y). B, Most anterior appearance of the spinal trigeminal tract of Maseko et al. 2013 (blue; coronal section; their plate Z). Note the much smaller diameter of the spinal trigeminal tract compared to the trigeminal nerve shown in C, which argues against the continuity of the two structures. Indeed, our peripherin-antibody staining showed that the spinal trigeminal tract of Maseko corresponds to the olivo-cerebellar tract and is discontinuous with the trigeminal nerve. C, Plot of the trigeminal nerve and olivo-cerebellar tracts (the spinal trigeminal tract according to Maseko et al. 2013) diameter along the anterior-posterior axis. The trigeminal nerve is much larger in diameter than the olivocerebellar tract (the spinal trigeminal tract according to Maseko et al. 2013). C, D measurements, for which sections are shown in panels C and D respectively. The olivocerebellar tract (the spinal trigeminal tract according to Maseko et al. 2013) has a consistent diameter; data replotted from Maseko et al. 2013. At mm 25 the inferior olive appears. D, Trigeminal nerve entry in the brain of African elephant Bibi; our data, coronal section, the trigeminal nerve is outlined in orange, note the large diameter. E, Most anterior appearance of the olivo-cerebellar tract in the brain of African elephant Bibi; our data, coronal section, approximately 3 mm posterior to the section shown in A, the olivocerebellar tract is outlined in blue. Note the smaller diameter of the olivo-cerebellar tract compared to the trigeminal nerve, which argues against the continuity of the two structures. F, Plot of the trigeminal nerve and olivo-cerebellar tract diameter along the anterior-posterior axis. The nerve and olivo-cerebellar tract are discontinuous and the trigeminal nerve is much larger in diameter than the olivocerebellar tract (the spinal trigeminal tract according to Maseko et al. 2013); our data. D, E measurements, for which sections are shown in panels D and E respectively. At mm 27 the inferior olive appears. G, In the rat the trigeminal nerve is continuous in size with the spinal trigeminal tract. Data replotted from Paxinos and Watson.

      Reviewer 2 (Public Review):

      As indicated in my previous review of this manuscript (see above), it is my opinion that the authors have misidentified, and indeed switched, the inferior olivary nuclear complex (IO) and the trigeminal nuclear complex (Vsens). It is this specific point only that I will address in this second review, as this is the crucial aspect of this paper - if the identification of these nuclear complexes in the elephant brainstem by the authors is incorrect, the remainder of the paper does not have any scientific validity.

      Comment: We agree with the referee that it is most important to sort out, the inferior olivary nuclear complex (IO) and the trigeminal nuclear complex, respectively.Change: We did additional experimental work to resolve this matter as detailed at the beginning of our response. Specifically, we ascertained that elephant climbing fibers are strongly peripherin-positive. Based on elephant climbing fiber peripherin-reactivity we delineated the elephant olivo-cerebellar tract. We find that the olivo-cerebellar connects to the structure we refer to as inferior olive to the cerebellum (the referee refers to this structure as the trigeminal nuclear complex). We also found that the trigeminal nucleus (the structure the referee refers to as inferior olive) appears to receive no climbing fibers. We provide indications that the tracing of the trigeminal nerve into the olivo-cerebellar tract by Maseko et al. 2023 was erroneous (Author response image 1). These novel findings support our ideas but are very difficult to reconcile with the referee’s partitioning scheme.

      The authors, in their response to my initial review, claim that I "bend" the comparative evidence against them. They further claim that as all other mammalian species exhibit a "serrated" appearance of the inferior olive, and as the elephant does not exhibit this appearance, that what was previously identified as the inferior olive is actually the trigeminal nucleus and vice versa. 

      For convenience, I will refer to IOM and VsensM as the identification of these structures according to Maseko et al (2013) and other authors and will use IOR and VsensR to refer to the identification forwarded in the study under review. <br /> The IOM/VsensR certainly does not have a serrated appearance in elephants. Indeed, from the plates supplied by the authors in response (Referee Fig. 2), the cytochrome oxidase image supplied and the image from Maseko et al (2013) shows a very similar appearance. There is no doubt that the authors are identifying structures that closely correspond to those provided by Maseko et al (2013). It is solely a contrast in what these nuclear complexes are called and the functional sequelae of the identification of these complexes (are they related to the trunk sensation or movement controlled by the cerebellum?) that is under debate.

      Elephants are part of the Afrotheria, thus the most relevant comparative data to resolve this issue will be the identification of these nuclei in other Afrotherian species. Below I provide images of these nuclear complexes, labelled in the standard nomenclature, across several Afrotherian species. 

      (A) Lesser hedgehog tenrec (Echinops telfairi) 

      Tenrecs brains are the most intensively studied of the Afrotherian brains, these extensive neuroanatomical studies undertaken primarily by Heinz Künzle. Below I append images (coronal sections stained with cresol violet) of the IO and Vsens (labelled in the standard mammalian manner) in the lesser hedgehog tenrec. It should be clear that the inferior olive is located in the ventral midline of the rostral medulla oblongata (just like the rat) and that this nucleus is not distinctly serrated. The Vsens is located in the lateral aspect of the medulla skirted laterally by the spinal trigeminal tract (Sp5). These images and the labels indicating structures correlate precisely with that provide by Künzle (1997, 10.1016, see his Figure 1K,L. Thus, in the first case of a related species, there is no serrated appearance of the inferior olive, the location of the inferior olive is confirmed through connectivity with the superior colliculus (a standard connection in mammals) by Künzle (1997), and the location of Vsens is what is considered to be typical for mammals. This is in agreement with the authors, as they propose that ONLY the elephants show the variations they report. 

      (B) Giant otter shrew (Potomogale velox) 

      The otter shrews are close relatives of the Tenrecs. Below I append images of cresyl violet (left column) and myelin (right column) stained coronal sections through the brainstem with the IO, Vsens and Sp5 labelled as per standard mammalian anatomy. Here we see hints of the serration of the IO as defined by the authors, but we also see many myelin stripes across the IO. Vsens is located laterally and skirted by the Sp5. This is in agreement with the authors, as they propose that ONLY the elephants show the variations they report.

      (C) Four-toed sengi (Petrodromus tetradactylus) 

      The sengis are close relatives of the Tenrecs and otter shrews, these three groups being part of the Afroinsectiphilia, a distinct branch of the Afrotheria. Below I append images of cresyl violet (left column) and myelin (right column) stained coronal sections through the brainstem with the IO, Vsens and Sp5 labelled as per standard mammalian anatomy. Here we see vague hints of the serration of the IO (as defined by the authors), and we also see many myelin stripes across the IO. Vsens is located laterally and skirted by the Sp5. This is in agreement with the authors, as they propose that ONLY the elephants show the variations they report. 

      (D) Rock hyrax (Procavia capensis) 

      The hyraxes, along with the sirens and elephants form the Paenungulata branch of the Afrotheria. Below I append images of cresyl violet (left column) and myelin (right column) stained coronal sections through the brainstem with the IO, Vsens and Sp5 labelled as per the standard mammalian anatomy. Here we see hints of the serration of the IO (as defined by the authors), but we also see evidence of a more "bulbous" appearance of subnuclei of the IO (particularly the principal nucleus), and we also see many myelin stripes across the IO. Vsens is located laterally and skirted by the Sp5. This is in agreement with the authors, as they propose that ONLY the elephants show the variations they report. 

      (E) West Indian manatee (Trichechus manatus) 

      The sirens are the closest extant relatives of the elephants in the Afrotheria. Below I append images of cresyl violet (top) and myelin (bottom) stained coronal sections (taken from the University of Wisconsin-Madison Brain Collection, https://brainmuseum.org, and while quite low in magnification they do reveal the structures under debate) through the brainstem with the IO, Vsens and Sp5 labelled as per standard mammalian anatomy. Here we see the serration of the IO (as defined by the authors). Vsens is located laterally and skirted by the Sp5. This is in agreement with the authors, as they propose that ONLY the elephants show the variations they report.

      These comparisons and the structural identification, with which the authors agree as they only distinguish the elephants from the other Afrotheria, demonstrate that the appearance of the IO can be quite variable across mammalian species, including those with a close phylogenetic affinity to the elephants. Not all mammal species possess a "serrated" appearance of the IO. Thus, it is more than just theoretically possible that the IO of the elephant appears as described prior to this study. 

      So what about elephants? Below I append a series of images from coronal sections through the African elephant brainstem stained for Nissl, myelin, and immunostained for calretinin. These sections are labelled according to standard mammalian nomenclature. In these complete sections of the elephant brainstem, we do not see a serrated appearance of the IOM (as described previously and in the current study by the authors). Rather the principal nucleus of the IOM appears to be bulbous in nature. In the current study, no image of myelin staining in the IOM/VsensR is provided by the authors. However, in the images I provide, we do see the reported myelin stripes in all stains - agreement between the authors and reviewer on this point. The higher magnification image to the bottom left of the plate shows one of the IOM/VsensR myelin stripes immunostained for calretinin, and within the myelin stripes axons immunopositive for calretinin are seen (labelled with an arrow). The climbing fibres of the elephant cerebellar cortex are similarly calretinin immunopositive (10.1159/000345565). In contrast, although not shown at high magnification, the fibres forming the Sp5 in the elephant (in the Maseko description, unnamed in the description of the authors) show no immunoreactivity to calretinin. 

      Comment: We appreciate the referee’s additional comments. We concede the possibility that some relatives of elephants have a less serrated inferior olive than most other mammals. We maintain, however, that the elephant inferior olive (our Figure 1J) has the serrated appearance seen in the vast majority of mammals.

      Change: None.

      Peripherin Immunostaining 

      In their revised manuscript the authors present immunostaining of peripherin in the elephant brainstem. This is an important addition (although it does replace the only staining of myelin provided by the authors which is unusual as the word myelin is in the title of the paper) as peripherin is known to specifically label peripheral nerves. In addition, as pointed out by the authors, peripherin also immunostains climbing fibres (Errante et al., 1998). The understanding of this staining is important in determining the identification of the IO and Vsens in the elephant, although it is not ideal for this task as there is some ambiguity. Errante and colleagues (1998; Fig. 1) show that climbing fibres are peripherin-immunopositive in the rat. But what the authors do not evaluate is the extensive peripherin staining in the rat Sp5 in the same paper (Errante et al, 1998, Fig. 2). The image provided by the authors of their peripherin immunostaining (their new Figure 2) shows what I would call the Sp5 of the elephant to be strongly peripherin immunoreactive, just like the rat shown in Errant et al (1998), and more over in the precise position of the rat Sp5! This makes sense as this is where the axons subserving the "extraordinary" tactile sensitivity of the elephant trunk would be found (in the standard model of mammalian brainstem anatomy). Interestingly, the peripherin immunostaining in the elephant is clearly lamellated...this coincides precisely with the description of the trigeminal sensory nuclei in the elephant by Maskeo et al (2013) as pointed out by the authors in their rebuttal. Errante et al (1998) also point out peripherin immunostaining in the inferior olive, but according to the authors this is only "weakly present" in the elephant IOM/VsensR. This latter point is crucial. Surely if the elephant has an extraordinary sensory innervation from the trunk, with 400 000 axons entering the brain, the VsensR/IOM should be highly peripherin-immunopositive, including the myelinated axon bundles?! In this sense, the authors argue against their own interpretation - either the elephant trunk is not a highly sensitive tactile organ, or the VsensR is not the trigeminal nuclei it is supposed to be. 

      Comment: We made sure that elephant climbing fibers are strongly peripherin-positive (our revised Figure 2). As we noted in already our previous ms, we see weak diffuse peripherin-reactivity in the trigeminal nucleus (the inferior olive according to the referee), but no peripherin-reactive axon bundles (i.e. climbing fibers) that are seen in the inferior olive of other species. We also see no peripherin-reactive axon bundles (i.e. the olivo-cerebellar tract) arriving in the trigeminal nucleus as the tissue surrounding the trigeminal nucleus is devoid of peripherin-reactivity. Again, this finding is incompatible with the referee’s ideas. As far as we can tell, the trigeminal fibers are not reactive for peripherin in the elephant, i.e. we did not observe peripherin-reactivity very close to the nerve entry, but unfortunately, we did not stain for peripherin-reactivity into the nerve. As the referee alludes to the absence of peripherin-reactivity in the trigeminal tract is a difference between rodents and elephants.

      Change: Our novel Figure 2.

      Summary: 

      (1) Comparative data of species closely related to elephants (Afrotherians) demonstrates that not all mammals exhibit the "serrated" appearance of the principal nucleus of the inferior olive. 

      (2) The location of the IO and Vsens as reported in the current study (IOR and VsensR) would require a significant, and unprecedented, rearrangement of the brainstem in the elephants independently. I argue that the underlying molecular and genetic changes required to achieve this would be so extreme that it would lead to lethal phenotypes. Arguing that the "switcheroo" of the IO and Vsens does occur in the elephant (and no other mammals) and thus doesn't lead to lethal phenotypes is a circular argument that cannot be substantiated. 

      (3) Myelin stripes in the subnuclei of the inferior olivary nuclear complex are seen across all related mammals as shown above. Thus, the observation made in the elephant by the authors in what they call the VsensR, is similar to that seen in the IO of related mammals, especially when the IO takes on a more bulbous appearance. These myelin stripes are the origin of the olivocerebellar pathway, and are indeed calretinin immunopositive in the elephant as I show. 

      (4) What the authors see aligns perfectly with what has been described previously, the only difference being the names that nuclear complexes are being called. But identifying these nuclei is important, as any functional sequelae, as extensively discussed by the authors, is entirely dependent upon accurately identifying these nuclei. 

      (4) The peripherin immunostaining scores an own goal - if peripherin is marking peripheral nerves (as the authors and I believe it is), then why is the VsensR/IOM only "weakly positive" for this stain? This either means that the "extraordinary" tactile sensitivity of the elephant trunk is non-existent, or that the authors have misinterpreted this staining. That there is extensive staining in the fibre pathway dorsal and lateral to the IOR (which I call the spinal trigeminal tract), supports the idea that the authors have misinterpreted their peripherin immunostaining.

      (5) Evolutionary expediency. The authors argue that what they report is an expedient way in which to modify the organisation of the brainstem in the elephant to accommodate the "extraordinary" tactile sensitivity. I disagree. As pointed out in my first review, the elephant cerebellum is very large and comprised of huge numbers of morphologically complex neurons. The inferior olivary nuclei in all mammals studied in detail to date, give rise to the climbing fibres that terminate on the Purkinje cells of the cerebellar cortex. It is more parsimonious to argue that, in alignment with the expansion of the elephant cerebellum (for motor control of the trunk), the inferior olivary nuclei (specifically the principal nucleus) have had additional neurons added to accommodate this cerebellar expansion. Such an addition of neurons to the principal nucleus of the inferior olive could readily lead to the loss of the serrated appearance of the principal nucleus of the inferior olive, and would require far less modifications in the developmental genetic program that forms these nuclei. This type of quantitative change appears to be the primary way in which structures are altered in the mammalian brainstem. 

      Comment: We still disagree with the referee. We note that our conclusions rest on the analysis of 8 elephant brainstems, which we sectioned in three planes and stained with a variety of metabolic and antibody stains and in which assigned two structures (the inferior olive and the trigeminal nucleus). Most of the evidence cited by the referee stems from a single paper, in which 147 structures were identified based on the analysis of a single brainstem sectioned in one plane and stained with a limited set of antibodies. Our synopsis of the evidence is the following.

      (1) We agree with the referee that concerning brainstem position our scheme of a ventromedial trigeminal nucleus and a dorsolateral inferior olive deviates from the usual mammalian position of these nuclei (i.e. a dorsolateral trigeminal nucleus and a ventromedial inferior olive).

      (2) Cytoarchitectonics support our partitioning scheme. The compact cellular appearance of our ventromedial trigeminal nucleus is characteristic of trigeminal nuclei. The serrated appearance of our dorsolateral inferior olive is characteristic of the mammalian inferior olive; we acknowledge that the referee claims exceptions here. To our knowledge, nobody has described a mammalian trigeminal nucleus with a serrated appearance (which would apply to the elephant in case the trigeminal nucleus is situated dorsolaterally).

      (3) Metabolic staining (Cyto-chrome-oxidase reactivity) supports our partitioning scheme. Specifically, our ventromedial trigeminal nucleus shows intense Cyto-chrome-oxidase reactivity as it is seen in the trigeminal nuclei of trigeminal tactile experts.

      (4) Isomorphism. The myelin stripes on our ventromedial trigeminal nucleus are isomorphic to trunk wrinkles. Isomorphism is a characteristic of somatosensory brain structures (barrel, barrelettes, nose-stripes, etc) and we know of no case, where such isomorphism was misleading.

      (5) The large-scale organization of our ventromedial trigeminal nuclei in anterior-posterior repeats is characteristic of the mammalian trigeminal nuclei. To our knowledge, no such organization has ever been reported for the inferior olive.

      (6) Connectivity analysis supports our partitioning scheme. According to our delineation of the elephant olivo-cerebellar tract, our dorsolateral inferior olive is connected via peripherin-positive climbing fibers to the cerebellum. In contrast, our ventromedial trigeminal nucleus (the referee’s inferior olive) is not connected via climbing fibers to the cerebellum.

      Change: As discussed, we advanced further evidence in this revision. Our partitioning scheme (a ventromedial trigeminal nucleus and a dorsolateral inferior olive) is better supported by data and makes more sense than the referee’s suggestion (a dorsolateral trigeminal nucleus and a ventromedial inferior olive). It should be published.

      Reviewer #3 (Public Review):

      Summary: 

      The study claims to investigate trunk representations in elephant trigeminal nuclei located in the brainstem. The researchers identify large protrusions visible from the ventral surface of the brainstem, which they examined using a range of histological methods. However, this ventral location is usually where the inferior olivary complex is found, which challenges the author's assertions about the nucleus under analysis. They find that this brainstem nucleus of elephants contains repeating modules, with a focus on the anterior and largest unit which they define as the putative nucleus principalis trunk module of the trigeminal. The nucleus exhibits low neuron density, with glia outnumbering neurons significantly. The study also utilizes synchrotron X-ray phase contrast tomography to suggest that myelin-stripe-axons traverse this module. The analysis maps myelin-rich stripes in several specimens and concludes that based on their number and patterning that they likely correspond with trunk folds; however this conclusion is not well supported if the nucleus has been misidentified. 

      Comment: The referee provides a summary of our work. The referee also notes that the correct identification of the trigeminal nucleus is critical to the message of our paper.

      Change: In line with these assessments we focused our revision efforts on the issue of trigeminal nucleus identification, please see our introductory comments and our response to Referee 2.

      Strengths: 

      The strength of this research lies in its comprehensive use of various anatomical methods, including Nissl staining, myelin staining, Golgi staining, cytochrome oxidase labeling, and synchrotron X-ray phase contrast tomography. The inclusion of quantitative data on cell numbers and sizes, dendritic orientation and morphology, and blood vessel density across the nucleus adds a quantitative dimension. Furthermore, the research is commendable for its high-quality and abundant images and figures, effectively illustrating the anatomy under investigation.

      Comment: We appreciate this positive assessment.

      Change: None

      Weaknesses: 

      While the research provides potentially valuable insights if revised to focus on the structure that appears to be inferior olivary nucleus, there are certain additional weaknesses that warrant further consideration. First, the suggestion that myelin stripes solely serve to separate sensory or motor modules rather than functioning as an "axonal supply system" lacks substantial support due to the absence of information about the neuronal origins and the termination targets of the axons. Postmortem fixed brain tissue limits the ability to trace full axon projections. While the study acknowledges these limitations, it is important to exercise caution in drawing conclusions about the precise role of myelin stripes without a more comprehensive understanding of their neural connections. 

      Comment: We understand these criticisms and the need for cautious interpretation. As we noted previously, we think that the Elife-publishing scheme, where critical referee commentary is published along with our ms, will make this contribution particularly valuable.

      Change: Our additional efforts to secure the correct identification of the trigeminal nucleus.

      Second, the quantification presented in the study lacks comparison to other species or other relevant variables within the elephant specimens (i.e., whole brain or brainstem volume). The absence of comparative data to different species limits the ability to fully evaluate the significance of the findings. Comparative analyses could provide a broader context for understanding whether the observed features are unique to elephants or more common across species. This limitation in comparative data hinders a more comprehensive assessment of the implications of the research within the broader field of neuroanatomy. Furthermore, the quantitative comparisons between African and Asian elephant specimens should include some measure of overall brain size as a covariate in the analyses. Addressing these weaknesses would enable a richer interpretation of the study's findings. 

      Comment: We understand, why the referee asks for additional comparative data, which would make our study more meaningful. We note that we already published a quantitative comparison of African and Asian elephant facial nuclei (Kaufmann et al. 2022). The quantitative differences between African and Asian elephant facial nuclei are similar in magnitude to what we observed here for the trigeminal nucleus, i.e. African elephants have about 10-15% more facial nucleus neurons than Asian elephants. The referee also notes that data on overall elephant brain size might be important for interpreting our data. We agree with this sentiment and we are preparing a ms on African and Asian elephant brain size. We find – unexpectedly given the larger body size of African elephants – that African elephants have smaller brains than Asian elephants. The finding might imply that African elephants, which have more facial nucleus neurons and more trigeminal nucleus trunk module neurons, are neurally more specialized in trunk control than Asian elephants.

      Change: We are preparing a further ms on African and Asian elephant brain size, a first version of this work has been submitted.

      Reviewer #4 (Public Review): 

      Summary: 

      The authors report a novel isomorphism in which the folds of the elephant trunk are recognizably mapped onto the principal sensory trigeminal nucleus in the brainstem. Further, they identifiy the enlarged nucleus as being situated in this species in an unusual ventral midline position. 

      Comment: The referee summarizes our work.

      Change: None.

      Strengths: 

      The identity of the purported trigeminal nucleus and the isomorphic mapping with the trunk folds is supported by multiple lines of evidence: enhanced staining for cytochrome oxidase, an enzyme associated with high metabolic activity; dense vascularization, consistent with high metabolic activity; prominent myelinated bundles that partition the nucleus in a 1:1 mapping of the cutaneous folds in the trunk periphery; near absence of labeling for the anti-peripherin antibody, specific for climbing fibers, which can be seen as expected in the inferior olive; and a high density of glia.

      Comment: The referee again reviews some of our key findings.

      Change: None. 

      Weaknesses: 

      Despite the supporting evidence listed above, the identification of the gross anatomical bumps, conspicuous in the ventral midline, is problematic. This would be the standard location of the inferior olive, with the principal trigeminal nucleus occupying a more dorsal position. This presents an apparent contradiction which at a minimum needs further discussion. Major species-specific specializations and positional shifts are well-documented for cortical areas, but nuclear layouts in the brainstem have been considered as less malleable. 

      Comment: The referee notes that our discrepancy with referee 2, needs to be addressed with further evidence and discussion, given the unusual position of both inferior olive and trigeminal nucleus in the partitioning scheme and that the mammalian brainstem tends to be positionally conservative. We agree with the referee. We note that – based on the immense size of the elephant trigeminal ganglion (50 g), half the size of a monkey brain – it was expected that the elephant trigeminal nucleus ought to be exceptionally large.

      Change: We did additional experimental work to resolve this matter: (i) We ascertained that elephant climbing fibers are strongly peripherin-positive. (ii) Based on elephant climbing fiber peripherin-reactivity we delineated the elephant olivo-cerebellar tract. We find that the olivo-cerebellar connects to the structure we refer to as inferior olive to the cerebellum. (iii) We also found that the trigeminal nucleus (the structure the referee refers to as inferior olive) appears to receive no climbing fibers. (iv) We provide indications that the tracing of the trigeminal nerve into the olivo-cerebellar tract by Maseko et al. 2023 was erroneous (Referee-Figure 1). These novel findings support our ideas.

      Reviewer #5 (Public Review): 

      After reading the manuscript and the concerns raised by reviewer 2 I see both sides of the argument - the relative location of trigeminal nucleus versus the inferior olive is quite different in elephants (and different from previous studies in elephants), but when there is a large disproportionate magnification of a behaviorally relevant body part at most levels of the nervous system (certainly in the cortex and thalamus), you can get major shifting in location of different structures. In the case of the elephant, it looks like there may be a lot of shifting. Something that is compelling is that the number of modules separated but the myelin bands correspond to the number of trunk folds which is different in the different elephants. This sort of modular division based on body parts is a general principle of mammalian brain organization (demonstrated beautifully for the cuneate and gracile nucleus in primates, VP in most of species, S1 in a variety of mammals such as the star nosed mole and duck-billed platypus). I don't think these relative changes in the brainstem would require major genetic programming - although some surely exists. Rodents and elephants have been independently evolving for over 60 million years so there is a substantial amount of time for changes in each l lineage to occur.

      I agree that the authors have identified the trigeminal nucleus correctly, although comparisons with more out groups would be needed to confirm this (although I'm not suggesting that the authors do this). I also think the new figure (which shows previous divisions of the brainstem versus their own) allows the reader to consider these issues for themselves. When reviewing this paper, I actually took the time to go through atlases of other species and even look at some of my own data from highly derived species. Establishing homology across groups based only on relative location is tough especially when there appears to be large shifts in relative location of structures. My thoughts are that the authors did an extraordinary amount of work on obtaining, processing and analyzing this extremely valuable tissue. They document their work with images of the tissue and their arguments for their divisions are solid. I feel that they have earned the right to speculate - with qualifications - which they provide. 

      Comment: The referee summarizes our work and appears to be convinced by the line of our arguments. We are most grateful for this assessment. We add, again, that the skeptical assessment of referee 2 will be published as well and will give the interested reader the possibility to view another perspective on our work.

      Change: None. 

      Recommendations for the authors: 

      Reviewer #1 (Recommendations For The Authors):

      With this manuscript being virtually identical to the previous version, it is possible that some of the definitive conclusions about having identified the elephant trigeminal nucleus and trunk representation should be moderated in a more nuanced manner, especially given the careful and experienced perspective from reviewers with first hand knowledge elephant neuroanatomy.

      Comment: We agree that both our first and second revisions were very much centered on the debate of the correct identification of the trigeminal nucleus and that our ms did not evolve as much in other regards. This being said we agree with Referee 2 that we needed to have this debate. We also think we advanced important novel data in this context (the delineation of elephant olivo-cerebellar tract through the peripherin-antibody).

      Changes: Our revised Figure 2. 

      The peripherin staining adds another level of argument to the authors having identified the trigeminal brainstem instead of the inferior olive, if differential expression of peripherin is strong enough to distinguish one structure from the other.

      Comment: We think we showed too little peripherin-antibody staining in our previous revision. We have now addressed this problem.

      Changes: Our revised Figure 2, i.e. the delineation of elephant olivo-cerebellar tract through the peripherin-antibody).

      There are some minor corrections to be made with the addition of Fig. 2., including renumbering the figures in the manuscript (e.g., 406, 521). 

      I continue to appreciate this novel investigation of the elephant brainstem and find it an interesting and thorough study, with the use of classical and modern neuroanatomical methods.

      Comment: We are thankful for this positive assessment.

      Reviewer #2 (Recommendations For The Authors):

      I do realise the authors are very unhappy with me and the reviews I have submitted. I do apologise if feelings have been hurt, and I do understand the authors put in a lot of hard work and thought to develop what they have; however, it is unfortunate that the work and thoughts are not correct. Science is about the search for the truth and sometimes we get it wrong. This is part of the scientific process and why most journals adhere to strict review processes of scientific manuscripts. As I said previously, the authors can use their data to write a paper describing and quantifying Golgi staining of neurons in the principal olivary nucleus of the elephant that should be published in a specialised journal and contextualised in terms of the motor control of the trunk and the large cerebellum of the elephant. 

      Comment: We appreciate the referee’s kind words. Also, no hard feelings from our side, this is just a scientific debate. In our experience, neuroanatomical debates are resolved by evidence and we note that we provide evidence strengthening our identification of the trigeminal nucleus and inferior olive. As far as we can tell from this effort and the substantial evidence accumulated, the referee is wrong.

      Reviewer #4 (Recommendations For The Authors):

      As a new reviewer, I have benefited from reading the previous reviews and Author response, even while having several new comments to add. 

      (1) The identification of the inferior olive and trigeminal nuclei is obviously center stage. An enlargement of the trigeminal nuclei is not necessarily problematic, given the published reports on the dramatic enlargement of the trigeminal nerve (Purkart et al., 2022). At issue is the conspicuous relocation of the trigeminal nuclei that is being promoted by Reveyaz et al. Conspicuous rearrangements are not uncommon; for example, primary sensory cortical fields in different species (fig. 1 in H.H.A. Oelschlager for dolphins; S. De Vreese et al. (2023) for cetaceans, L. Krubitzer on various species, in the context of evolution). The difficult point here concerns what looks like a rather conspicuous gross anatomical rearrangement, in BRAINSTEM - the assumption being that the brainstem bauplan is going to be specifically conservative and refractory to gross anatomical rearrangement. 

      Comment: We agree with the referee that the brainstem rearrangements are unexpected. We also think that the correct identification of nuclei needs to be at the center of our revision efforts.

      Change: Our revision provided further evidence (delineation of the olivo-cerebellar tract, characterization of the trigeminal nerve entry) about the identity of the nuclei we studied.

      Why would a major nucleus shift to such a different location? and how? Can ex vivo DTI provide further support of the correct identification? Is there other "disruption" in the brainstem? What occupies the traditional position of the trigeminal nuclei? An atlas-equivalent coronal view of the entire brainstem would be informative. The Authors have assembled multiple criteria to support their argument that the ventral "bumps" are in fact a translocated trigeminal principal nucleus: enhanced CO staining, enhanced vascularization, enhanced myelination (via Golgi stains and tomography), very scant labeling for a climbing fiber specific antibody ( anti-peripherin), vs. dense staining of this in the alternative structure that they identify as IO; and a high density of glia. Admittedly, this should be sufficient, but the proposed translocation (in the BRAINSTEM) is sufficiently startling that this is arguably NOT sufficient. <br /> The terminology of "putative" is helpful, but a more cogent presentation of the results and more careful discussion might succeed in winning over at least some of a skeptical readership. 

      Comment: We do not know, what led to the elephant brainstem rearrangements we propose. If the trigeminal nuclei had expanded isometrically in elephants from the ancestral pattern, one would have expected a brain with big lateral bumps, not the elephant brain with its big ventromedial bumps. We note, however, that very likely the expansion of the elephant trigeminal nuclei did not occur isometrically. Instead, the neural representation of the elephant nose expanded dramatically and in rodents the nose is represented ventromedially in the brainstem face representation. Thus, we propose a ‘ventromedial outgrowth model’ according to which the elephant ventromedial trigeminal bumps result from a ventromedially direct outgrowth of the ancestral ventromedial nose representation.

      We advanced substantially more evidence to support our partitioning scheme, including the delineation of the olivo-cerebellar tract based on peripherin-reactivity. We also identified problems in previous partitioning schemes, such as the claim that the trigeminal nerve continues into the ~4x smaller olivocerebellar tract (Referee-Figure 1C, D); we think such a flow of fibers, (which is also at odds with peripherin-antibody-reactivity and the appearance of nerve and olivocerebellar tract), is highly unlikely if not physically impossible. With all that we do not think that we overstate our case in our cautiously presented ms.

      Change: We added evidence on the identification of elephant trigeminal nuclei and inferior olive.

      (2) Role of myelin. While the photos of myelin are convincing, it would be nice to have further documentation. Gallyas? Would antibodies to MBP work? What is the myelin distribution in the "standard" trigeminal nuclei (human? macaque or chimpanzee?). What are alternative sources of the bundles? Regardless, I think it would be beneficial to de-emphasize this point about the role of myelin in demarcating compartments. <br /> I would in fact suggest an alternative (more neutral) title that might highlight instead the isomorphic feature; for example, "An isomorphic representation of Trunk folds in the Elephant Trigeminal Nucleus." The present title stresses myelin, but figure 1 already focuses on CO. Additionally, the folds are actually mentioned almost in passing until later in the manuscript. I recommend a short section on these at the beginning of the Results to serve as a useful framework.

      Here I'm inclined to agree with the Reviewer, that the Authors' contention that the myelin stipes serve PRIMARILY to separate trunk-fold domains is not particularly compelling and arguably a distraction. The point can be made, but perhaps with less emphasis. After all, the fact that myelin has multiple roles is well-established, even if frequently overlooked. In addition, the Authors might make better use of an extensive relevant literature related to myelin as a compartmental marker; for example, results and discussion in D. Haenelt....N. Weiskopf (eLife, 2023), among others. Another example is the heavily myelinated stria of Gennari in primate visual cortex, consisting of intrinsic pyramidal cell axons, but where the role of the myelination has still not been elucidated. 

      Comment: (1) Documentation of myelin. We note that we show further identification of myelinated fibers by the fluorescent dye fluomyelin in Figure 4B. We also performed additional myelin stains as the gold-myelin stain after the protocol of Schmued (Referee-Figure 2). In the end, nothing worked quite as well to visualize myelin-stripes as the bright-field images shown in Figure 4A and it is only the images that allowed us to match myelin-stripes to trunk folds. Hence, we focus our presentation on these images.

      (2) Title: We get why the referee envisions an alternative title. This being said, we would like to stick with our current title, because we feel it highlights the major novelty we discovered.

      (3) We agree with many of the other comments of the referee on myelin phenomenology. We missed the Haenelt reference pointed out by the referee and think it is highly relevant to our paper

      Change: 1. Review image 2. Inclusion of the Haenelt-reference.

      Author response image 2.

      Myelin stripes of the elephant trunk module visualized by Gold-chloride staining according to Schmued. A, Low magnification micrograph of the trunk module of African elephant Indra stained with AuCl according to Schmued. The putative finger is to the left, proximal is to the right. Myelin stripes can easily be recognized. The white box indicates the area shown in B. B, high magnification micrograph of two myelin stripes. Individual gold-stained (black) axons organized in myelin stripes can be recognized.

      Schmued, L. C. (1990). A rapid, sensitive histochemical stain for myelin in frozen brain sections. Journal of Histochemistry & Cytochemistry,38(5), 717-720.

      Are the "bumps" in any way "analogous" to the "brain warts" seen in entorhinal areas of some human brains (G. W. van Hoesen and A. Solodkin (1993)? 

      Comment: We think this is a similar phenomenon.

      Change: We included the Hoesen and A. Solodkin (1993) reference in our discussion.

      At least slightly more background (ie, a separate section or, if necessary, supplement) would be helpful, going into more detail on the several subdivisions of the ION and if these undergo major alterations in the elephant.

      Comment: The strength of the paper is the detailed delineation of the trunk module, based on myelin stripes and isomorphism. We don’t think we have strong evidence on ION subdivisions, because it appears the trigeminal tract cannot be easily traced in elephants. Accordingly, we find it difficult to add information here.

      Change: None.

      Is there evidence from the literature of other conspicuous gross anatomical translocations, in any species, especially in subcortical regions? 

      Comment: The best example that comes to mind is the star-nosed mole brainstem. There is a beautiful paper comparing the star-nosed mole brainstem to the normal mole brainstem (Catania et al 2011). The principal trigeminal nucleus in the star-nosed mole is far more rostral and also more medial than in the mole; still, such rearrangements are minor compared to what we propose in elephants.

      Catania, Kenneth C., Duncan B. Leitch, and Danielle Gauthier. "A star in the brainstem reveals the first step of cortical magnification." PloS one 6.7 (2011): e22406.

      Change: None.

      (3) A major point concerns the isomorphism between the putative trigeminal nuclei and the trunk specialization. I think this can be much better presented, at least with more discussion and other examples. The Authors mention about the rodent "barrels," but it seemed strange to me that they do not refer to their own results in pig (C. Ritter et al., 2023) nor the work from Ken Catania, 2002 (star-nosed mole; "fingerprints in the brain") or other that might be appropriate. I concur with the Reviewer that there should be more comparative data. 

      Comment: We agree.

      Change: We added a discussion of other isomorphisms including the the star-nosed mole to our paper.

      (4) Textual organization could be improved. 

      The Abstract all-important Introduction is a longish, semi "run-on" paragraph. At a minimum this should be broken up. The last paragraph of the Introduction puts forth five issues, but these are only loosely followed in the Results section. I think clarity and good organization is of the upmost importance in this manuscript. I recommend that the Authors begin the Results with a section on the trunk folds (currently figure 5, and discussion), continue with the several points related to the identification of the trigeminal nuclei, and continue with a parallel description of ION with more parallel data on the putative trigeminal and IO structures (currently referee Table 1, but incorporate into the text and add higher magnification of nucleus-specific cell types in the IO and trigeminal nuclei). Relevant comparative data should be included in the Discussion.

      Comment: 1. We agree with the referee that our abstract needed to be revised. 2. We also think that our ms was heavily altered by the insertion of the new Figure 2, which complemented Figure 1 from our first submission and is concerned with the identification of the inferior olive. From a standpoint of textual flow such changes were not ideal, but the revisions massively added to the certainty with which we identify the trigeminal nuclei. Thus, although we are not as content as we were with the flow, we think the ms advanced in the revision process and we would like to keep the Figure sequence as is. 3. We already noted above that we included additional comparative evidence.

      Change: 1. We revised our abstract. 2. We added comparative evidence.

      Reviewer #5 (Recommendations For The Authors): 

      The data is invaluable and provides insights into some of the largest mammals on the planet. 

      Comment: We are incredibly thankful for this positive assessment.

    2. Author Response

      eLife assessment

      This potentially valuable study uses classic neuroanatomical techniques and synchrotron X-ray tomography to investigate the mapping of the trunk within the brainstem nuclei of the elephant brain. Given its unique specializations, understanding the somatosensory projections from the elephant trunk would be of general interest to evolutionary neurobiologists, comparative neuroscientists, and animal behavior scientists. However, the anatomical analysis is inadequate to support the authors' conclusion that they have identified the elephant trigeminal sensory nuclei rather than a different brain region, specifically the inferior olive.

      Comment: We are happy that our paper is considered to be potentially valuable. Also, the editors highlight the potential interest of our work for evolutionary neurobiologists, comparative neuroscientists, and animal behavior scientists. The editors are more negative when it comes to our evidence on the identification of the trigeminal nucleus vs the inferior olive. We have five comments on this assessment. (i) We think this assessment is heavily biased by the comments of referee 2. We will show that the referee’s comments are more about us than about our paper. Hence, the referee failed to do their job (refereeing our paper) and should not have succeeded in leveling our paper. (ii) We have no ad hoc knock-out experiments to distinguish the trigeminal nucleus vs the inferior olive. Such experiments (extracellular recording & electrolytic lesions, viral tracing would be done in a week in mice, but they cannot and should not be done in elephants. (iii) We have extraordinary evidence. Nobody has ever described a similarly astonishing match of body (trunk folds) and myeloarchitecture in the trigeminal system before. (iv) We will show that our assignment of the trigeminal nucleus vs the inferior olive is more plausible than the current hypothesis about the assignment of the trigeminal nucleus vs the inferior olive as defended by referee 2. We think this is why it is important to publish our paper. (v) We think eLife is the perfect place for our publication because the deviating views of referee 2 are published along.

      Change: We performed additional peripherin-antibody staining to differentiate the inferior olive and trigeminal nucleus. Peripherin is a cytoskeletal protein that is found in peripheral nerves and climbing fibers. Specifically, climbing fibers of various species (mouse, rabbit, pig, cow, and human; Errante et al., 1998) are stained intensely with peripherin-antibodies. What is tricky for our purposes is that there is also some peripherin-antibody reactivity in the trigeminal nuclei (Errante et al., 1998). Such peripherin-antibody reactivity is weaker, however, and lacks the distinct axonal bundle signature that stems from the strong climbing fiber peripherin-reactivity as seen in the inferior olive (Errante et al., 1998). As can be seen in Author response image 1, we observe peripherin-reactivity in axonal bundles (i.e. in putative climbing fibers), in what we think is the inferior olive. We also observe weak peripherin-reactivity, in what we think is the trigeminal nucleus, but not the distinct and strong labeling of axonal bundles. These observations are in line with our ideas but are difficult to reconcile with the views of the referee. Specifically, the lack of peripherin-reactive axon bundles suggests that there are no climbing fibres in what the referee thinks is the inferior olive.

      Errante, L., Tang, D., Gardon, M., Sekerkova, G., Mugnaini, E., & Shaw, G. (1998). The intermediate filament protein peripherin is a marker for cerebellar climbing fibres. Journal of neurocytology, 27, 69-84.

      Author response image 1.

      The putative inferior olive but not the putative trigeminal nucleus contains peripherin-positive axon bundles (presumptive climbing fibers). (A) Overview picture of a brainstem section stained with anti-peripherin-antibodies (white color). Anti-peripherin-antibodies stain climbing fibers in a wide variety of mammals. The section comes from the posterior brainstem of African elephant cow Bibi; in this posterior region, both putative inferior olive and trigeminal nucleus are visible. Note the bright staining of the dorsolateral nucleus, the putative inferior olive according to Reveyaz et al., and the trigeminal nucleus according to Maseko et al., 2013. (B) High magnification view of the dorsolateral nucleus (corresponding to the upper red rectangle in A). Anti-peripherin-positive axon bundles (putative climbing fibers) are seen in support of the inferior olive hypothesis of Reveyaz et al. (C) High magnification view of the ventromedial nucleus (corresponding to the lower red rectangle in A). The ventromedial nucleus is weakly positive for peripherin but contains no anti-peripherin-positive axon bundles (i.e. no putative climbing fibers) in support of the trigeminal nucleus hypothesis of Reveyaz et al. Note that myelin stripes – weakly visible as dark omissions – are clearly anti-peripherin-negative.

      Reviewer #1:

      Summary:

      This fundamental study provides compelling neuroanatomical evidence underscoring the sensory function of the trunk in African and Asian elephants. Whereas myelinated tracts are classically appreciated as mediating neuronal connections, the authors speculate that myelinated bundles provide functional separation of trunk folds and display elaboration related to the "finger" projections. The authors avail themselves of many classical neuroanatomical techniques (including cytochrome oxidase stains, Golgi stains, and myelin stains) along with modern synchrotron X-ray tomography. This work will be of interest to evolutionary neurobiologists, comparative neuroscientists, and the general public, with its fascinating exploration of the brainstem of an icon sensory specialist.

      Comment: We are incredibly grateful for this positive assessment.

      Changes: None.

      Strengths:

      • The authors made excellent use of the precious sample materials from 9 captive elephants.

      • The authors adopt a battery of neuroanatomical techniques to comprehensively characterize the structure of the trigeminal subnuclei and properly re-examine the "inferior olive".

      • Based on their exceptional histological preparation, the authors reveal broadly segregated patterns of metabolic activity, similar to the classical "barrel" organization related to rodent whiskers.

      Comment: The referee provides a concise summary of our findings.

      Changes: None.

      Weaknesses:

      • As the authors acknowledge, somewhat limited functional description can be provided using histological analysis (compared to more invasive techniques).

      • The correlation between myelinated stripes and trunk fold patterns is intriguing, and Figure 4 presents this idea beautifully. I wonder - is the number of stripes consistent with the number of trunk folds? Does this hold for both species?

      Comment: We agree with the referee’s assessment. We note that cytochrome-oxidase staining is an at least partially functional stain, as it reveals constitutive metabolic activity. A significant problem of the work in elephants is that our recording possibilities are limited, which in turn limits functional analysis. As indicated in Figure 4 for the African elephant Indra, there was an excellent match of trunk folds and myelin stripes. Asian elephants have more, and less conspicuous trunk folds than African elephants. As illustrated in Figure 6, Asian elephants have more, and less conspicuous myelin stripes. Thus, species differences in myelin stripes correlate with species differences in trunk folds.

      Changes: We clarify the relation of myelin stripe and trunk fold patterns in our discussion of Figure 6.  

      Reviewer #2 (Public Review):

      The authors describe what they assert to be a very unusual trigeminal nuclear complex in the brainstem of elephants, and based on this, follow with many speculations about how the trigeminal nuclear complex, as identified by them, might be organized in terms of the sensory capacity of the elephant trunk.

      Comment: We agree with the referee’s assessment that the putative trigeminal nucleus described in our paper is highly unusual in size, position, vascularization, and myeloarchitecture. This is why we wrote this paper. We think these unusual features reflect the unique facial specializations of elephants, i.e. their highly derived trunk. Because we have no access to recordings from the elephant brainstem, we cannot back up all our functional interpretations with electrophysiological evidence; it is therefore fair to call them speculative.

      Changes: None.

      The identification of the trigeminal nuclear complex/inferior olivary nuclear complex in the elephant brainstem is the central pillar of this manuscript from which everything else follows, and if this is incorrect, then the entire manuscript fails, and all the associated speculations become completely unsupported.

      Comment: We agree.

      Changes: None.

      The authors note that what they identify as the trigeminal nuclear complex has been identified as the inferior olivary nuclear complex by other authors, citing Shoshani et al. (2006; 10.1016/j.brainresbull.2006.03.016) and Maseko et al (2013; 10.1159/000352004), but fail to cite either Verhaart and Kramer (1958; PMID 13841799) or Verhaart (1962; 10.1515/9783112519882-001). These four studies are in agreement, but the current study differs.

      Comment & Change: We were not aware of the papers of Verhaart and included them in the revised ms.

      Let's assume for the moment that the four previous studies are all incorrect and the current study is correct. This would mean that the entire architecture and organization of the elephant brainstem is significantly rearranged in comparison to ALL other mammals, including humans, previously studied (e.g. Kappers et al. 1965, The Comparative Anatomy of the Nervous System of Vertebrates, Including Man, Volume 1 pp. 668-695) and the closely related manatee (10.1002/ar.20573). This rearrangement necessitates that the trigeminal nuclei would have had to "migrate" and shorten rostrocaudally, specifically and only, from the lateral aspect of the brainstem where these nuclei extend from the pons through to the cervical spinal cord (e.g. the Paxinos and Watson rat brain atlases), the to the spatially restricted ventromedial region of specifically and only the rostral medulla oblongata. According to the current paper, the inferior olivary complex of the elephant is very small and located lateral to their trigeminal nuclear complex, and the region from where the trigeminal nuclei are located by others appears to be just "lateral nuclei" with no suggestion of what might be there instead.

      Comment: We have three comments here:

      1) The referee correctly notes that we argue the elephant brainstem underwent fairly major rearrangements. In particular, we argue that the elephant inferior olive was displaced laterally, by a very large cell mass, which we argue is an unusually large trigeminal nucleus. To our knowledge, such a large compact cell mass is not seen in the ventral brain stem of any other mammal.

      2) The referee makes it sound as if it is our private idea that the elephant brainstem underwent major rearrangements and that the rest of the evidence points to a conventional ‘rodent-like’ architecture. This is far from the truth, however. Already from the outside appearance (see our Figure 1B and Figure 6A) it is clear that the elephant brainstem has huge ventral bumps not seen in any other mammal. An extraordinary architecture also holds at the organizational level of nuclei. Specifically, the facial nucleus – the most carefully investigated nucleus in the elephant brainstem – has an appearance distinct from that of the facial nuclei of all other mammals (Maseko et al., 2013; Kaufmann et al., 2022). If both the overall shape and the constituting nuclei of the brainstem are very different from other mammals, it is very unlikely if not impossible that the elephant brainstem follows in all regards a conventional ‘rodent-like’ architecture.

      3) The inferior olive is an impressive nucleus in the partitioning scheme we propose (Author response image 1). In fact – together with the putative trigeminal nucleus we describe – it’s the most distinctive nucleus in the elephant brainstem. We have not done volumetric measurements and cell counts here, but think this is an important direction for future work. What has informed our work is that the inferior olive nucleus we describe has the serrated organization seen in the inferior olive of all mammals. We will discuss these matters in depth below.

      Changes: None.

      Such an extraordinary rearrangement of brainstem nuclei would require a major transformation in the manner in which the mutations, patterning, and expression of genes and associated molecules during development occur. Such a major change is likely to lead to lethal phenotypes, making such a transformation extremely unlikely. Variations in mammalian brainstem anatomy are most commonly associated with quantitative changes rather than qualitative changes (10.1016/B978-0-12-804042-3.00045-2).

      Comment: We have two comments here:

      1) The referee claims that it is impossible that the elephant brainstem differs from a conventional brainstem architecture because this would lead to lethal phenotypes etc. Following our previous response, this argument does not hold. It is out of the question that the elephant brainstem looks very different from the brainstem of other mammals. Yet, it is also evident that elephants live. The debate we need to have is not if the elephant brainstem differs from other mammals, but how it differs from other mammals.

      2). In principle we agree with the referee’s thinking that the model of the elephant brainstem that is most likely correct is the one that requires the least amount of rearrangements to other mammals. We therefore prepared a comparison of the model the referee is proposing (Maseko et al., 2013; see Author response table 1 below) with our proposition. We scored these models on their similarity to other mammals. We find that the referee’s ideas (Maseko et al., 2013) require more rearrangements relative to other mammals than our suggestion.

      Changes: Inclusion of Author response table 1, which we discuss in depth below.

      The impetus for the identification of the unusual brainstem trigeminal nuclei in the current study rests upon a previous study from the same laboratory (10.1016/j.cub.2021.12.051) that estimated that the number of axons contained in the infraorbital branch of the trigeminal nerve that innervate the sensory surfaces of the trunk is approximately 400 000. Is this number unusual? In a much smaller mammal with a highly specialized trigeminal system, the platypus, the number of axons innervating the sensory surface of the platypus bill skin comes to 1 344 000 (10.1159/000113185). Yet, there is no complex rearrangement of the brainstem trigeminal nuclei in the brain of the developing or adult platypus (Ashwell, 2013, Neurobiology of Monotremes), despite the brainstem trigeminal nuclei being very large in the platypus (10.1159/000067195). Even in other large-brained mammals, such as large whales that do not have a trunk, the number of axons in the trigeminal nerve ranges between 400,000 and 500,000 (10.1007/978-3-319-47829-6_988-1). The lack of comparative support for the argument forwarded in the previous and current study from this laboratory, and that the comparative data indicates that the brainstem nuclei do not change in the manner suggested in the elephant, argues against the identification of the trigeminal nuclei as outlined in the current study. Moreover, the comparative studies undermine the prior claim of the authors, informing the current study, that "the elephant trigeminal ganglion ... point to a high degree of tactile specialization in elephants" (10.1016/j.cub.2021.12.051). While clearly, the elephant has tactile sensitivity in the trunk, it is questionable as to whether what has been observed in elephants is indeed "truly extraordinary".

      Comment: These comments made us think that the referee is not talking about the paper we submitted, but that the referee is talking about us and our work in general. Specifically, the referee refers to the platypus and other animals dismissing our earlier work, which argued for a high degree of tactile specialization in elephants. We think the referee’s intuitions are wrong and our earlier work is valid.

      Changes: We prepared a Author response image 2 (below) that puts the platypus brain, a monkey brain, and the elephant trigeminal ganglion (which contains a large part of the trunk innervating cells) in perspective.

      Author response image 2.

      The elephant trigeminal ganglion is comparatively large. Platypus brain, monkey brain, and elephant ganglion. The elephant has two trigeminal ganglia, which contain the first-order somatosensory neurons. They serve mainly for tactile processing and are large compared to a platypus brain (from the comparative brain collection) and are similar in size to a monkey brain. The idea that elephants might be highly specialized for trunk touch is also supported by the analysis of the sensory nerves of these animals (Purkart et al., 2022). Specifically, we find that the infraorbital nerve (which innervates the trunk) is much thicker than the optic nerve (which mediates vision) and the vestibulocochlear nerve (which mediates hearing). Thus, not everything is large about elephants; instead, the data argue that these animals are heavily specialized for trunk touch.

      But let's look more specifically at the justification outlined in the current study to support their identification of the unusually located trigeminal sensory nuclei of the brainstem.

      (1) Intense cytochrome oxidase reactivity.

      (2) Large size of the putative trunk module.

      (3) Elongation of the putative trunk module.

      (4) The arrangement of these putative modules corresponds to elephant head anatomy.

      (5) Myelin stripes within the putative trunk module that apparently match trunk folds.

      (6) Location apparently matches other mammals.

      (7) Repetitive modular organization apparently similar to other mammals.

      (8) The inferior olive described by other authors lacks the lamellated appearance of this structure in other mammals.

      Comment: We agree those are key issues.

      Changes: None.

      Let's examine these justifications more closely.

      (1) Cytochrome oxidase histochemistry is typically used as an indicative marker of neuronal energy metabolism. The authors indicate, based on the "truly extraordinary" somatosensory capacities of the elephant trunk, that any nuclei processing this tactile information should be highly metabolically active, and thus should react intensely when stained for cytochrome oxidase. We are told in the methods section that the protocols used are described by Purkart et al (2022) and Kaufmann et al (2022). In neither of these cited papers is there any description, nor mention, of the cytochrome oxidase histochemistry methodology, thus we have no idea of how this histochemical staining was done. To obtain the best results for cytochrome oxidase histochemistry, the tissue is either processed very rapidly after buffer perfusion to remove blood or in recently perfusion-fixed tissue (e.g., 10.1016/0165-0270(93)90122-8). Given: (1) the presumably long post-mortem interval between death and fixation - "it often takes days to dissect elephants"; (2) subsequent fixation of the brains in 4% paraformaldehyde for "several weeks"; (3) The intense cytochrome oxidase reactivity in the inferior olivary complex of the laboratory rat (Gonzalez-Lima, 1998, Cytochrome oxidase in neuronal metabolism and Alzheimer's diseases); and (4) The lack of any comparative images from other stained portions of the elephant brainstem; it is difficult to support the justification as forwarded by the authors. The histochemical staining observed is likely background reactivity from the use of diaminobenzidine in the staining protocol. Thus, this first justification is unsupported.

      Comment: The referee correctly notes the description of our cytochrome-oxidase reactivity staining was lacking. This is a serious mistake of ours for which we apologize very much. The referee then makes it sound as if we messed up our cytochrome-oxidase staining, which is not the case. All successful (n = 3; please see our technical comments in the recommendation section) cytochrome-oxidase stainings were done with elephants with short post-mortem times (≤ 2 days) to brain removal/cooling and only brief immersion fixation (≤ 1 day). Cytochrome-oxidase reactivity in elephant brains appears to be more sensitive to quenching by fixation than is the case for rodent brains. We think it is a good idea to include a cytochrome-oxidase staining overview picture because we understood from the referee’s comments that we need to compare our partitioning scheme of the brainstem with that of other authors. To this end, we add a cytochrome-oxidase staining overview picture (Author response image 3) along with an alternative interpretation from Maseko et al., 2013.

      Changes: 1) We added details on our cytochrome-oxidase reactivity staining protocol and the cytochrome-oxidase reactivity in the elephant brain in general recommendation.

      2) We provide a detailed discussion of the technicalities of cytochrome-oxidase staining below in the recommendation section, where the referee raised further criticisms.

      3) We include a cytochrome-oxidase staining overview picture (Author response image 2) along with an alternative interpretation from Maseko et al., 2013.

      Author response image 3.

      Cytochrome-oxidase staining overview along with the Maseko et al. (2013) scheme Left, coronal cytochrome-oxidase staining overview from African elephant cow Indra; the section is taken a few millimeters posterior to the facial nucleus. Brown is putatively neural cytochrome-reactivity, and white is the background. Black is myelin diffraction and (seen at higher resolution, when you zoom in) erythrocyte cytochrome-reactivity in blood vessels (see our Figure 1E-G); such blood vessel cytochrome-reactivity is seen, because we could not perfuse the animal. There appears to be a minimal outside-in-fixation artifact (i.e. a more whitish/non-brownish appearance of the section toward the borders of the brain). This artifact is not seen in sections from Indra that we processed earlier or in other elephant brains processed at shorter post-mortem/fixation delays (see our Figure 1C). Right, coronal partitioning scheme of Maseko et al. (2013) for the elephant brainstem at an approximately similar anterior-posterior level.

      The same structures can be recognized left and right. The section is taken at an anterior-posterior level, where we encounter the trigeminal nuclei in pretty much all mammals. Note that the neural cytochrome reactivity is very high, in what we refer to as the trigeminal-nuclei-trunk-module and what Maseko et al. refer to as inferior olive. Myelin stripes can be recognized here as white omissions.

      At the same time, the cytochrome-oxidase-reactivity is very low in what Maseko et al. refer to as trigeminal nuclei. The indistinct appearance and low cytochrome-oxidase-reactivity of the trigeminal nuclei in the scheme of Maseko et al. (2013) is unexpected because trigeminal nuclei stain intensely for cytochrome-oxidase-reactivity in most mammals and because the trigeminal nuclei represent the elephant’s most important body part, the trunk. Staining patterns of the trigeminal nuclei as identified by Maseko et al. (2013) are very different at more posterior levels; we will discuss this matter below.

      Justifications (2), (3), and (4) are sequelae from justification (1). In this sense, they do not count as justifications, but rather unsupported extensions.

      Comment: These are key points of our paper that the referee does not discuss.

      Changes: None.

      (4) and (5) These are interesting justifications, as the paper has clear internal contradictions, and (5) is a sequelae of (4). The reader is led to the concept that the myelin tracts divide the nuclei into sub-modules that match the folding of the skin on the elephant trunk. One would then readily presume that these myelin tracts are in the incoming sensory axons from the trigeminal nerve. However, the authors note that this is not the case: "Our observations on trunk module myelin stripes are at odds with this view of myelin. Specifically, myelin stripes show no tapering (which we would expect if axons divert off into the tissue). More than that, there is no correlation between myelin stripe thickness (which presumably correlates with axon numbers) and trigeminal module neuron numbers. Thus, there are numerous myelinated axons, where we observe few or no trigeminal neurons. These observations are incompatible with the idea that myelin stripes form an axonal 'supply' system or that their prime function is to connect neurons. What do myelin stripe axons do, if they do not connect neurons? We suggest that myelin stripes serve to separate rather than connect neurons." So, we are left with the observation that the myelin stripes do not pass afferent trigeminal sensory information from the "truly extraordinary" trunk skin somatic sensory system, and rather function as units that separate neurons - but to what end? It appears that the myelin stripes are more likely to be efferent axonal bundles leaving the nuclei (to form the olivocerebellar tract). This justification is unsupported.

      Comment: The referee cites some of our observations on myelin stripes, which we find unusual. We stand by the observations and comments. The referee does not discuss the most crucial finding we report on myelin stripes, namely that they correspond remarkably well to trunk folds.

      Changes: None.

      (6) The authors indicate that the location of these nuclei matches that of the trigeminal nuclei in other mammals. This is not supported in any way. In ALL other mammals in which the trigeminal nuclei of the brainstem have been reported they are found in the lateral aspect of the brainstem, bordered laterally by the spinal trigeminal tract. This is most readily seen and accessible in the Paxinos and Watson rat brain atlases. The authors indicate that the trigeminal nuclei are medial to the facial nerve nucleus, but in every other species, the trigeminal sensory nuclei are found lateral to the facial nerve nucleus. This is most salient when examining a close relative, the manatee (10.1002/ar.20573), where the location of the inferior olive and the trigeminal nuclei matches that described by Maseko et al (2013) for the African elephant. This justification is not supported.

      Comment: The referee notes that we incorrectly state that the position of the trigeminal nuclei matches that of other mammals. We think this criticism is justified.

      Changes: We prepared a comparison of the Maseko et al. (2013) scheme of the elephant brainstem with our scheme of the elephant brainstem (see Author response table 1). Here we acknowledge the referee’s argument and we also changed the manuscript accordingly.

      (7) The dual to quadruple repetition of rostrocaudal modules within the putative trigeminal nucleus as identified by the authors relies on the fact that in the neurotypical mammal, there are several trigeminal sensory nuclei arranged in a column running from the pons to the cervical spinal cord, these include (nomenclature from Paxinos and Watson in roughly rostral to caudal order) the Pr5VL, Pr5DM, Sp5O, Sp5I, and Sp5C. However, these nuclei are all located far from the midline and lateral to the facial nerve nucleus, unlike what the authors describe in the elephants. These rostrocaudal modules are expanded upon in Figure 2, and it is apparent from what is shown that the authors are attributing other brainstem nuclei to the putative trigeminal nuclei to confirm their conclusion. For example, what they identify as the inferior olive in Figure 2D is likely the lateral reticular nucleus as identified by Maseko et al (2013). This justification is not supported.

      Comment: The referee again compares our findings to the scheme of Maseko et al. (2013) and rejects our conclusions on those grounds. We think such a comparison of our scheme is needed, indeed.

      Changes: We prepared a comparison of the Maseko et al. (2013) scheme of the elephant brainstem with our scheme of the elephant brainstem (see Author response table 1).

      (8) In primates and related species, there is a distinct banded appearance of the inferior olive, but what has been termed the inferior olive in the elephant by other authors does not have this appearance, rather, and specifically, the largest nuclear mass in the region (termed the principal nucleus of the inferior olive by Maseko et al, 2013, but Pr5, the principal trigeminal nucleus in the current paper) overshadows the partial banded appearance of the remaining nuclei in the region (but also drawn by the authors of the current paper). Thus, what is at debate here is whether the principal nucleus of the inferior olive can take on a nuclear shape rather than evince a banded appearance. The authors of this paper use this variance as justification that this cluster of nuclei could not possibly be the inferior olive. Such a "semi-nuclear/banded" arrangement of the inferior olive is seen in, for example, giraffe (10.1016/j.jchemneu.2007.05.003), domestic dog, polar bear, and most specifically the manatee (a close relative of the elephant) (brainmuseum.org; 10.1002/ar.20573). This justification is not supported.

      Comment: We carefully looked at the brain sections referred to by the referee in the brainmuseum.org collection. We found contrary to the referee’s claims that dogs, polar bears, and manatees have a perfectly serrated (a cellular arrangement in curved bands) appearance of the inferior olive. Accordingly, we think the referee is not reporting the comparative evidence fairly and we wonder why this is the case.

      Changes: None.

      Thus, all the justifications forwarded by the authors are unsupported. Based on methodological concerns, prior comparative mammalian neuroanatomy, and prior studies in the elephant and closely related species, the authors fail to support their notion that what was previously termed the inferior olive in the elephant is actually the trigeminal sensory nuclei. Given this failure, the justifications provided above that are sequelae also fail. In this sense, the entire manuscript and all the sequelae are not supported.

      Comment: We disagree. To summarize:

      (1) Our description of the cytochrome oxidase staining lacked methodological detail, which we have now added; the cytochrome oxidase reactivity data are great and support our conclusions.

      (2)–(5)The referee does not really discuss our evidence on these points.

      (6) We were wrong and have now fixed this mistake.

      (7) The referee asks for a comparison to the Maseko et al. (2013) scheme (agreed, see Author response image 4 4 and Author response table 1).

      (8) The referee bends the comparative evidence against us.

      Changes: None.

      A comparison of the elephant brainstem partitioning schemes put forward by Maseko et al 2013 and by Reveyaz et al.

      To start with, we would like to express our admiration for the work of Maseko et al. (2013). These authors did pioneering work on obtaining high-quality histology samples from elephants. Moreover, they made a heroic neuroanatomical effort, in which they assigned 147 brain structures to putative anatomical entities. Most of their data appear to refer to staining in a single elephant and one coronal sectioning plane. The data quality and the illustration of results are excellent.

      We studied mainly two large nuclei in six (now 7) elephants in three (coronal, parasagittal, and horizontal) sectioning planes. The two nuclei in question are the two most distinct nuclei in the elephant brainstem, namely an anterior ventromedial nucleus (the trigeminal trunk module in our terminology; the inferior olive in the terminology of Maseko et al., 2013) and a more posterior lateral nucleus (the inferior olive in our terminology; the posterior part of the trigeminal nuclei in the terminology of Maseko et al., 2013).

      Author response image 4 gives an overview of the two partitioning schemes for inferior olive/trigeminal nuclei along with the rodent organization (see below).

      Author response image 4.

      Overview of the brainstem organization in rodents & elephants according to Maseko et. (2013) and Reveyaz et al. (this paper).

      The strength of the Maseko et al. (2013) scheme is the excellent match of the position of elephant nuclei to the position of nuclei in the rodent (Author response image 4). We think this positional match reflects the fact that Maseko et al. (2013) mapped a rodent partitioning scheme on the elephant brainstem. To us, this is a perfectly reasonable mapping approach. As the referee correctly points out, the positional similarity of both elephant inferior olive and trigeminal nuclei to the rodent strongly argues in favor of the Maseko et al. (2013), because brainstem nuclei are positionally very conservative.

      Other features of the Maseko et al. (2013) scheme are less favorable. The scheme marries two cyto-architectonically very distinct divisions (an anterior indistinct part) and a super-distinct serrated posterior part to be the trigeminal nuclei. We think merging entirely distinct subdivisions into one nucleus is a byproduct of mapping a rodent partitioning scheme on the elephant brainstem. Neither of the two subdivisions resemble the trigeminal nuclei of other mammals. The cytochrome oxidase staining patterns differ markedly across the anterior indistinct part (see our Author response image 4) and the posterior part of the trigeminal nuclei and do not match with the intense cytochrome oxidase reactivity of other mammalian trigeminal nuclei (Referee Figure 3). Our anti-peripherin staining indicates that there probably no climbing fibers, in what Maseko et al. think. is inferior olive; this is a potentially fatal problem for the hypothesis. The posterior part of Maseko et al. (2013) trigeminal nuclei has a distinct serrated appearance that is characteristic of the inferior olive in other mammals. Moreover, the inferior olive of Maseko et al. (2013) lacks the serrated appearance of the inferior olive seen in pretty much all mammals; this is a serious problem.

      The partitioning scheme of Reveyaz et al. comes with poor positional similarity but avoids the other problems of the Maseko et al. (2013) scheme. Our explanation for the positionally deviating location of trigeminal nuclei is that the elephant grew one of the if not the largest trigeminal systems of all mammals. As a result, the trigeminal nuclei grew through the floor of the brainstem. We understand this is a post hoc just-so explanation, but at least it is an explanation.

      The scheme of Reveyaz et al. was derived in an entirely different way from the Maseko model. Specifically, we were convinced that the elephant trigeminal nuclei ought to be very special because of the gigantic trigeminal ganglia (Purkart et al., 2022). Cytochrome-oxidase staining revealed a large distinct nucleus with an elongated shape. Initially, we were freaked out by the position of the nucleus and the fact that it was referred to as inferior olive by other authors. When we found an inferior-olive-like nucleus at a nearby (although at an admittedly unusual) location, we were less worried. We then optimized the visualization of myelin stripes (brightfield imaging etc.) and were able to collect an entire elephant trunk along with the brain (African elephant cow Indra). When we made the one-to-one match of Indra’s trunk folds and myelin stripes (Figure 4) we were certain that we had identified the trunk module of the trigeminal nuclei. We already noted at the outset of our rebuttal that we now consider such certainty a fallacy of overconfidence. In light of the comments of Referee 2, we feel that a further discussion of our ideas is warranted. A strength of the Reveyaz model is that nuclei look like single anatomical entities. The trigeminal nuclei look like trigeminal nuclei of other mammals, the trunk module has a striking resemblance to the trunk and the inferior olive looks like the inferior olive of other mammals.

      We evaluated the fit of the two models in the form of a table (Author response table 1; below). Unsurprisingly, Author response table 1 aligns with our views of elephant brainstem partitioning.

      Author response table 1.

      Qualitative evaluation of elephant brainstem partitioning schemes

      ++ = Very attractive; + = attractive; - = unattractive; -- = very unattractive We scored features that are clear and shared by all mammals – as far as we know them – as very attractive. We scored features that are clear and are not shared by all mammals – as far as we know them – as very unattractive. Attractive features are either less clear or less well-shared features. Unattractive features are either less clear or less clearly not shared features.

      Author response table 1 suggests two conclusions to us. (i) The Reveyaz et al. model has mainly favorable properties. The Maseko et al. (2013) model has mainly unfavorable properties. Hence, the Reveyaz et al. model is more likely to be true. (ii) The outcome is not black and white, i.e., both models have favorable and unfavorable properties. Accordingly, we overstated our case in our initial submission and toned down our claims in the revised manuscript.

      What the authors have not done is to trace the pathway of the large trigeminal nerve in the elephant brainstem, as was done by Maseko et al (2013), which clearly shows the internal pathways of this nerve, from the branch that leads to the fifth mesencephalic nucleus adjacent to the periventricular grey matter, through to the spinal trigeminal tract that extends from the pons to the spinal cord in a manner very similar to all other mammals. Nor have they shown how the supposed trigeminal information reaches the putative trigeminal nuclei in the ventromedial rostral medulla oblongata. These are but two examples of many specific lines of evidence that would be required to support their conclusions. Clearly, tract tracing methods, such as cholera toxin tracing of peripheral nerves cannot be done in elephants, thus the neuroanatomy must be done properly and with attention to detail to support the major changes indicated by the authors.

      Comment: The referee claims that Maseko et al. (2013) showed by ‘tract tracing’ that the structures they refer to trigeminal nuclei receive trigeminal input. This statement is at least slightly misleading. There is nothing of what amounts to proper ‘tract tracing’ in the Maseko et al. (2013) paper, i.e. tracing of tracts with post-mortem tracers. We tried proper post-mortem tracing but failed (no tracer transport) probably as a result of the limitations of our elephant material. What Maseko et al. (2013) actually did is look a bit for putative trigeminal fibers and where they might go. We also used this approach. In our hands, such ‘pseudo tract tracing’ works best in unstained material under bright field illumination, because myelin is very well visualized. In such material, we find: (i) massive fiber tracts descending dorsoventrally roughly from where both Maseko et al. 2013 and we think the trigeminal tract runs. (ii) These fiber tracts run dorsoventrally and approach, what we think is the trigeminal nuclei from lateral.

      Changes: Ad hoc tract tracing see above.

      So what are these "bumps" in the elephant brainstem?

      Four previous authors indicate that these bumps are the inferior olivary nuclear complex. Can this be supported?

      The inferior olivary nuclear complex acts "as a relay station between the spinal cord (n.b. trigeminal input does reach the spinal cord via the spinal trigeminal tract) and the cerebellum, integrating motor and sensory information to provide feedback and training to cerebellar neurons" (https://www.ncbi.nlm.nih.gov/books/NBK542242/). The inferior olivary nuclear complex is located dorsal and medial to the pyramidal tracts (which were not labeled in the current study by the authors but are clearly present in Fig. 1C and 2A) in the ventromedial aspect of the rostral medulla oblongata. This is precisely where previous authors have identified the inferior olivary nuclear complex and what the current authors assign to their putative trigeminal nuclei. The neurons of the inferior olivary nuclei project, via the olivocerebellar tract to the cerebellum to terminate in the climbing fibres of the cerebellar cortex.

      Comment: We agree with the referee that in the Maseko et al. (2013) scheme the inferior olive is exactly where we expect it from pretty much all other mammals. Hence, this is a strong argument in favor of the Maseko et al. (2013) scheme and a strong argument against the partitioning scheme suggested by us.

      Changes: Please see our discussion above.

      Elephants have the largest (relative and absolute) cerebellum of all mammals (10.1002/ar.22425), this cerebellum contains 257 x109 neurons (10.3389/fnana.2014.00046; three times more than the entire human brain, 10.3389/neuro.09.031.2009). Each of these neurons appears to be more structurally complex than the homologous neurons in other mammals (10.1159/000345565; 10.1007/s00429-010-0288-3). In the African elephant, the neurons of the inferior olivary nuclear complex are described by Maseko et al (2013) as being both calbindin and calretinin immunoreactive. Climbing fibres in the cerebellar cortex of the African elephant are clearly calretinin immunopositive and also are likely to contain calbindin (10.1159/000345565). Given this, would it be surprising that the inferior olivary nuclear complex of the elephant is enlarged enough to create a very distinct bump in exactly the same place where these nuclei are identified in other mammals?

      Comment: We agree with the referee that it is possible and even expected from other mammals that there is an enlargement of the inferior olive in elephants. Hence, a priori one might expect the ventral brain stem bumps to the inferior olive, this is perfectly reasonable and is what was done by previous authors. The referee also refers to calbindin and calretinin antibody reactivity. Such antibody reactivity is indeed in line with the referee’s ideas and we considered these findings in our Referee Table 1. The problem is, however, that neither calbindin nor calretinin antibody reactivity are highly specific and indeed both nuclei in discussion (trigeminal nuclei and inferior olive) show such reactivity. Unlike the peripherin-antibody staining advanced by us, calbindin nor calretinin antibody reactivity cannot distinguish the two hypotheses debated.

      Changes: Please see our discussion above.

      What about the myelin stripes? These are most likely to be the origin of the olivocerebellar tract and probably only have a coincidental relationship with the trunk. Thus, given what we know, the inferior olivary nuclear complex as described in other studies, and the putative trigeminal nuclear complex as described in the current study, is the elephant inferior olivary nuclear complex. It is not what the authors believe it to be, and they do not provide any evidence that discounts the previous studies. The authors are quite simply put, wrong. All the speculations that flow from this major neuroanatomical error are therefore science fiction rather than useful additions to the scientific literature.

      Comment: It is unlikely that the myelin stripes are the origin of the olivocerebellar tract as suggested by the referee. Specifically, the lack of peripherin-reactivity indicates that these fibers are not climbing fibers (Referee Figure 1). In general, we feel the referee does not want to discuss the myelin stripes and obviously thinks we made up the strange correspondence of myelin stripes and trunk folds.

      Changes: Please see our discussion above.

      What do the authors actually have?

      The authors have interesting data, based on their Golgi staining and analysis, of the inferior olivary nuclear complex in the elephant.

      Comment: The referee reiterates their views.

      Changes: None.

      Reviewer #3 (Public Review):

      Summary:

      The study claims to investigate trunk representations in elephant trigeminal nuclei located in the brainstem. The researchers identified large protrusions visible from the ventral surface of the brainstem, which they examined using a range of histological methods. However, this ventral location is usually where the inferior olivary complex is found, which challenges the author's assertions about the nucleus under analysis. They find that this brainstem nucleus of elephants contains repeating modules, with a focus on the anterior and largest unit which they define as the putative nucleus principalis trunk module of the trigeminal. The nucleus exhibits low neuron density, with glia outnumbering neurons significantly. The study also utilizes synchrotron X-ray phase contrast tomography to suggest that myelin-stripe-axons traverse this module. The analysis maps myelin-rich stripes in several specimens and concludes that based on their number and patterning they likely correspond with trunk folds; however, this conclusion is not well supported if the nucleus has been misidentified.

      Comment: The referee gives a concise summary of our findings. The referee acknowledges the depth of our analysis and also notes our cellular results. The referee – in line with the comments of Referee 2 – also points out that a misidentification of the nucleus under study is potentially fatal for our analysis. We thank the referee for this fair assessment.

      Changes: We feel that we need to alert the reader more broadly to the misidentification concern. We think the critical comments of Referee 2, which will be published along with our manuscript, will go a long way in doing so. We think the eLife publishing format is fantastic in this regard. We will also include pointers to these concerns in the revised manuscript.

      Strengths:

      The strength of this research lies in its comprehensive use of various anatomical methods, including Nissl staining, myelin staining, Golgi staining, cytochrome oxidase labeling, and synchrotron X-ray phase contrast tomography. The inclusion of quantitative data on cell numbers and sizes, dendritic orientation and morphology, and blood vessel density across the nucleus adds a quantitative dimension. Furthermore, the research is commendable for its high-quality and abundant images and figures, effectively illustrating the anatomy under investigation.

      Comment: Again, a very fair and balanced set of comments. We are thankful for these comments.

      Changes: None.

      Weaknesses:

      While the research provides potentially valuable insights if revised to focus on the structure that appears to be the inferior olivary nucleus, there are certain additional weaknesses that warrant further consideration. First, the suggestion that myelin stripes solely serve to separate sensory or motor modules rather than functioning as an "axonal supply system" lacks substantial support due to the absence of information about the neuronal origins and the termination targets of the axons. Postmortem fixed brain tissue limits the ability to trace full axon projections. While the study acknowledges these limitations, it is important to exercise caution in drawing conclusions about the precise role of myelin stripes without a more comprehensive understanding of their neural connections.

      Comment: The referee points out a significant weakness of our study, namely our limited understanding of the origin and targets of the axons constituting the myelin stripes. We are very much aware of this problem and this is also why we directed high-powered methodology like synchrotron X-ray tomograms to elucidate the structure of myelin stripes. Such analysis led to advances, i.e., we now think, what looks like stripes are bundles and we understand the constituting axons tend to transverse the module. Such advances are insufficient, however, to provide a clear picture of myelin stripe connectivity.

      Changes: We think solving the problems raised by the referee will require long-term methodological advances and hence we will not be able to solve these problems in the current revision. Our long-term plans for confronting these issues are the following: (i) Improving our understanding of long-range connectivity by post-mortem tracing and MR-based techniques such as Diffusion-Tensor-Imaging. (ii) Improving our understanding of mid and short-range connectivity by applying even larger synchrotron X-ray tomograms and possible serial EM.

      Second, the quantification presented in the study lacks comparison to other species or other relevant variables within the elephant specimens (i.e., whole brain or brainstem volume). The absence of comparative data for different species limits the ability to fully evaluate the significance of the findings. Comparative analyses could provide a broader context for understanding whether the observed features are unique to elephants or more common across species. This limitation in comparative data hinders a more comprehensive assessment of the implications of the research within the broader field of neuroanatomy. Furthermore, the quantitative comparisons between African and Asian elephant specimens should include some measure of overall brain size as a covariate in the analyses. Addressing these weaknesses would enable a richer interpretation of the study's findings.

      Comment: The referee suggests another series of topics, which include the analysis of brain parts volumes or overall brain size. We agree these are important issues, but we also think such questions are beyond the scope of our study.

      Changes: We hope to publish comparative data on elephant brain size and shape later this year.  

    3. Author response:

      The following is the authors’ response to the original reviews.

      We are thankful for the handling of our manuscript. The following is a summary of our response and what we have done:

      (1) We are most thankful for the very thorough evaluation of our manuscript.

      (2) We were a bit shocked by the very negative commentary of referee 2.

      (3) We think, what put referee 2 off so much is that we were overconfident in the strength of our conclusions. We consider such overconfidence a big mistake. We have revised the manuscript to fix this problem.

      (4) We respond in great depth to all criticism and also go into technicalities.

      (5) We consider the possibility of a mistake. Yet, we carefully weighed the evidence advanced by referee 2 and by us and found that a systematic review supports our conclusions. Hence, we also resist the various attempts to crush our paper.

      (6) We added evidence (peripherin-antibody staining; our novel Figure 2) that suggests we correctly identified the inferior olive.

      (7) The eLife format – in which critical commentary is published along with the paper – is a fantastic venue to publish, what appears to be a surprisingly controversial issue.

      eLife assessment

      This potentially valuable study uses classic neuroanatomical techniques and synchrotron X-ray tomography to investigate the mapping of the trunk within the brainstem nuclei of the elephant brain. Given its unique specializations, understanding the somatosensory projections from the elephant trunk would be of general interest to evolutionary neurobiologists, comparative neuroscientists, and animal behavior scientists. However, the anatomical analysis is inadequate to support the authors' conclusion that they have identified the elephant trigeminal sensory nuclei rather than a different brain region, specifically the inferior olive.

      Comment: We are happy that our paper is considered to be potentially valuable. Also, the editors highlight the potential interest of our work for evolutionary neurobiologists, comparative neuroscientists, and animal behavior scientists. The editors are more negative when it comes to our evidence on the identification of the trigeminal nucleus vs the inferior olive. We have five comments on this assessment. (i) We think this assessment is heavily biased by the comments of referee 2. We show that the referee’s comments are more about us than about our paper. Hence, the referee failed to do their job (refereeing our paper) and should not have succeeded in leveling our paper. (ii) We have no ad hoc knock-out experiments to distinguish the trigeminal nucleus vs the inferior olive. Such experiments (extracellular recording & electrolytic lesions, viral tracing would be done in a week in mice, but they cannot and should not be done in elephants. (iii) We have extraordinary evidence. Nobody has ever described a similarly astonishing match of body (trunk folds) and myeloarchitecture in the brain before. (iv) We show that our assignment of the trigeminal nucleus vs the inferior olive is more plausible than the current hypothesis about the assignment of the trigeminal nucleus vs the inferior olive as defended by referee 2. We think this is why it is important to publish our paper. (v) We think eLife is the perfect place for our publication because the deviating views of referee 2 are published along.

      Change: We performed additional peripherin-antibody staining to differentiate the inferior olive and trigeminal nucleus. Peripherin is a cytoskeletal protein that is found in peripheral nerves and climbing fibers. Specifically, climbing fibers of various species (mouse, rabbit, pig, cow, and human; Errante et al., 1998) are stained intensely with peripherin-antibodies. What is tricky for our purposes is that there is also some peripherin-antibody reactivity in the trigeminal nuclei (Errante et al., 1998). Such peripherin-antibody reactivity is weaker, however, and lacks the distinct axonal bundle signature that stems from the strong climbing fiber peripherin-reactivity as seen in the inferior olive (Errante et al., 1998). As can be seen in our novel Figure 2, we observe peripherin-reactivity in axonal bundles (i.e. in putative climbing fibers), in what we think is the inferior olive. We also observe weak peripherin-reactivity, in what we think is the trigeminal nucleus, but not the distinct and strong labeling of axonal bundles. These observations are in line with our ideas but are difficult to reconcile with the views of the referee. Specifically, the lack of peripherin-reactive axon bundles suggests that there are no climbing fibers in what the referee thinks is the inferior olive.

      Errante, L., Tang, D., Gardon, M., Sekerkova, G., Mugnaini, E., & Shaw, G. (1998). The intermediate filament protein peripherin is a marker for cerebellar climbing fibres. Journal of neurocytology, 27, 69-84.

      Reviewer #1 :

      Summary:

      This fundamental study provides compelling neuroanatomical evidence underscoring the sensory function of the trunk in African and Asian elephants. Whereas myelinated tracts are classically appreciated as mediating neuronal connections, the authors speculate that myelinated bundles provide functional separation of trunk folds and display elaboration related to the "finger" projections. The authors avail themselves of many classical neuroanatomical techniques (including cytochrome oxidase stains, Golgi stains, and myelin stains) along with modern synchrotron X-ray tomography. This work will be of interest to evolutionary neurobiologists, comparative neuroscientists, and the general public, with its fascinating exploration of the brainstem of an icon sensory specialist. 

      Comment: We are incredibly grateful for this positive assessment.

      Changes: None.

      Strengths: 

      - The authors made excellent use of the precious sample materials from 9 captive elephants. 

      - The authors adopt a battery of neuroanatomical techniques to comprehensively characterize the structure of the trigeminal subnuclei and properly re-examine the "inferior olive".

      - Based on their exceptional histological preparation, the authors reveal broadly segregated patterns of metabolic activity, similar to the classical "barrel" organization related to rodent whiskers. 

      Comment: The referee provides a concise summary of our findings.

      Changes: None.

      Weaknesses: 

      - As the authors acknowledge, somewhat limited functional description can be provided using histological analysis (compared to more invasive techniques). 

      - The correlation between myelinated stripes and trunk fold patterns is intriguing, and Figure 4 presents this idea beautifully. I wonder - is the number of stripes consistent with the number of trunk folds? Does this hold for both species? 

      Comment: We agree with the referee’s assessment. We note that cytochrome-oxidase staining is an at least partially functional stain, as it reveals constitutive metabolic activity. A significant problem of the work in elephants is that our recording possibilities are limited, which in turn limits functional analysis. As indicated in Figure 5 (our former Figure 4) for the African elephant Indra, there was an excellent match of trunk folds and myelin stripes. Asian elephants have more, and less conspicuous trunk folds than African elephants. As illustrated in Figure 7, Asian elephants have more, and less conspicuous myelin stripes. Thus, species differences in myelin stripes correlate with species differences in trunk folds.

      Changes: We clarify the relation of myelin stripe and trunk fold patterns in our description of Figure 7.

      Reviewer #2 (Public Review): 

      The authors describe what they assert to be a very unusual trigeminal nuclear complex in the brainstem of elephants, and based on this, follow with many speculations about how the trigeminal nuclear complex, as identified by them, might be organized in terms of the sensory capacity of the elephant trunk.

      Comment: We agree with the referee’s assessment that the putative trigeminal nucleus described in our paper is highly unusual in size, position, vascularization, and myeloarchitecture. This is why we wrote this paper. We think these unusual features reflect the unique facial specializations of elephants, i.e. their highly derived trunk. Because we have no access to recordings from the elephant brainstem, we cannot back up all our functional interpretations with electrophysiological evidence; it is therefore fair to call them speculative.

      Changes: None.

      The identification of the trigeminal nuclear complex/inferior olivary nuclear complex in the elephant brainstem is the central pillar of this manuscript from which everything else follows, and if this is incorrect, then the entire manuscript fails, and all the associated speculations become completely unsupported. 

      Comment: We agree.

      Changes: None.

      The authors note that what they identify as the trigeminal nuclear complex has been identified as the inferior olivary nuclear complex by other authors, citing Shoshani et al. (2006; 10.1016/j.brainresbull.2006.03.016) and Maseko et al (2013; 10.1159/000352004), but fail to cite either Verhaart and Kramer (1958; PMID 13841799) or Verhaart (1962; 10.1515/9783112519882-001). These four studies are in agreement, but the current study differs.

      Comment & Change: We were not aware of the papers of Verhaart and included them in the revised manusript.

      Let's assume for the moment that the four previous studies are all incorrect and the current study is correct. This would mean that the entire architecture and organization of the elephant brainstem is significantly rearranged in comparison to ALL other mammals, including humans, previously studied (e.g. Kappers et al. 1965, The Comparative Anatomy of the Nervous System of Vertebrates, Including Man, Volume 1 pp. 668-695) and the closely related manatee (10.1002/ar.20573). This rearrangement necessitates that the trigeminal nuclei would have had to "migrate" and shorten rostrocaudally, specifically and only, from the lateral aspect of the brainstem where these nuclei extend from the pons through to the cervical spinal cord (e.g. the Paxinos and Watson rat brain atlases), the to the spatially restricted ventromedial region of specifically and only the rostral medulla oblongata. According to the current paper, the inferior olivary complex of the elephant is very small and located lateral to their trigeminal nuclear complex, and the region from where the trigeminal nuclei are located by others appears to be just "lateral nuclei" with no suggestion of what might be there instead.

      Comment: We have three comments here:

      (1) The referee correctly notes that we argue the elephant brainstem underwent fairly major rearrangements. In particular, we argue that the elephant inferior olive was displaced laterally, by a very large cell mass, which we argue is an unusually large trigeminal nucleus. To our knowledge, such a large compact cell mass is not seen in the ventral brain stem of any other mammal.

      (2) The referee makes it sound as if it is our private idea that the elephant brainstem underwent major rearrangements and that the rest of the evidence points to a conventional ‘rodent-like’ architecture. This is far from the truth, however. Already from the outside appearance (see our Figure 1B and Figure 7A) it is clear that the elephant brainstem has huge ventral bumps not seen in any other mammal. An extraordinary architecture also holds at the organizational level of nuclei. Specifically, the facial nucleus – the most carefully investigated nucleus in the elephant brainstem – has an appearance distinct from that of the facial nuclei of all other mammals (Maseko et al., 2013; Kaufmann et al., 2022). If both the overall shape and the constituting nuclei of the brainstem are very different from other mammals, it is very unlikely if not impossible that the elephant brainstem follows in all regards a conventional ‘rodent-like’ architecture.

      (3) The inferior olive is an impressive nucleus in the partitioning scheme we propose (Figure 2). In fact – together with the putative trigeminal nucleus we describe – it’s the most distinctive nucleus in the elephant brainstem. We have not done volumetric measurements and cell counts here, but think this is an important direction for future work. What has informed our work is that the inferior olive nucleus we describe has the serrated organization seen in the inferior olive of all mammals. We will discuss these matters in depth below.

      Changes: None.

      Such an extraordinary rearrangement of brainstem nuclei would require a major transformation in the manner in which the mutations, patterning, and expression of genes and associated molecules during development occur. Such a major change is likely to lead to lethal phenotypes, making such a transformation extremely unlikely. Variations in mammalian brainstem anatomy are most commonly associated with quantitative changes rather than qualitative changes (10.1016/B978-0-12-804042-3.00045-2). 

      Comment: We have two comments here:

      (1) The referee claims that it is impossible that the elephant brainstem differs from a conventional brainstem architecture because this would lead to lethal phenotypes etc. Following our previous response, this argument does not hold. It is out of the question that the elephant brainstem looks very different from the brainstem of other mammals. Yet, it is also evident that elephants live. The debate we need to have is not if the elephant brainstem differs from other mammals, but how it differs from other mammals.

      (2) In principle we agree with the referee’s thinking that the model of the elephant brainstem that is most likely to be correct is the one that requires the least amount of rearrangements to other mammals. We therefore prepared a comparison of the model the referee is proposing (Maseko et al., 2013; see Referee Table 1 below) with our proposition. We scored these models on their similarity to other mammals. We find that the referee’s ideas (Maseko et al., 2013) require more rearrangements relative to other mammals than our suggestion.

      Changes: Inclusion of Referee Table 1, which we discuss in depth below.

      The impetus for the identification of the unusual brainstem trigeminal nuclei in the current study rests upon a previous study from the same laboratory (10.1016/j.cub.2021.12.051) that estimated that the number of axons contained in the infraorbital branch of the trigeminal nerve that innervate the sensory surfaces of the trunk is approximately 400 000. Is this number unusual? In a much smaller mammal with a highly specialized trigeminal system, the platypus, the number of axons innervating the sensory surface of the platypus bill skin comes to 1 344 000 (10.1159. Yet, there is no complex rearrangement of the brainstem trigeminal nuclei in the brain of the developing or adult platypus (Ashwell, 2013, Neurobiology of Monotremes), despite the brainstem trigeminal nuclei being very large in the platypus (10.1159/000067195). Even in other large-brained mammals, such as large whales that do not have a trunk, the number of axons in the trigeminal nerve ranges between 400,000 and 500,000 (10.1007. The lack of comparative support for the argument forwarded in the previous and current study from this laboratory, and that the comparative data indicates that the brainstem nuclei do not change in the manner suggested in the elephant, argues against the identification of the trigeminal nuclei as outlined in the current study. Moreover, the comparative studies undermine the prior claim of the authors, informing the current study, that "the elephant trigeminal ganglion ... point to a high degree of tactile specialization in elephants" (10.1016/j.cub.2021.12.051). While clearly, the elephant has tactile sensitivity in the trunk, it is questionable as to whether what has been observed in elephants is indeed "truly extraordinary".

      Comment: These comments made us think that the referee is not talking about the paper we submitted, but that the referee is talking about us and our work in general. Specifically, the referee refers to the platypus and other animals dismissing our earlier work, which argued for a high degree of tactile specialization in elephants. We think the referee’s intuitions are wrong and our earlier work is valid.

      Changes: We prepared a Author response image 1 (below) that puts the platypus brain, a monkey brain, and the elephant trigeminal ganglion (which contains a large part of the trunk innervating cells) in perspective.

      Author response image 1.

      The elephant trigeminal ganglion is comparatively large. Platypus brain, monkey brain, and elephant ganglion. The elephant has two trigeminal ganglia, which contain the first-order somatosensory neurons. They serve mainly for tactile processing and are large compared to a platypus brain (from the comparative brain collection) and are similar in size to a monkey brain. The idea that elephants might be highly specialized for trunk touch is also supported by the analysis of the sensory nerves of these animals (Purkart et al., 2022). Specifically, we find that the infraorbital nerve (which innervates the trunk) is much thicker than the optic nerve (which mediates vision) and the vestibulocochlear nerve (which mediates hearing). Thus, not everything is large about elephants; instead, the data argue that these animals are heavily specialized for trunk touch.

      But let's look more specifically at the justification outlined in the current study to support their identification of the unusually located trigeminal sensory nuclei of the brainstem. 

      (1) Intense cytochrome oxidase reactivity.

      (2) Large size of the putative trunk module.

      (3) Elongation of the putative trunk module.

      (4) The arrangement of these putative modules corresponds to elephant head

      anatomy. 

      (5) Myelin stripes within the putative trunk module that apparently match trunk folds. <br /> (6) Location apparently matches other mammals.

      (7) Repetitive modular organization apparently similar to other mammals. <br /> (8) The inferior olive described by other authors lacks the lamellated appearance of this structure in other mammals.

      Comment: We agree those are key issues.

      Changes: None.

      Let's examine these justifications more closely.

      (1) Cytochrome oxidase histochemistry is typically used as an indicative marker of neuronal energy metabolism. The authors indicate, based on the "truly extraordinary" somatosensory capacities of the elephant trunk, that any nuclei processing this tactile information should be highly metabolically active, and thus should react intensely when stained for cytochrome oxidase. We are told in the methods section that the protocols used are described by Purkart et al (2022) and Kaufmann et al (2022). In neither of these cited papers is there any description, nor mention, of the cytochrome oxidase histochemistry methodology, thus we have no idea of how this histochemical staining was done. To obtain the best results for cytochrome oxidase histochemistry, the tissue is either processed very rapidly after buffer perfusion to remove blood or in recently perfusion-fixed tissue (e.g., 10.1016/0165-0270(93)90122-8). Given: (1) the presumably long post-mortem interval between death and fixation - "it often takes days to dissect elephants"; (2) subsequent fixation of the brains in 4% paraformaldehyde for "several weeks"; (3) The intense cytochrome oxidase reactivity in the inferior olivary complex of the laboratory rat (Gonzalez-Lima, 1998, Cytochrome oxidase in neuronal metabolism and Alzheimer's diseases); and (4) The lack of any comparative images from other stained portions of the elephant brainstem; it is difficult to support the justification as forwarded by the authors. The histochemical staining observed is likely background reactivity from the use of diaminobenzidine in the staining protocol. Thus, this first justification is unsupported. 

      Comment: The referee correctly notes the description of our cytochrome-oxidase reactivity staining was lacking. This is a serious mistake of ours for which we apologize very much. The referee then makes it sound as if we messed up our cytochrome-oxidase staining, which is not the case. All successful (n = 3; please see our technical comments in the recommendation section) cytochrome-oxidase stainings were done with elephants with short post-mortem times (≤ 2 days) to brain removal/cooling and only brief immersion fixation (≤ 1 day). Cytochrome-oxidase reactivity in elephant brains appears to be more sensitive to quenching by fixation than is the case for rodent brains. We think it is a good idea to include a cytochrome-oxidase staining overview picture because we understood from the referee’s comments that we need to compare our partitioning scheme of the brainstem with that of other authors. To this end, we add a cytochrome-oxidase staining overview picture (Author response image 3) along with an alternative interpretation from Maseko et al., 2013.

      Changes: (1) We added details on our cytochrome-oxidase reactivity staining protocol and the cytochrome-oxidase reactivity in the elephant brain in the manuscript and in our response to the general recommendations.

      (2) We provide a detailed discussion of the technicalities of cytochrome-oxidase staining below in the recommendation section, where the referee raised further criticisms.

      (3) We include a cytochrome-oxidase staining overview picture (Author response image 2) along with an alternative interpretation from Maseko et al., 2013.

      Author response image 2.

      Cytochrome-oxidase staining overview. Coronal cytochrome-oxidase staining overview from African elephant cow Indra; the section is taken a few millimeters posterior to the facial nucleus. Brown is putatively neural cytochrome-reactivity, and white is the background. Black is myelin diffraction and (seen at higher resolution, when you zoom in) erythrocyte cytochrome-reactivity in blood vessels (see our Figure 1E-G); such blood vessel cytochrome-reactivity is seen, because we could not perfuse the animal. There appears to be a minimal outside-in-fixation artifact (i.e. a more whitish/non-brownish appearance of the section toward the borders of the brain). This artifact is not seen in sections from Indra that we processed earlier or in other elephant brains processed at shorter post-mortem/fixation delays (see our Figure 1C).

      The same structures can be recognized in Author response image 2 and Supplememntary figure 36 of Maseko et al. (2013). The section is taken at an anterior-posterior level, where we encounter the trigeminal nuclei in pretty much all mammals. Note that the neural cytochrome reactivity is very high, in what we refer to as the trigeminal-nuclei-trunk-module and what Maseko et al. refer to as inferior olive. Myelin stripes can be recognized here as white omissions.

      At the same time, the cytochrome-oxidase-reactivity is very low in what Maseko et al. refer to as trigeminal nuclei. The indistinct appearance and low cytochrome-oxidase-reactivity of the trigeminal nuclei in the scheme of Maseko et al. (2013) is unexpected because trigeminal nuclei stain intensely for cytochrome-oxidase-reactivity in most mammals and because the trigeminal nuclei represent the elephant’s most important body part, the trunk. Staining patterns of the trigeminal nuclei as identified by Maseko et al. (2013) are very different at more posterior levels; we will discuss this matter below.

      Justifications (2), (3), and (4) are sequelae from justification (1). In this sense, they do not count as justifications, but rather unsupported extensions. 

      Comment: These are key points of our paper that the referee does not discuss.

      Changes: None.

      (4) and (5) These are interesting justifications, as the paper has clear internal contradictions, and (5) is a sequelae of (4). The reader is led to the concept that the myelin tracts divide the nuclei into sub-modules that match the folding of the skin on the elephant trunk. One would then readily presume that these myelin tracts are in the incoming sensory axons from the trigeminal nerve. However, the authors note that this is not the case: "Our observations on trunk module myelin stripes are at odds with this view of myelin. Specifically, myelin stripes show no tapering (which we would expect if axons divert off into the tissue). More than that, there is no correlation between myelin stripe thickness (which presumably correlates with axon numbers) and trigeminal module neuron numbers. Thus, there are numerous myelinated axons, where we observe few or no trigeminal neurons. These observations are incompatible with the idea that myelin stripes form an axonal 'supply' system or that their prime function is to connect neurons. What do myelin stripe axons do, if they do not connect neurons? We suggest that myelin stripes serve to separate rather than connect neurons." So, we are left with the observation that the myelin stripes do not pass afferent trigeminal sensory information from the "truly extraordinary" trunk skin somatic sensory system, and rather function as units that separate neurons - but to what end? It appears that the myelin stripes are more likely to be efferent axonal bundles leaving the nuclei (to form the olivocerebellar tract). This justification is unsupported.

      Comment: The referee cites some of our observations on myelin stripes, which we find unusual. We stand by the observations and comments. The referee does not discuss the most crucial finding we report on myelin stripes, namely that they correspond remarkably well to trunk folds.

      Changes: None.

      (6) The authors indicate that the location of these nuclei matches that of the trigeminal nuclei in other mammals. This is not supported in any way. In ALL other mammals in which the trigeminal nuclei of the brainstem have been reported they are found in the lateral aspect of the brainstem, bordered laterally by the spinal trigeminal tract. This is most readily seen and accessible in the Paxinos and Watson rat brain atlases. The authors indicate that the trigeminal nuclei are medial to the facial nerve nucleus, but in every other species, the trigeminal sensory nuclei are found lateral to the facial nerve nucleus. This is most salient when examining a close relative, the manatee (10.1002/ar.20573), where the location of the inferior olive and the trigeminal nuclei matches that described by Maseko et al (2013) for the African elephant. This justification is not supported. 

      Comment: The referee notes that we incorrectly state that the position of the trigeminal nuclei matches that of other mammals. We think this criticism is justified.

      Changes: We prepared a comparison of the Maseko et al. (2013) scheme of the elephant brainstem with our scheme of the elephant brainstem (see below Referee Table 1). Here we acknowledge the referee’s argument and we also changed the manuscript accordingly.

      (7) The dual to quadruple repetition of rostrocaudal modules within the putative trigeminal nucleus as identified by the authors relies on the fact that in the neurotypical mammal, there are several trigeminal sensory nuclei arranged in a column running from the pons to the cervical spinal cord, these include (nomenclature from Paxinos and Watson in roughly rostral to caudal order) the Pr5VL, Pr5DM, Sp5O, Sp5I, and Sp5C. However, these nuclei are all located far from the midline and lateral to the facial nerve nucleus, unlike what the authors describe in the elephants. These rostrocaudal modules are expanded upon in Figure 2, and it is apparent from what is shown that the authors are attributing other brainstem nuclei to the putative trigeminal nuclei to confirm their conclusion. For example, what they identify as the inferior olive in Figure 2D is likely the lateral reticular nucleus as identified by Maseko et al (2013). This justification is not supported.

      Comment: The referee again compares our findings to the scheme of Maseko et al. (2013) and rejects our conclusions on those grounds. We think such a comparison of our scheme is needed, indeed.

      Changes: We prepared a comparison of the Maseko et al. (2013) scheme of the elephant brainstem with our scheme of the elephant brainstem (see below Referee Table 1).

      (8) In primates and related species, there is a distinct banded appearance of the inferior olive, but what has been termed the inferior olive in the elephant by other authors does not have this appearance, rather, and specifically, the largest nuclear mass in the region (termed the principal nucleus of the inferior olive by Maseko et al, 2013, but Pr5, the principal trigeminal nucleus in the current paper) overshadows the partial banded appearance of the remaining nuclei in the region (but also drawn by the authors of the current paper). Thus, what is at debate here is whether the principal nucleus of the inferior olive can take on a nuclear shape rather than evince a banded appearance. The authors of this paper use this variance as justification that this cluster of nuclei could not possibly be the inferior olive. Such a "semi-nuclear/banded" arrangement of the inferior olive is seen in, for example, giraffe (10.1016/j.jchemneu.2007.05.003), domestic dog, polar bear, and most specifically the manatee (a close relative of the elephant) (brainmuseum.org; 10.1002/ar.20573). This justification is not supported. 

      Comment: We carefully looked at the brain sections referred to by the referee in the brainmuseum.org collection. We found contrary to the referee’s claims that dogs, polar bears, and manatees have a perfectly serrated (a cellular arrangement in curved bands) appearance of the inferior olive. Accordingly, we think the referee is not reporting the comparative evidence fairly and we wonder why this is the case.

      Changes: None.

      Thus, all the justifications forwarded by the authors are unsupported. Based on methodological concerns, prior comparative mammalian neuroanatomy, and prior studies in the elephant and closely related species, the authors fail to support their notion that what was previously termed the inferior olive in the elephant is actually the trigeminal sensory nuclei. Given this failure, the justifications provided above that are sequelae also fail. In this sense, the entire manuscript and all the sequelae are not supported.

      Comment: We disagree. To summarize:

      (1) Our description of the cytochrome oxidase staining lacked methodological detail, which we have now added; the cytochrome oxidase reactivity data are great and support our conclusions.

      (2)–(5)The referee does not really discuss our evidence on these points.

      (6) We were wrong and have now fixed this mistake.

      (7) The referee asks for a comparison to the Maseko et al. (2013) scheme (agreed, see Referee Table 1).

      (8) The referee bends the comparative evidence against us.

      Changes: None.

      A comparison of the elephant brainstem partitioning schemes put forward by Maseko et al 2013 and by Reveyaz et al.

      To start with, we would like to express our admiration for the work of Maseko et al. (2013). These authors did pioneering work on obtaining high-quality histology samples from elephants. Moreover, they made a heroic neuroanatomical effort, in which they assigned 147 brain structures to putative anatomical entities. Most of their data appear to refer to staining in a single elephant and one coronal sectioning plane. The data quality and the illustration of results are excellent.

      We studied mainly two large nuclei in six (now 7) elephants in three (coronal, parasagittal, and horizontal) sectioning planes. The two nuclei in question are the two most distinct nuclei in the elephant brainstem, namely an anterior ventromedial nucleus (the trigeminal trunk module in our terminology; the inferior olive in the terminology of Maseko et al., 2013) and a more posterior lateral nucleus (the inferior olive in our terminology; the posterior part of the trigeminal nuclei in the terminology of Maseko et al., 2013).

      Author response image 3 gives an overview of the two partitioning schemes for inferior olive/trigeminal nuclei along with the rodent organization (see below).

      Author response image 3.

      Overview of the brainstem organization in rodents & elephants

      The strength of the Maseko et al. (2013) scheme is the excellent match of the position of elephant nuclei to the position of nuclei in the rodent (Author response image 3). We think this positional match reflects the fact that Maseko et al. (2013) mapped a rodent partitioning scheme on the elephant brainstem. To us, this is a perfectly reasonable mapping approach. As the referee correctly points out, the positional similarity of both elephant inferior olive and trigeminal nuclei to the rodent strongly argues in favor of the Maseko et al. (2013), because brainstem nuclei are positionally very conservative.

      Other features of the Maseko et al. (2013) scheme are less favorable. The scheme marries two cyto-architectonically very distinct divisions (an anterior indistinct part) and a super-distinct serrated posterior part to be the trigeminal nuclei. We think merging entirely distinct subdivisions into one nucleus is a byproduct of mapping a rodent partitioning scheme on the elephant brainstem. Neither of the two subdivisions resemble the trigeminal nuclei of other mammals. The cytochrome oxidase staining patterns differ markedly across the anterior indistinct part (see our Author response image 3) and the posterior part of the trigeminal nuclei and do not match with the intense cytochrome oxidase reactivity of other mammalian trigeminal nuclei (Author response image 2). Our anti-peripherin staining (the novel Figure 2 of our manuscript) indicates that there probably no climbing fibers, in what Maseko et al. think. is inferior olive; this is a potentially fatal problem for the hypothesis. The posterior part of Maseko et al. (2013) trigeminal nuclei has a distinct serrated appearance that is characteristic of the inferior olive in other mammals. Moreover, the inferior olive of Maseko et al. (2013) lacks the serrated appearance of the inferior olive seen in pretty much all mammals; this is a serious problem.

      The partitioning scheme of Reveyaz et al. comes with poor positional similarity but avoids the other problems of the Maseko et al. (2013) scheme. Our explanation for the positionally deviating location of trigeminal nuclei is that the elephant grew one of the if not the largest trigeminal systems of all mammals. As a result, the trigeminal nuclei grew through the floor of the brainstem. We understand this is a post hoc just-so explanation, but at least it is an explanation.

      The scheme of Reveyaz et al. was derived in an entirely different way from the Maseko model. Specifically, we were convinced that the elephant trigeminal nuclei ought to be very special because of the gigantic trigeminal ganglia (Purkart et al., 2022). Cytochrome-oxidase staining revealed a large distinct nucleus with an elongated shape. Initially, we were freaked out by the position of the nucleus and the fact that it was referred to as inferior olive by other authors. When we found an inferior-olive-like nucleus at a nearby (although at an admittedly unusual) location, we were less worried. We then optimized the visualization of myelin stripes (brightfield imaging etc.) and were able to collect an entire elephant trunk along with the brain (African elephant cow Indra). When we made the one-to-one match of Indra’s trunk folds and myelin stripes (former Figure 4, now Figure 5) we were certain that we had identified the trunk module of the trigeminal nuclei. We already noted at the outset of our rebuttal that we now consider such certainty a fallacy of overconfidence. In light of the comments of Referee 2, we feel that a further discussion of our ideas is warranted.

      A strength of the Reveyaz model is that nuclei look like single anatomical entities. The trigeminal nuclei look like trigeminal nuclei of other mammals, the trunk module has a striking resemblance to the trunk and the inferior olive looks like the inferior olive of other mammals.

      We evaluated the fit of the two models in the form of a table (Author response table 1; below). Unsurprisingly, Author response table 1 aligns with our views of elephant brainstem partitioning.

      Author response table 1

      Qualitative evaluation of elephant brainstem partitioning schemes

      ++ = Very attractive; + = attractive; - = unattractive; -- = very unattractive

      We scored features that are clear and shared by all mammals – as far as we know them – as very attractive.

      We scored features that are clear and are not shared by all mammals – as far as we know them – as very unattractive.

      Attractive features are either less clear or less well-shared features.

      Unattractive features are either less clear or less clearly not shared features.

      Author response table 1 suggests two conclusions to us. (i) The Reveyaz et al. model has mainly favorable properties. The Maseko et al. (2013) model has mainly unfavorable properties. Hence, the Reveyaz et al. model is more likely to be true. (ii) The outcome is not black and white, i.e., both models have favorable and unfavorable properties. Accordingly, we overstated our case in our initial submission and toned down our claims in the revised manuscript.

      What the authors have not done is to trace the pathway of the large trigeminal nerve in the elephant brainstem, as was done by Maseko et al (2013), which clearly shows the internal pathways of this nerve, from the branch that leads to the fifth mesencephalic nucleus adjacent to the periventricular grey matter, through to the spinal trigeminal tract that extends from the pons to the spinal cord in a manner very similar to all other mammals. Nor have they shown how the supposed trigeminal information reaches the putative trigeminal nuclei in the ventromedial rostral medulla oblongata. These are but two examples of many specific lines of evidence that would be required to support their conclusions. Clearly, tract tracing methods, such as cholera toxin tracing of peripheral nerves cannot be done in elephants, thus the neuroanatomy must be done properly and with attention to detail to support the major changes indicated by the authors. 

      Comment: The referee claims that Maseko et al. (2013) showed by ‘tract tracing’ that the structures they refer to trigeminal nuclei receive trigeminal input. This statement is at least slightly misleading. There is nothing of what amounts to proper ‘tract tracing’ in the Maseko et al. (2013) paper, i.e. tracing of tracts with post-mortem tracers. We tried proper post-mortem tracing but failed (no tracer transport) probably as a result of the limitations of our elephant material. What Maseko et al. (2013) actually did is look a bit for putative trigeminal fibers and where they might go. We also used this approach. In our hands, such ‘pseudo tract tracing’ works best in unstained material under bright field illumination, because myelin is very well visualized. In such material, we find: (i) massive fiber tracts descending dorsoventrally roughly from where both Maseko et al. 2013 and we think the trigeminal tract runs. (ii) These fiber tracts run dorsoventrally and approach, what we think is the trigeminal nuclei from lateral.

      Changes: Ad hoc tract tracing see above.

      So what are these "bumps" in the elephant brainstem? 

      Four previous authors indicate that these bumps are the inferior olivary nuclear complex. Can this be supported?

      The inferior olivary nuclear complex acts "as a relay station between the spinal cord (n.b. trigeminal input does reach the spinal cord via the spinal trigeminal tract) and the cerebellum, integrating motor and sensory information to provide feedback and training to cerebellar neurons" (https://www.ncbi.nlm.nih.gov/books/NBK542242/). The inferior olivary nuclear complex is located dorsal and medial to the pyramidal tracts (which were not labeled in the current study by the authors but are clearly present in Fig. 1C and 2A) in the ventromedial aspect of the rostral medulla oblongata. This is precisely where previous authors have identified the inferior olivary nuclear complex and what the current authors assign to their putative trigeminal nuclei. The neurons of the inferior olivary nuclei project, via the olivocerebellar tract to the cerebellum to terminate in the climbing fibres of the cerebellar cortex.

      Comment: We agree with the referee that in the Maseko et al. (2013) scheme the inferior olive is exactly where we expect it from pretty much all other mammals. Hence, this is a strong argument in favor of the Maseko et al. (2013) scheme and a strong argument against the partitioning scheme suggested by us.

      Changes: Please see our discussion above.

      Elephants have the largest (relative and absolute) cerebellum of all mammals (10.1002/ar.22425), this cerebellum contains 257 x109 neurons (10.3389/fnana.2014.00046; three times more than the entire human brain, 10.3389/neuro.09.031.2009). Each of these neurons appears to be more structurally complex than the homologous neurons in other mammals (10.1159/000345565; 10.1007/s00429-010-0288-3). In the African elephant, the neurons of the inferior olivary nuclear complex are described by Maseko et al (2013) as being both calbindin and calretinin immunoreactive. Climbing fibres in the cerebellar cortex of the African elephant are clearly calretinin immunopositive and also are likely to contain calbindin (10.1159/000345565). Given this, would it be surprising that the inferior olivary nuclear complex of the elephant is enlarged enough to create a very distinct bump in exactly the same place where these nuclei are identified in other mammals? 

      Comment: We agree with the referee that it is possible and even expected from other mammals that there is an enlargement of the inferior olive in elephants. Hence, a priori one might expect the ventral brain stem bumps to the inferior olive, this is perfectly reasonable and is what was done by previous authors. The referee also refers to calbindin and calretinin antibody reactivity. Such antibody reactivity is indeed in line with the referee’s ideas and we considered these findings in our Referee Table 1. The problem is, however, that neither calbindin nor calretinin antibody reactivity are highly specific and indeed both nuclei in discussion (trigeminal nuclei and inferior olive) show such reactivity. Unlike the peripherin-antibody staining advanced by us, calbindin nor calretinin antibody reactivity cannot distinguish the two hypotheses debated.

      Changes: Please see our discussion above.

      What about the myelin stripes? These are most likely to be the origin of the olivocerebellar tract and probably only have a coincidental relationship with the trunk. Thus, given what we know, the inferior olivary nuclear complex as described in other studies, and the putative trigeminal nuclear complex as described in the current study, is the elephant inferior olivary nuclear complex. It is not what the authors believe it to be, and they do not provide any evidence that discounts the previous studies. The authors are quite simply put, wrong. All the speculations that flow from this major neuroanatomical error are therefore science fiction rather than useful additions to the scientific literature. 

      Comment: It is unlikely that the myelin stripes are the origin of the olivocerebellar tract as suggested by the referee. Specifically, the lack of peripherin-reactivity indicates that these fibers are not climbing fibers (our novel Figure 2). In general, we feel the referee does not want to discuss the myelin stripes and obviously thinks we made up the strange correspondence of myelin stripes and trunk folds.

      Changes: Please see our discussion above.

      What do the authors actually have? 

      The authors have interesting data, based on their Golgi staining and analysis, of the inferior olivary nuclear complex in the elephant.

      Comment: The referee reiterates their views.

      Changes: None.

      Reviewer #3 (Public Review):

      Summary: 

      The study claims to investigate trunk representations in elephant trigeminal nuclei located in the brainstem. The researchers identified large protrusions visible from the ventral surface of the brainstem, which they examined using a range of histological methods. However, this ventral location is usually where the inferior olivary complex is found, which challenges the author's assertions about the nucleus under analysis. They find that this brainstem nucleus of elephants contains repeating modules, with a focus on the anterior and largest unit which they define as the putative nucleus principalis trunk module of the trigeminal. The nucleus exhibits low neuron density, with glia outnumbering neurons significantly. The study also utilizes synchrotron X-ray phase contrast tomography to suggest that myelin-stripe-axons traverse this module. The analysis maps myelin-rich stripes in several specimens and concludes that based on their number and patterning they likely correspond with trunk folds; however, this conclusion is not well supported if the nucleus has been misidentified.

      Comment: The referee gives a concise summary of our findings. The referee acknowledges the depth of our analysis and also notes our cellular results. The referee – in line with the comments of Referee 2 – also points out that a misidentification of the nucleus under study is potentially fatal for our analysis. We thank the referee for this fair assessment.

      Changes: We feel that we need to alert the reader more broadly to the misidentification concern. We think the critical comments of Referee 2, which will be published along with our manuscript, will go a long way in doing so. We think the eLife publishing format is fantastic in this regard. We will also include pointers to these concerns in the revised manuscript.

      Strengths: 

      The strength of this research lies in its comprehensive use of various anatomical methods, including Nissl staining, myelin staining, Golgi staining, cytochrome oxidase labeling, and synchrotron X-ray phase contrast tomography. The inclusion of quantitative data on cell numbers and sizes, dendritic orientation and morphology, and blood vessel density across the nucleus adds a quantitative dimension. Furthermore, the research is commendable for its high-quality and abundant images and figures, effectively illustrating the anatomy under investigation.

      Comment: Again, a very fair and balanced set of comments. We are thankful for these comments.

      Changes: None.

      Weaknesses: 

      While the research provides potentially valuable insights if revised to focus on the structure that appears to be the inferior olivary nucleus, there are certain additional weaknesses that warrant further consideration. First, the suggestion that myelin stripes solely serve to separate sensory or motor modules rather than functioning as an "axonal supply system" lacks substantial support due to the absence of information about the neuronal origins and the termination targets of the axons. Postmortem fixed brain tissue limits the ability to trace full axon projections. While the study acknowledges these limitations, it is important to exercise caution in drawing conclusions about the precise role of myelin stripes without a more comprehensive understanding of their neural connections.

      Comment: The referee points out a significant weakness of our study, namely our limited understanding of the origin and targets of the axons constituting the myelin stripes. We are very much aware of this problem and this is also why we directed high-powered methodology like synchrotron X-ray tomograms to elucidate the structure of myelin stripes. Such analysis led to advances, i.e., we now think, what looks like stripes are bundles and we understand the constituting axons tend to transverse the module. Such advances are insufficient, however, to provide a clear picture of myelin stripe connectivity.

      Changes: We think solving the problems raised by the referee will require long-term methodological advances and hence we will not be able to solve these problems in the current revision. Our long-term plans for confronting these issues are the following: (i) Improving our understanding of long-range connectivity by post-mortem tracing and MR-based techniques such as Diffusion-Tensor-Imaging. (ii) Improving our understanding of mid and short-range connectivity by applying even larger synchrotron X-ray tomograms and possible serial EM.

      Second, the quantification presented in the study lacks comparison to other species or other relevant variables within the elephant specimens (i.e., whole brain or brainstem volume). The absence of comparative data for different species limits the ability to fully evaluate the significance of the findings. Comparative analyses could provide a broader context for understanding whether the observed features are unique to elephants or more common across species. This limitation in comparative data hinders a more comprehensive assessment of the implications of the research within the broader field of neuroanatomy. Furthermore, the quantitative comparisons between African and Asian elephant specimens should include some measure of overall brain size as a covariate in the analyses. Addressing these weaknesses would enable a richer interpretation of the study's findings.

      Comment: The referee suggests another series of topics, which include the analysis of brain parts volumes or overall brain size. We agree these are important issues, but we also think such questions are beyond the scope of our study.

      Changes: We hope to publish comparative data on elephant brain size and shape later this year.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      I realize that elephant brains are a limiting resource in this project, along with the ability to perform functional investigations. However, I believe that Prof. Jon Kaas (Vanderbilt University) has one or more series of Nissl-stained brainstems from elephants. These might be of potential interest, as they were previously used to explore general patterns of trigeminal brainstem organization in a comparative manner (see Sawyer and Sarko, 2017, "Comparative Anatomy and Evolution of the Somatosensory Brain Stem" in the Evolution of Nervous System series) and might shed light on the positioning of the trigeminal complex and IO, with parts of the trigeminal nerve itself still attached to these sections.

      Comment: The referee suggests adding data from more elephants and we think this is a great suggestion because our ns are small. We followed this advice. We agree we need more comparative neuroanatomy of elephants and the urgency of this matter is palpable in the heated debate we have with Referee 2. Specifically, we need more long-range and short-range analysis of elephant brains.

      Changes: We plan to include data in the revised manuscript about cytoarchitectonics (Nissl), cytochrome-oxidase reactivity, and possibly also antibody reactivity from an additional animal, i.e., from the African elephant cow Bibi. The quality of this specimen is excellent and the post-mortem time to brain extraction was very short.

      We also have further plans for connectivity analysis (see our response above), but such data will not become available fast enough for the revision.

      Other recommendations: 

      - A general schematic showing input from trunk to PrV to the trigeminal subnuclei (as well as possibly ascending connections) might be informative to the reader, in terms of showing which neural relay is being examined.

      Comment: We think this is a very good suggestion in principle, but we were not satisfied with the schematics we came up with.

      Changes: None.

      - Perhaps a few more sentences described the significance of synchrotron tomography for those who may be unfamiliar.

      Comment & Change: We agree and implement this suggestion.

      - "Belly-shaped" trunk module description is unclear on page 9. 

      Comment & Change: We clarified this matter.

      - Typo on the last sentence of page 9. 

      Comment & Change: We fixed this mistake.

      Reviewer #2 (Recommendations For The Authors): 

      The data is only appropriate a specialized journal and is limited to the Golgi analysis of neurons within the inferior olivary complex of the elephant. This reviewer considers that the remainder of the work is speculation and that the paper in its current version is not salvageable.

      Comment: Rather than suggesting changes, the referee makes it clear that the referee does not want to see our paper published. We think this desire to reject is not rooted in a lack of quality of our work. In fact, we did an immense amount of work (detailed cytoarchitectonic analysis of six (now seven) elephant brainstems rather than one as in the case of our predecessors), cell counts, and X-ray tomography. Instead, we think the problem is rooted in the fact that we contradict the referee. To us, such suppression of diverging opinions – provided they are backed up with data – is a scientifically deeply unhealthy attitude. Science lives from the debate and this is why we did not exclude any referees even though we knew that our results do not align with the views of all of the few actors in the field.

      Changes: We think the novel eLife publishing scheme was developed to prevent such abuse. We look forward to having our data published along with the harsh comments of the referee. The readers and subsequent scientific work will determine who’s right and who’s wrong.

      In order to convince readers of the grand changes to the organization of the brainstem in a species suggested by the authors the data presented needs to be supported. It is not. 

      Comment: Again, this looks to us like more of the ‘total-rejection-commentary’ than like an actual recommendation.

      Changes: None.

      The protocol for the cytochrome oxidase histochemistry is not available in the locations indicated by the authors, and it is very necessary to provide this, as I fully believe that the staining obtained is not real, given the state of the tissue used. 

      Comment: We apologize again for not including the necessary details on our cytochrome-oxidase staining.

      From these comments (and the initial comments above) it appears that the referee is uncertain about the validity of cytochrome-oxidase staining. We (M.B., the senior author) have been doing this particular stain for approximately three decades. The referee being unfamiliar with cytochrome-oxidase staining is fine, but we can’t comprehend how the referee then comes to the ‘full belief’ that our staining patterns are ‘not real’ when the visual evidence indicates the opposite. We feel the referee does not want to believe our data.

      From hundreds of permutations, we can assure the referee that cytochrome-oxidase staining can go wrong in many ways. The most common failure outcome in elephants is a uniform light brown stain after hours or days of the cytochrome-oxidase reaction. This outcome is closely associated with long ≥2 days post-mortem/fixation times and reflects the quenching of cytochrome-oxidases by fixation. Interestingly, cytochrome-oxidase staining in elephant brains is distinctly more sensitive to quenching by fixation than cytochrome-oxidase staining in rodent brains. Another, more rare failure of cytochrome-oxidase staining comes as entirely white or barely colored sections; this outcome is usually associated with a bad reagent (most commonly old DAB, but occasionally also old or bad catalase, in case you are using a staining protocol with catalase). Another nasty cytochrome-oxidase staining outcome is smeary all-black sections. In this case, a black precipitate sticks to sections and screws up the staining (filtering and more gradual heating of the staining solution usually solve this problem). Thus, you can get uniformly white, uniformly light brown, and smeary black sections as cytochrome-oxidase staining failures. What you never get from cytochrome-oxidase staining as an artifact are sections with a strong brown to lighter brown differential contrast. All sections with strong brown to lighter brown differential contrast (staining successes) show one and the same staining pattern in a given brain area, i.e., brownish barrels in the rodent cortex, brownish barrelettes (trigeminal nuclei) in the rodent brainstem, brownish putative trunk modules/inferior olives (if we believe the referee) in the elephant brainstem. Cytochrome-oxidase reactivity is in this regard remarkably different from antibody staining. In antibody staining you can get all kinds of interesting differential contrast staining patterns, which mean nothing. Such differential contrast artifacts in antibody staining arise as a result of insufficient primary antibody specificity, the secondary antibody binding non-specifically, and of what have you not reasons. The reason that the brown differential contrast of cytochrome-oxidase reaction is pretty much fool-proof, relates to the histochemical staining mechanism, which is based on the supply of specific substrates to a universal mitochondrial enzyme. The ability to reveal mitochondrial metabolism and the universal and ‘fool-proof’ staining qualities make the cytochrome-oxidase reactivity a fantastic tool for comparative neuroscience, where you always struggle with insufficient information about antigen reactivity.

      We also note that the contrast of cytochrome-oxidase reactivity seen in the elephant brainstem is spectacular. As the Referee can see in our Figure 1C we observe a dark brown color in the putative trunk module, with the rest of the brain being close to white. Such striking cytochrome-oxidase reactivity contrast has been observed only very rarely in neuroanatomy: (i) In the rest of the elephant brain (brainstem, thalamus cortex) we did not observe as striking contrast as in the putative trunk module (the inferior olive according to the referee). (ii) In decades of work with rodents, we have rarely seen such differential activity. For example, cortical whisker-barrels (a classic CO-staining target) in rodents usually come out as dark brown against a light brown background.

      What all of this commentary means is that patterns revealed by differential cytochrome-oxidase staining in the elephant brain stem are real.

      Changes: We added details on our cytochrome-oxidase reactivity staining protocol and commented on cytochrome-oxidase reactivity in the elephant brain in general.

      The authors need to recognize that the work done in Africa on elephant brains is of high quality and should not be blithely dismissed by the authors - this stinks of past colonial "glory", especially as the primary author on these papers is an African female.

      Comment: The referee notes that we unfairly dismiss the work of African scientists and that our paper reflects a continuation of our horrific colonial past because we contradict the work of an African woman. We think such commentary is meant to be insulting and prefer to return to the scientific discourse. We are staunch supporters of diversity in science. It is simply untrue, that we do not acknowledge African scientists or the excellent work done in Africa on elephant brains. For example, we cite no less than four papers from the Manger group. We refer countless times in the manuscript to these papers, because these papers are highly relevant to our work. We indeed disagree with two anatomical assignments made by Maseko et al., 2013. Such differences should not be overrated, however. As we noted before, such differences relate to only 2 out of 147 anatomical assignments made by these authors. More generally, discussing and even contradicting papers is the appropriate way to acknowledge scientists. We already expressed we greatly admire the pioneering work of the Manger group. In our view, the perfusion of elephants in the field is a landmark experiment in comparative neuroanatomy. We closely work with colleagues in Africa and find them fantastic collaborators. When the referee is accusing us of contradicting the work of an African woman, the referee is unfairly and wrongly accusing us of attacking a scientist’s identity. More generally, we feel the discussion should focus on the data presented.

      Changes: None.

      In addition, perfusing elephants in the field with paraformaldehyde shortly after death is not a problem "partially solved" when it comes to collecting elephant tissue (n.b., with the right tools the brain of the elephant can be removed in under 2 hours). It means the problem IS solved. This is evidenced by the quality of the basic anatomical, immuno-, and Golgi-staining of the elephant tissue collected in Africa.

      Comment: This is not a recommendation. We repeat: In our view, the perfusion of elephants in the field by the Manger group is a landmark experiment in comparative neuroanatomy. Apart, from that, we think the referee got our ‘partially solved comment’ the wrong way. It is perhaps worthwhile to recall the context of this quote. We first describe the numerous limitations of our elephant material; admitting these limitations is about honesty. Then, we wanted to acknowledge previous authors who either paved the way for elephant neuroanatomy (Shoshani) or did a better job than we did (Manger; see the above landmark experiment). These citations were meant as an appreciation of our predecessors’ work and by far not meant to diminish their work. Why did we say that the problems of dealing with elephant material are only partially solved? Because elephant neuroanatomy is hard and the problems associated with it are by no means solved. Many previous studies rely on single specimen and our possibilities of accessing, removing, processing, and preserving elephant brains are limited and inferior to the conditions elsewhere. Doing a mouse brain is orders of magnitude easier than doing an elephant brain (because the problems of doing mouse anatomy are largely solved), yet it is hard to publish a paper with six elephant brains because the referees expect evidence at least half as good as what you get in mice.

      Changes: We replaced the ‘partially solved’ sentence.

      The authors need to give credit where credit is due - the elephant cerebellum is clearly at the core of controlling trunk movement, and as much as primary sensory and final stage motor processing is important, the complexity required for the neural programs needed to move the trunk either voluntarily or in response to stimuli, is being achieved by the cerebellum. The inferior olive is part of this circuit and is accordingly larger than one would expect.

      Comment: We think it is very much possible that the elephant cerebellum is important in trunk control.

      Changes: We added a reference to the elephant cerebellum in the introduction of our manuscript.

    1. Author Response:

      Reviewer #1 (Public Review):

      Force sensing and gating mechanisms of the mechanically activated ion channels is an area of broad interest in the field of mechanotransduction. These channels perform important biological functions by converting mechanical force into electrical signals. To understand their underlying physiological processes, it is important to determine gating mechanisms, especially those mediated by lipids. The authors in this manuscript describe a mechanism for mechanically induced activation of TREK-1 (TWIK-related K+ channel. They propose that force induced disruption of ganglioside (GM1) and cholesterol causes relocation of TREK-1 associated with phospholipase D2 (PLD2) to 4,5-bisphosphate (PIP2) clusters, where PLD2 catalytic activity produces phosphatidic acid that can activate the channel. To test their hypothesis, they use dSTORM to measure TREK-1 and PLD2 colocalization with either GM1 or PIP2. They find that shear stress decreases TREK-1/PLD2 colocalization with GM1 and relocates to cluster with PIP2. These movements are affected by TREK-1 C-terminal or PLD2 mutations suggesting that the interaction is important for channel re-location. The authors then draw a correlation to cholesterol suggesting that TREK-1 movement is cholesterol dependent. It is important to note that this is not the only method of channel activation and that one not involving PLD2 also exists. Overall, the authors conclude that force is sensed by ordered lipids and PLD2 associates with TREK-1 to selectively gate the channel. Although the proposed mechanism is solid, some concerns remain.

      1) Most conclusions in the paper heavily depend on the dSTORM data. But the images provided lack resolution. This makes it difficult for the readers to assess the representative images.

      The images were provided are at 300 dpi. Perhaps the reviewer is referring to contrast in Figure 2? We are happy to increase the contrast or resolution.

      As a side note, we feel the main conclusion of the paper, mechanical activation of TREK-1 through PLD2, depended primarily on the electrophysiology in Figure 1b-c, not the dSTORM. But both complement each other.

      2) The experiments in Figure 6 are a bit puzzling. The entire premise of the paper is to establish gating mechanism of TREK-1 mediated by PLD2; however, the motivation behind using flies, which do not express TREK-1 is puzzling.

      The fly experiment shows that PLD mechanosensitivity is more evolutionarily conserved than TREK-1 mechanosensitivity. We should have made this clearer.

      -Figure 6B, the image is too blown out and looks over saturated. Unclear whether the resolution in subcellular localization is obvious or not.

      Figure 6B is a confocal image, it is not dSTORM. There is no dSTORM in Figure 6. This should have been made clear in the figure legend. For reference, only a few cells would fit in the field of view with dSTORM.

      -Figure 6C-D, the differences in activity threshold is 1 or less than 1g. Is this physiologically relevant? How does this compare to other conditions in flies that can affect mechanosensitivity, for example?

      Yes, 1g is physiologically relevant. It is almost the force needed to wake a fly from sleep (1.2-3.2g). See ref 33. Murphy Nature Pro. 2017.

      3) 70mOsm is a high degree of osmotic stress. How confident are the authors that a. cell health is maintained under this condition and b. this does indeed induce membrane stretch? For example, does this stimulation activate TREK-1?

      Yes, osmotic swell activates TREK1. This was shown in ref 19 (Patel et al 1998). We agree the 70 mOsm is a high degree of stress. This needs to be stated better in the paper.

      Reviewer #2 (Public Review):

      This manuscript by Petersen and colleagues investigates the mechanistic underpinnings of activation of the ion channel TREK-1 by mechanical inputs (fluid shear or membrane stretch) applied to cells. Using a combination of super-resolution microscopy, pair correlation analysis and electrophysiology, the authors show that the application of shear to a cell can lead to changes in the distribution of TREK-1 and the enzyme PhospholipaseD2 (PLD2), relative to lipid domains defined by either GM1 or PIP2. The activation of TREK-1 by mechanical stimuli was shown to be sensitized by the presence of PLD2, but not a catalytically dead xPLD2 mutant. In addition, the activity of PLD2 is increased when the molecule is more associated with PIP2, rather than GM1 defined lipid domains. The presented data do not exclude direct mechanical activation of TREK-1, rather suggest a modulation of TREK-1 activity, increasing sensitivity to mechanical inputs, through an inherent mechanosensitivity of PLD2 activity. The authors additionally claim that PLD2 can regulate transduction thresholds in vivo using Drosophila melanogaster behavioural assays. However, this section of the manuscript overstates the experimental findings, given that it is unclear how the disruption of PLD2 is leading to behavioural changes, given the lack of a TREK-1 homologue in this organism and the lack of supporting data on molecular function in the relevant cells.

      We agree, the downstream effectors of PLD2 mechanosensitivity are not known in the fly. Other anionic lipids have been shown to mediate pain see ref 46 and 47. We do not wish to make any claim beyond PLD2 being an in vivo contributor to a fly’s response to mechanical force.

      That said we do believe we have established a molecular function at the cellular level. We showed PLD is robustly mechanically activated in a cultured fly cell line (BG2-c2) Figure 6a of the manuscript. And our previous publication established mechanosensation of PLD (Petersen et. al. Nature Com 2016) through mechanical disruption of the lipids. At a minimum, the experiments show PLDs mechanosensitivity is evolutionarily better conserved across species than TREK1.

      This work will be of interest to the growing community of scientists investigating the myriad mechanisms that can tune mechanical sensitivity of cells, providing valuable insight into the role of functional PLD2 in sensitizing TREK-1 activation in response to mechanical inputs, in some cellular systems.

      The authors convincingly demonstrate that, post application of shear, an alteration in the distribution of TREK-1 and mPLD2 (in HEK293T cells) from being correlated with GM1 defined domains (no shear) to increased correlation with PIP2 defined membrane domains (post shear). These data were generated using super-resolution microscopy to visualise, at sub diffraction resolution, the localisation of labelled protein, compared to labelled lipids. The use of super-resolution imaging enabled the authors to visualise changes in cluster association that would not have been achievable with diffraction limited microscopy. However, the conclusion that this change in association reflects TREK-1 leaving one cluster and moving to another overinterprets these data, as the data were generated from static measurements of fixed cells, rather than dynamic measurements capturing molecular movements.

      When assessing molecular distribution of endogenous TREK-1 and PLD2, these molecules are described as "well correlated: in C2C12 cells" however it is challenging to assess what "well correlated" means, precisely in this context. This limitation is compounded by the conclusion that TREK-1 displayed little pair correlation with GM1 and the authors describe a "small amount of TREK-1 trafficked to PIP2". As such, these data may suggest that the findings outlined for HEK293T cells may be influenced by artefacts arising from overexpression.

      The changes in TREK-1 sensitivity to mechanical activation could also reflect changes in the amount of TREK-1 in the plasma membrane. The authors suggest that the presence of a leak currently accounts for the presence of TREK-1 in the plasma membrane, however they do not account for whether there are significant changes in the membrane localisation of the channel in the presence of mPLD2 versus xPLD2. The supplementary data provide some images of fluorescently labelled TREK-1 in cells, and the authors state that truncating the c-terminus has no effect on expression at the plasma membrane, however these data provide inadequate support for this conclusion. In addition, the data reporting the P50 should be noted with caution, given the lack of saturation of the current in response to the stimulus range.

      We thank the reviewer for his/her concern about expression levels. We did test TREK-1 expression. mPLD decreases TREK-1 expression ~two-fold (see Author response image 1). We did not include the mPLD data since TREK-1 was mechanically activated with mPLD. For expression to account for the loss of TREK-1 stretch current (Figure 1b), xPLD would need to block surface expression of TREK-1. The opposite was true, xPLD2 increased TREK-1 expression increased (see Figure S2c). Furthermore, we tested the leak current of TREK-1 at 0 mV and 0 mmHg of stretch. Basal leak current was no different with xPLD2 compared to endogenous PLD (Figure 1d; red vs grey bars respectively) suggesting TREK-1 is in the membrane and active when xPLD2 is present. If anything, the magnitude of the effect with xPLD would be larger if the expression levels were equal.

      Author response image 1.

      TREK expression at the plasma membrane. TREK-1 Fluorescence was measured by GFP at points along the plasma membrane. Over expression of mouse PLD2 (mPLD) decrease the amount of full-length TREK-1 (FL TREK) on the surface more than 2-fold compared to endogenously expressed PLD (enPLD) or truncated TREK (TREKtrunc) which is missing the PLD binding site in the C-terminus. Over expression of mPLD had no effect on TREKtrunc.

      Finally, by manipulating PLD2 in D. melanogaster, the authors show changes in behaviour when larvae are exposed to either mechanical or electrical inputs. The depletion of PLD2 is concluded to lead to a reduction in activation thresholds and to suggest an in vivo role for PA lipid signaling in setting thresholds for both mechanosensitivity and pain. However, while the data provided demonstrate convincing changes in behaviour and these changes could be explained by changes in transduction thresholds, these data only provide weak support for this specific conclusion. As the authors note, there is no TREK-1 in D. melanogaster, as such the reported findings could be accounted for by other explanations, not least including potential alterations in the activation threshold of Nav channels required for action potential generation. To conclude that the outcomes were in fact mediated by changes in mechanotransduction, the authors would need to demonstrate changes in receptor potential generation, rather than deriving conclusions from changes in behaviour that could arise from alterations in resting membrane potential, receptor potential generation or the activity of the voltage gated channels required for action potential generation.

      We are willing to restrict the conclusion about the fly behavior as the reviewers see fit. We have shown PLD is mechanosensitivity in a fly cell line, and when we knock out PLD from a fly, the animal exhibits a mechanosensation phenotype.

      This work provides further evidence of the astounding flexibility of mechanical sensing in cells. By outlining how mechanical activation of TREK-1 can be sensitised by mechanical regulation of PLD2 activity, the authors highlight a mechanism by which TREK-1 sensitivity could be regulated under distinct physiological conditions.

      Reviewer #3 (Public Review):

      The manuscript "Mechanical activation of TWIK-related potassium channel by nanoscopic movement and second messenger signaling" presents a new mechanism for the activation of TREK-1 channel. The mechanism suggests that TREK1 is activated by phosphatidic acids that are produced via a mechanosensitive motion of PLD2 to PIP2-enriched domains. Overall, I found the topic interesting, but several typos and unclarities reduced the readability of the manuscript. Additionally, I have several major concerns on the interpretation of the results. Therefore, the proposed mechanism is not fully supported by the presented data. Lastly, the mechanism is based on several previous studies from the Hansen lab, however, the novelty of the current manuscript is not clearly stated. For example, in the 2nd result section, the authors stated, "fluid shear causes PLD2 to move from cholesterol dependent GM1 clusters to PIP2 clusters and this activated the enzyme". However, this is also presented as a new finding in section 3 "Mechanism of PLD2 activation by shear."

      For PLD2 dependent TREK-1 activation. Overall, I found the results compelling. However, two key results are missing. 1. Does HEK cells have endogenous PLD2? If so, it's hard to claim that the authors can measure PLD2-independent TREK1 activation.

      Yes, there is endogenous PLD (enPLD). We calculated the relative expression of xPLD2 vs enPLD. xPLD2 is >10x more abundant (Fig. S3d of Pavel et al PNAS 2020, ref 14 of the current manuscript). Hence, as with anesthetic sensitivity, we expect the xPLD to out compete the endogenous PLD, which is what we see. This should have been described more carefully in this paper and the studies pointed out that establish this conclusion.

      1. Does the plasma membrane trafficking of TREK1 remain the same under different conditions (PLD2 overexpression, truncation)? From Figure S2, the truncated TREK1 seem to have very poor trafficking. The change of trafficking could significantly contribute to the interpretation of the data in Figure 1.

      If the PLD2 binding site is removed (TREK-1trunc), yes, the trafficking to the plasma membrane is unaffected by the expression of xPLD and mPLD (Figure R1 above). For full length TREK1 (FL-TREK-1), co-expression of mPLD decreases TREK expression (Figure R1) and co-expression with xPLD increases TREK expression (Figure S2). This is exactly opposite of what one would expect if surface expression accounted for the change in pressure currents. Hence, we conclude surface expression does not account for loss of TREK-1 mechanosensitivity with xPLD2.

      For shear-induced movement of TREK1 between nanodomains. The section is convincing, however I'm not an expert on super-resolution imaging. Also, it would be helpful to clarify whether the shear stress was maintained during fixation. If not, what is the time gap between reduced shear and the fixed state. lastly, it's unclear why shear flow changes the level of TREK1 and PIP2.

      Shear was maintained during the fixing. We do not know why shear changes PIP2 and TREK-1 levels. Presumably endocytosis and or release of other lipid modifying enzymes affect the system. The change in TREK-1 levels appears to be directly through an interaction with PLD as TREKtrunc is not affected by over expression of xPLD or mPLD.

      For the mechanism of PLD2 activation by shear. I found this section not convincing. Therefore, the question of how does PLD2 sense mechanical force on the membrane is not fully addressed. Particularly, it's hard to imagine an acute 25% decrease cholesterol level by shear - where did the cholesterol go? Details on the measurements of free cholesterol level is unclear and additional/alternative experiments are needed to prove the reduction in cholesterol by shear.

      The question “how does PLD2 sense mechanical force on the membrane” we addressed and published in Nature Comm. In 2016. The title of that paper is “Kinetic disruption of lipid rafts is a mechanosensor for phospholipase D” see ref 13 Petersen et. al. PLD is a soluble protein associated to the membrane through palmitoylation. There is no transmembrane domain, which narrows the possible mechanism of its mechanosensation to disruption.

      The Nature Comm. reviewer identified as “an expert in PLD signaling” wrote the following of our data and the proposed mechanism:

      "This is a provocative report that identifies several unique properties of phospholipase D2 (PLD2). It explains in a novel way some long established observations including that the enzyme is largely regulated by substrate presentation which fits nicely with the authors model of segregation of the two lipid raft domains (cholesterol ordered vs PIP2 containing). Although PLD has previously been reported to be involved in mechanosensory transduction processes (as cited by the authors) this is the first such report associating the enzyme with this type of signaling... It presents a novel model that is internally consistent with previous literature as well as the data shown in this manuscript. It suggests a new role for PLD2 as a force transduction tied to the physical structure of lipid rafts and uses parallel methods of disruption to test the predictions of their model."

      Regarding cholesterol. We use a fluorescent cholesterol oxidase assay which we described in the methods. This is an appropriate assay for determining cholesterol levels in a cell which we use routinely. We have published in multiple journals using this method, see references 28, 30, 31. Working out the metabolic fate of cholesterol after sheer is indeed interesting but well beyond the scope of this paper. Furthermore, we indirectly confirmed our finding using dSTORM cluster analysis (Figure 3d-e). The cluster analysis shows a decrease in GM1 cluster size consistent with our previous experiments where we chemically depleted cholesterol and saw a similar decrease in cluster size (see ref 13). All the data are internally consistent, and the cholesterol assay is properly done. We see no reason to reject the data.

      Importantly, there is no direct evidence for "shear thinning" of the membrane and the authors should avoid claiming shear thinning in the abstract and summary of the manuscript.

      We previously established a kinetic model for PLD2 activation see ref 13 (Petersen et al Nature Comm 2016). In that publication we discussed both entropy and heat as mechanisms of disruption. Here we controlled for heat which narrowed that model to entropy (i.e., shear thinning) (see Figure 3c). We provide an overall justification below. But this is a small refinement of our previous paper, and we prefer not to complicate the current paper. We believe the proper rheological term is shear thinning. The following justification, which is largely adapted from ref 13, could be added to the supplement if the reviewer wishes.

      Justification: To establish shear thinning in a biological membrane, we initially used a soluble enzyme that has no transmembrane domain, phospholipase D2 (PLD2). PLD2 is a soluble enzyme and associated with the membrane by palmitate, a saturated 16 carbon lipid attached to the enzyme. In the absence of a transmembrane domain, mechanisms of mechanosensation involving hydrophobic mismatch, tension, midplane bending, and curvature can largely be excluded. Rather the mechanism appears to be a change in fluidity (i.e., kinetic in nature). GM1 domains are ordered, and the palmate forms van der Waals bonds with the GM1 lipids. The bonds must be broken for PLD to no longer associate with GM1 lipids. We established this in our 2016 paper, ref 13. In that paper we called it a kinetic effect, however we did not experimentally distinguish enthalpy (heat) vs. entropy (order). Heat is Newtonian and entropy (i.e., shear thinning) is non-Newtonian. In the current study we paid closer attention to the heat and ruled it out (see Figure 3c and methods). We could propose a mechanism based on kinetic disruption, but we know the disruption is not due to melting of the lipids (enthalpy), which leaves shear thinning (entropy) as the plausible mechanism.

      The authors should also be aware that hypotonic shock is a very dirty assay for stretching the cell membrane. Often, there is only a transient increase in membrane tension, accompanied by many biochemical changes in the cells (including acidification, changes of concentration etc). Therefore, I would not consider this as definitive proof that PLD2 can be activated by stretching membrane.

      Comment noted. We trust the reviewer is correct. In 1998 osmotic shock was used to activate the channel. We only intended to show that the system is consistent with previous electrophysiologic experiments.

    1. Author response:

      The following is the authors’ response to the current reviews.

      We thank you for sending our manuscript for the second round of review.  We are encouraged by the comments from reviewer #2 that our supplementary work on naïve T cells and antibody blockade work satisfied their previous concerns and is important for our work.

      The Editors raised concerns that we have shared preliminary data on Nrn1 and AMPAR double knockout mice.  We apologize for our enthusiasm for these studies.  Because of the publication model by eLife, we shared that data not because we needed to persuade the reviewer for publication purposes but rather to agree with the reviewer that the molecular target of Nrn1 is important, and we are progressing in understanding this subject.


      The following is the authors’ response to the original reviews.

      To Reviewer #1:

      Thank you for your thorough review and comments on our work, which you described as “the role of neuritin in T cell biology studied here is new and interesting.”.  We have summarized your comments into two categories: biology and investigation approach, experimental rigor, and data presentation.

      Biology and Investigation approach comments:

      (1) Questions regarding the T cell anergy model:

      Major point “(4) Figure 1E-H. The authors assume that this immunization protocol induces anergic cells, but they provide no experimental evidence for this. It would be useful to show that T cells are indeed anergic in this model, especially those that are OVA-specific. The lack of IL-2 production by Cltr cells could be explained by the presence of fewer OVA-specific cells, rather than by an anergic status.”

      T cell anergy is a well-established concept first described by Schwartz’s group. It refers to the hyporesponsive T cell functional state in antigen-experienced CD4 T cells (Chappert and Schwartz, 2010; Fathman and Lineberry, 2007; Jenkins and Schwartz, 1987; Quill and Schwartz, 1987).  Anergic T cells are characterized by their inability to expand and to produce IL2 upon subsequent antigen re-challenge. In this paper, we have borrowed the existing in vivo T cell anergy induction model used by Mueller’s group for T cell anergy induction (Vanasek et al., 2006).  Specifically, Thy1.1+ Ctrl or Nrn1-/- TCR transgenic OTII cells were co-transferred with the congenically marked Thy1.2+ WT polyclonal Treg cells into TCR-/- mice.  After anergy induction, the congenically marked TCR transgenic T cells were recovered by sorting based on Thy1.1+ congenic marker, and subsequently re-stimulation ex vivo with OVA323-339 peptide. We evaluated the T cell anergic state based on OTII cell expansion in vivo and IL2 production upon OVA323-339 restimulation ex vivo.  

      “The authors assume that this immunization protocol induces anergic cells, but they provide no experimental evidence for this.”

      Because the anergy model by Mueller's group is well established (Vanasek et al., 2006), we did not feel that additional effort was required to validate this model as the reviewer suggested. Moreover, the limited IL2 production among the control cells upon restimulation confirms the validity of this model.

      “The lack of IL-2 production by Cltr cells could be explained by the presence of fewer OVAspecific cells, rather than by an anergic status”.

      Cells from Ctrl and Nrn1-/- mice on a homogeneous TCR transgenic (OTII) background were used in these experiments. The possibility that substantial variability of TCR expression or different expression levels of the transgenic TCR could have impacted IL2 production rather than anergy induction is unlikely.

      Overall, we used this in vivo anergy model to evaluate the Nrn1-/- T cell functional state in comparison to Ctrl cells under the anergy induction condition following the evaluation of Nrn1 expression, particularly in anergic T cells.  Through studies using this anergy model, we observed a significant change in Treg induction among OTII cells. We decided to pursue the role of Nrn1 in Treg cell development and function rather than the biology of T cell anergy as evidenced by subsequent experiments.

      Minor points “(6) On which markers are anergic cells sorted for RNAseq analysis?”

      Cells were sorted out based on their congenic marker marking Ctrl or Nrn1-/- OTII cells transferred into the host mice.  We did not specifically isolate anergic cells for sequencing.

      (2) Question regarding the validity of iTreg differentiation model.

      Major point: “(5) Figure 2A-C and Figure 3. The use of iTregs to try to understand what is happening in vivo is problematic. iTregs are cells that have probably no equivalent in vivo, and so may have no physiological relevance. In any case, they are different from pTreg cells generated in vivo. Working with pTreg may be challenging, that is why I would suggest generating data with purified nTreg. Moreover, it was shown in the article of Gonzalez-Figueroa 2021 that Nrn1-/- nTreg retained a normal suppressive function, which would not be what is concluded by the authors of this manuscript. Moreover, we do not even know what the % of Foxp3 cells is in the iTreg used (after differentiation and 20h of re-stimulation) and whether this % is the same between Ctlr and Nrn1 KO cells.”.

      We thank Reviewer #1 for their feedback. While it is true that iTregs made in vitro and in vivo generated pTregs display several distinctions (e. g., differences in Foxp3 expression stability, for example), we strongly disagree with this statement by Revieweer#1 “The use of iTregs to try to understand what is happening in vivo is problematic. iTregs are cells that have probably no equivalent in vivo, and so may have no physiological relevance.”  The induced Treg cell (iTreg) model was established over 20 years ago (Chen et al., 2003; Zheng et al., 2002), and the model is widely adopted with over 2000 citations. Further, it has been instrumental in understanding different aspects of regulatory T cell biology (Hurrell et al., 2022; John et al., 2022; Schmitt and Williams, 2013; Sugiura et al., 2022).   

      Because we have observed reduced pTreg generation in vivo, we choose to use the in vitro iTreg model system to understand the mechanistic changes involved in Treg cell differentiation and function, specifically, neuritin’s role in this process. We have made no claim that iTreg cell biology is identical to pTreg generated in vivo or nTreg cells. However, the iTreg culture system has proved to be a good in vitro system for deciphering molecular events involved in complex processes. As such, it remains a commonly used approach by many research groups in the Treg cell field (Hurrell et al., 2022; John et al., 2022; Sugiura et al., 2022). Moreover, applying the iTreg in vitro culture system has been instrumental in helping us identify the cell electrical state change in Nrn1-/- CD4 cells and revealed the biological link between Nrn1 and the ionotropic AMPA receptor (AMPAR), which we will discuss in the subsequent discussion. It is technically challenging to use nTreg cells for T cell electrical state studies due to their heterogeneous nature from development in an in vivo environment and the effect of manipulation during the nTreg cell isolation process, which can both affect the T cell electrical state.   

      “Moreover, it was shown in the article of Gonzalez-Figueroa 2021 that Nrn1-/- nTreg retained a normal suppressive function, which would not be what is concluded by the authors of this manuscript.” 

      We have also carried out nTreg studies in vitro in addition to iTreg cells. Similar to Gonzalez-Figueroa et al.'s findings, we did not observe differences in suppression function between Nrn1-/- and WT nTreg using the in vitro suppression assay. However, Nrn1-/- nTreg cells revealed reduced suppression function in vivo (Fig. 2D-L). In fact, Gonzalez-Figueroa et al. observed reduced plasma cell formation after OVA immunization in Treg-specific Nrn1-/- mice, implicating reduced suppression from Nrn1-/- follicular regulatory T (Tfr) cells. Thus, our observation of the reduced suppression function of Nrn1-/- nTreg toward effector T cell expansion, as presented in Fig. 2D-L, does not contradict the results from Gonzalez-Figueroa et al. Rather, the conclusions of these two studies agree that Nrn1 can play important roles in immune suppression observable in vivo that are not captured readily by the in vitro suppression assay.

      “Moreover, we do not even know what the % of Foxp3 cells is in the iTreg used (after differentiation and 20h of re-stimulation) and whether this % is the same between Ctlr and Nrn1 KO cells.”

      We have stated in the manuscript on page 7 line 208 that “Similar proportions of Foxp3+ cells were observed in Nrn1-/- and Ctrl cells under the iTreg culture condition, suggesting that Nrn1 deficiency does not significantly impact Foxp3+ cell differentiation”. In the revised manuscript, we will include the data on the proportion of Foxp3+ cells before iTreg restimulation.

      (3) Confirmation of transcriptomic data regarding amino acids or electrolytes transport change

      Minor point“(3) Would not it be possible to perform experiments showing the ability of cells to transport amino acids or electrolytes across the plasma membrane? This would be a more interesting demonstration than transcriptomic data.”

      We appreciate Review# 1’s suggestion regarding “perform experiments showing the ability of cells to transport amino acids or electrolytes across the plasma membrane”.  We have indeed already performed such experiments corroborating the transcriptomics data on differential amino acid and nutrient transporter expression. Specifically, we loaded either iTreg or Th0 cells with membrane potential (MP) dye and measured MP level change after adding the complete set of amino acids (complete AA).  Upon entry, the charge carried by AAs may transiently affect cell membrane potential. Different AA transporter expression patterns may show different MP change patterns upon AA entry, as we showed in Author response image 1. We observed reduced MP change in Nrn1-/- iTreg compared to the Ctrl, whereas in the context of Th0 cells, Nrn1-/- showed enhanced MP change than the Ctrl. We can certainly include these data in the revised manuscript.

      Author response image 1.

      Membrane potential change induced by amino acids entry. a. Nrn1-/- or WT iTreg cells loaded with MP dye and MP change was measured upon the addition of a complete set of AAs. b. Nrn1-/- or WT Th0 cells loaded with MP dye and MP change was measured upon the addition of a complete set of AAs.

      (4) EAE experiment data assessment

      Minor point ”(5) Figure 5F. How are cells re-stimulated? If polyclonal stimulation is used, the experiment is not interesting because the analysis is done with lymph node cells. This analysis should either be performed with cells from the CNS or with MOG restimulation with lymph node cells.”

      In the EAE study, the Nrn1-/- mice exhibit similar disease onset but a protracted non-resolving disease phenotype compared to the WT control mice.  Several reasons may contribute to this phenotype: 1. Enhanced T effector cell infiltration/persistence in the central nervous system (CNS); 2. Reduced Treg cell-mediated suppression to the T effector cells in the CNS; 3. Protracted non-resolving inflammation at the immunization site has the potential to continue sending T effector cells into CNS, contributing to persistent inflammation. Based on this reasoning, we examined the infiltrating T effector cell number and Treg cell proportion in the CNS.  We also restimulated cells from draining lymph nodes close to the inflammation site, looking for evidence of persistent inflammation.  When mice were harvested around day 16 after immunization, the inflammation at the local draining lymph node should be at the contraction stage.  We stimulated cells with PMA and ionomycin intended to observe all potential T effector cells involved in the draining lymph node rather than only MOG antigen-specific cells.  We disagree with Reviewer #1’s assumption that “This analysis should either be performed with cells from the CNS or with MOG restimulation with lymph node cells.”. We think the experimental approach we have taken has been appropriately tailored to the biological questions we intended to answer.

      Experimental rigor and data presentation.

      (1) data labeling and additional supporting data

      Major points

      (2) The authors use Nrn1+/+ and Nrn1+/- cells indiscriminately as control cells on the basis of similar biology between Nrn1+/+ and Nrn1+/- cells at homeostasis. However, it is quite possible that the Nrn1+/- cells have a phenotype in situations of in vitro activation or in vivo inflammation (cancer, EAE). It would be important to discriminate Nrn1+/- and Nrn1+/+ cells in the data or to show that both cell types have the same phenotype in these conditions too.

      (3) Figure 1A-D. Since the authors are using the Nrp1 KO mice, it would be important to confirm the specificity of the anti-Nrn1 mAb by FACS. Once verified, it would be important to add FACS results with this mAb in Figures 1A-C to have single-cell and quantitative data as well.

      Minor points  

      (1) Line 119, 120 of the text. It is said that one of the most up-regulated genes in anergic cells is Nrn1 but the data is not shown.

      (2) For all figures showing %, the titles of the Y axes are written in an odd way. For example, it is written "Foxp3% CD4". It would be more conventional and clearer to write "% Foxp3+ / CD4+" or "% Foxp3+ among CD4+".

      (4) For certain staining (Figure 3E, H) it would be important to show the raw data, in addition to MFI or % values.

      We can adapt the labeling and provide additional data, including Nrn1 staining on Treg cells and flow graphs for pmTOR and pS6 staining (Fig. 3H), as requested by Reviewer #1.

      (2) Experimental rigor:

      General comments:

      “However, it is disappointing that reading this manuscript leaves an impression of incomplete work done too quickly.”

      We were discouraged to receive the comment, “this manuscript leaves an impression of incomplete work done too quickly.” Our study of this novel molecule began without any existing biological tools such as antibodies, knockout mice, etc.  Over the past several years, we have established our own antibodies for Nrn1 detection, obtained and characterized Nrn1 knockout mice, and utilized multiple approaches to identify the molecular mechanism of Nrn1 function. Through the use of the in vitro iTreg system described in this manuscript, we identified the association of Nrn1 deficiency with cell electrical state change, potentially connected to AMPAR function. We have further corroborated our findings by generating Nrn1 and AMPAR T cell specific double knockout mice and confirmed that T cell specific AMPAR deletion could abrogate the phenotype caused by the Nrn1 deficiency (see Support Figure 2).  We did not include the double knockout data in the current manuscript because AMPAR function has not yet been studied thoroughly in T cell biology, and we feel this topic warrants examination in its own right.  However, the unpublished data support the finding that Nrn1 modulates the T cell electrical state and, consequently, metabolism, ultimately influencing tolerance and immunity.  In its current form, the manuscript represents the first characterization of the novel molecule Nrn1 in anergic cells, Tregs, and effector T cells. While this work has led to several exciting additional questions, we disagree that the novel characterization we have presented Is incomplete. We feel that our present data set, which squarely highlights Nrn1’s role as an important immune regulator while shedding unprecedented light on the molecular events involved, will be of considerable interest to a broad field of researchers.

      “Multiple models have been used, but none has been studied thoroughly enough to provide really conclusive and unambiguous data. For example, 5 different models were used to study T cells in vivo. It would have been preferable to use fewer, but to go further in the study of mechanisms.”

      We have indeed used multiple in vivo models to reveal Nrn1's function in Treg differentiation, Treg suppression function, T effector cell differentiation and function, and the overall impact on autoimmune disease. Because the impact of ion channel function is often context-dependent, we examined the biological outcome of Nrn1 deficiency in several in vivo contexts.  We would appreciate it if Reviewer#1 would provide a specific example, given the Nrn1 phenotype, of how to proceed deeper to investigate the electrical change in the in vivo models.

      “Major points

      (1) A real weakness of this work is the fact that in most of the results shown, there are few biological replicates with differences that are often small between Ctrl and Nrn1 -/-. The systematic use of student's t-test may lead to thinking that the differences are significant, which is often misleading given the small number of samples, which makes it impossible to know whether the distributions are Gaussian and whether a parametric test can be used. RNAseq bulk data are based on biological duplicates, which is open to criticism.”

      We respectfully disagree with Reviewer #1 on the question of statistical power and significance to our work. We have used 5-8 mice/group for each in vivo model and 3-4 technical replicates for the in vitro studies, with a minimum of 2-3 replicate experiments. These group sizes and replication numbers are in line with those seen in high-impact publications. While some differences between Ctrl and Nrn1-/- appear small, they have significant biological consequences, as evidenced by the various Nrn1-/- in vivo phenotypes. Furthermore, we believe we have subjected our data to the appropriate statistical tests to ensure rigorous analysis and representation of our findings.

      To Reviewer #2.

      We thank Reviewer #2 for the careful review of the manuscript. We especially appreciate the comments that “The characterizations of T cell Nrn1 expression both in vitro and in vivo are comprehensive and convincing. The in vivo functional studies of anergy development, Treg suppression, and EAE development are also well done to strengthen the notion that Nrn1 is an important regulator of CD4 responsiveness.”

      “The major weakness of this study stems from a lack of a clear molecular mechanism involving Nrn1. “  

      We fully understand this comment from Reviewer #2. The main mechanism we identified contributing to the functional defect of Nrn1-/- T cells involves novel effects on the electric and metabolic state of the cells. Although we referenced neuronal studies that indicate Nrn1 is the auxiliary protein for the ionotropic AMPA-type glutamate receptor (AMPAR) and may affect AMPAR function, we did not provide any evidence in this manuscript as the topic requires further in-depth study.   

      For the benefit of this discussion, we include our preliminary Nrn1 and AMPAR double knockout data (Author response image 2), which indicates that abrogating AMPAR expression can compensate for the defect caused by Nrn1 deficiency in vitro and in vivo. This preliminary data supports the notion that Nrn1 modulates AMPAR function, which causes changes in T cell electric and metabolic state, influencing T cell differentiation and function.  

      Author response image 2.

      Deletion of AMPAR expression in T cells compensates for the defect caused by Nrn1 deficiency. Nrn1-/- mice were crossed with T cell-specific AMPAR knockout mice (AMPARfl/flCD4Cre+) mice. The following mice were generated and used in the experiment: T cell specific AMPAR-knockout and Nrn1 knockout mice (AKONKO), Nrn1 knockout mice (AWTNKO), Ctrl mice (AWTNWT). a. Deletion of AMPAR compensates for the iTreg cell defect observed in Nrn1-/- CD4 cells. iTreg live cell proportion, cell number, and Ki67 expression among Foxp3+ cells 3 days after aCD3 restimulation. b. Deletion of AMPAR in T cells abrogates the enhanced autoimmune response in Nrn1-/- Mouse in the EAE disease model. Mouse relative weight change and disease score progression after EAE disease induction.  

      Ion channels can influence cell metabolism through multiple means (Vaeth and Feske, 2018; Wang et al., 2020). First, ion channels are involved in maintaining cell resting membrane potential. This electrical potential difference across the cell membrane is essential for various cellular processes, including metabolism (Abdul Kadir et al., 2018; Blackiston et al., 2009; Nagy et al., 2018; Yu et al., 2022). Second, ion channels facilitate the movement of ions across cell membranes. These ions are essential for various metabolic processes. For example, ions like calcium (Ca2+), potassium (K+), and sodium (Na+) play crucial roles in signaling pathways that regulate metabolism (Kahlfuss et al., 2020). Third, ion channel activity can influence cellular energy balance due to ATP consumption associated with ion transport to maintain ion balances (Erecińska and Dagani, 1990; Gerkau et al., 2019). This, in turn, can impact processes like ATP production, which is central to cellular metabolism. Thus, ion channel expression and function determine the cell’s bioelectric state and contribute to cell metabolism (Levin, 2021).

      Because the AMPAR function has not been thoroughly studied using a genetic approach in T cells, we do not intend to include the double knockout data in this manuscript before fully characterizing the T cell-specific AMPAR knockout mice.  

      “Although the biochemical and informatics studies are well-performed, it is my opinion that these results are inconclusive in part due to the absence of key "naive" control groups. This limits my ability to understand the significance of these data.

      Specifically, studies of the electrical and metabolic state of Nrn1-/- inducible Treg cells (iTregs) would benefit from similar data collected from wild-type and Nrn1-/- naive CD4 T cells.”

      We appreciate the reviewer’s comments. This comment reflects two concerns in data interpretation:

      (1) Are Nrn1-/- naïve T cells fundamentally different from WT cells? Does this fundamental difference contribute to the observed electrical and metabolic phenotype in iTreg or Th0 cells? This is a very good question we will perform the experiments as the reviewer suggested. While Nrn1 is expressed at a basal (low) level in naïve T cells, deletion of Nrn1 may cause changes in naïve T cell phenotype.   

      (2) Is the Nrn1-/- phenotype caused by Nrn1 functional deficiency or due to the secondary effect of Nrn1 deletion, such as non-physiological cell membrane structure changes?

      We have done the following experiment to address this concern.  We have cultured WT T cells in the presence of Nrn1 antibody and compared the outcome with Nrn1-/- iTreg cells (Figure 3-figure supplement 2D,E,F). WT iTreg cells under antibody blockade exhibited similar changes as Nrn1-/- iTreg cells, confirming the physiological relevance of the Nrn1-/- phenotype.

      Manuscript Revision based on the Reviewer’s suggestions:

      Reviewer #1:

      Major points (3) Figure 1A-D. Since the authors are using the Nrp1 KO mice, it would be important to confirm the specificity of the anti-Nrn1 mAb by FACS. 

      Following the suggestion by Reviewer#1, We have included the Nrn1 Ab staining on activated Nrn1-/- CD4 cells in Figure 1D. We have also added the staining of cell surface Nrn1 on Treg cells in Figure 1-figure supplement 1D.

      Major point: (5) “Moreover, we do not even know what the % of Foxp3 cells is in the iTreg used (after differentiation and 20h of re-stimulation) and whether this % is the same between Ctlr and Nrn1 KO cells.”

      In the revised manuscript, we have included the proportion of Foxp3+ cells among Nrn1-/- and ctrl iTreg cells developed under the iTreg culture condition in Figure 2A.

      Minor points  

      (2) For all figures showing %, the titles of the Y axes are written in an odd way. For example, it is written "Foxp3% CD4". It would be more conventional and clearer to write "% Foxp3+ / CD4+" or "% Foxp3+ among CD4+".

      Following reviewer#1’s suggestion, we have changed the Y-axis label in all the relevant figures.

      (3) Would not it be possible to perform experiments showing the ability of cells to transport amino acids or electrolytes across the plasma membrane? This would be a more interesting demonstration than transcriptomic data.”

      We appreciate Review# 1’s suggestion regarding “perform experiments showing the ability of cells to transport amino acids or electrolytes across the plasma membrane”.  We have used AAinduced cellular MP changes to confirm differential AA transporter expression patterns and their impact on cellular MP levels.  The data are included in the revised manuscript in Figure 3H and Figure 4K.

      (4) For certain staining (Figure 3E, H) it would be important to show the raw data, in addition to MFI or % values.

      We appreciated Reviewer #1’s suggestion and have included the histogram staining data for Figure 3E. We have moved the original Figure 3H to the supplemental figure and included the histogram staining data in Figure 3-figure supplement 1C.  Similarly, we have included the histogram staining data in Figure 4-figure supplement 1C.

      Reviewer#2:

      “Although the biochemical and informatics studies are well-performed, it is my opinion that these results are inconclusive in part due to the absence of key "naive" control groups. This limits my ability to understand the significance of these data.

      Specifically, studies of the electrical and metabolic state of Nrn1-/- inducible Treg cells (iTregs) would benefit from similar data collected from wild-type and Nrn1-/- naive CD4 T cells.”

      We greatly appreciate Reviewer#2’s suggestion and have carried out experiments on naïve CD4 cells derived from Nrn1-/- and WT mice. We have compared membrane potential, AA-induced MP change between Nrn1-/- and WT naïve T cells, and the metabolic state of Nrn1-/- and WT naïve T cells by carrying out glucose stress tests and mitochondria stress tests using a seahorse assay.  Moreover, to investigate whether the phenotype revealed in Nrn1-/- CD4 cells was caused by a secondary effect of cell membrane structure change due to Nrn1 deletion, we carried out Nrn1 antibody blockade in WT CD4 cells and investigated the phenotypic change. These new results are included in Figure 3-figure supplement 2.

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    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public Review):  

      Summary:

      In this study, Setogawa et al. employ an auditory discrimination task in freely moving rats, coupled with small animal imaging, electrophysiological recordings, and pharmacological inhibition/lesioning experiments to better understand the role of two striatal subregions: the anterior Dorsal Lateral Striatum (aDLS) and the posterior Ventrolateral Striatum (pVLS), during auditory discrimination learning. Attempting to better understand the contribution of different striatal subregions to sensory discrimination learning strikes me as a highly relevant and timely question, and the data presented in this study are certainly of major interest to the field. The authors have set up a robust behavioral task and systematically tackled the question about a striatal role in learning with multiple observational and manipulative techniques. Additionally, the structured approach the authors take by using neuroimaging to inform their pharmacological manipulation experiments and electrophysiological recordings is a strength.

      However, the results as they are currently presented are not easy to follow and could use some restructuring, especially the electrophysiology. Also, the main conclusion that the authors draw from the data, that aDLS and pVLS contribute to different phases of discrimination learning and influence the animal's response strategy in different ways, is not strongly supported by the data and deserves some additional caveats and limitations of the study in the discussion. 

      We appreciate the reviewer’s valuable feedback, which has been beneficial for improvement of our manuscript. In response to the reviewer’s comments, we have revised multiple parts of the manuscript, including explanations of electrophysiological data. We have also provided additional data to support our main conclusion and addressed caveats and limitations related to the data in the Discussion section. For more details, please refer to the responses to each comment.

      Comment 1: The authors have rigorously used PET neuroimaging, which is an interesting noninvasive method to track brain activity during behavioral states. However, in the case of a freely moving behavior where the scans are performed ~30 minutes after the behavioral task, it is unclear what conclusions can be drawn about task-specific brain activity. The study hinges on the neuroimaging findings that both areas of the lateral striatum (aDLS and pVLS) show increased activity during acquisition, but the DMS shows a reduction in activity during the late stages of behavior, and some of these findings are later validated with complementary experiments. However, the limitations of this technique can be further elaborated on in the discussion and the conclusions.

      As described in our response to the following two comments (a, b) from the reviewer, in the PET imaging study we first analyzed task-related activity by comparing <sup>18</sup>F-FDG uptake on different days of the auditory discrimination task with that on Day 4 of the single lever press task as a control. Next, we analyzed learning-dependent activity by comparing the uptake on different days of the discrimination task with that on Day 2 of the same task. Based on the results of both analyses, we concluded that the activity in the striatal subregions changes during the progress of discrimination learning. The behavioral significance of striatal subregions was tested by excitotoxic lesion and pharmacological blockade experiments. The explanation of imaging data analysis may have been insufficient to fully communicate dynamic changes in the activity of striatal subregions. Therefore, we have clarified our voxel-based statistical parametric analysis method to better explain the dynamic activity changes in the striatal subregions. Please refer to the following responses to comments 1 (a, b).

      Comment 1 (a): In commenting on the unilateral shifts in brain striatal activity during behavior, the authors use the single lever task as a control, where many variables affecting neuronal activity might be different than in the discriminatory task. The study might be better served using Day 2 measurements as a control against which to compare activity of all other sessions since the task structures are similar.

      We initially analyzed task-related activity by comparing <sup>18</sup>F-FDG uptake on one of Days 2, 6, 10, or 24 of auditory discrimination task with that on Day 4 of the single lever press task. This task was used as a control that does not require a decision process based on the auditory stimulus. We observed significant increases in the activity of the unilateral aDLS on Day 6 and in that of the bilateral pVLS on Day 10 of the discrimination task. We also observed a significant decrease in the unilateral DMS on Day 24 (see Figures 2F and 2G). Next, as suggested, we compared the uptake on one of Days 6, 10, or 24 with that on Day 2 as a control to evaluate learning-dependent activity. The activity showed significant increases in the bilateral aDLS on Day 6 and in the unilateral pVLS on Day 10, and a significant decrease in the bilateral DMS on Day 24 (see Figures 2H). 

      The reviewer has suggested a discrepancy in the activity of the unilateral or bilateral striatal subregions under certain conditions between the image data (shown in Figures 2F–H) and plot data (Figures 2J–L). This discrepancy is also suggested in the following Comment 1 (b). For example, in the image data the brain activity was increased in the unilateral (left) aDLS on Day 6 of the discrimination task as compared to Day 4 of the single lever task (Figure 2F). In the plot data, <sup>18</sup>F-FDG uptake reached a peak on Day 6 in both the left and right sides of the aDLS (Figure 2J), and the uptake in the left aDLS on Day 6 significantly increased relative to the value of the single lever press, whereas the value in the right aDLS on Day 6 tended to increase relative to that of the single lever press with no significant difference. The plot data showing the unilaterality in the aDLS activation relative to the single lever press are consistent with the image data. On the other hand, the <sup>18</sup>F-FDG uptake in the aDLS on Day 6 compared to the value on Day 2 was significantly increased in both sides. Similar observations were made in the activity in the pVLS on Day 10 compared to that on Day 2, as well as in the DMS activity on Day 24 relative to that of the single lever press. 

      Our analysis of both task-related and learning-dependent activities revealed dynamic changes in striatal subregions during discrimination learning. We investigated the brain regions in which <sup>18</sup>F-FDG uptake significantly increased or decreased during the learning processes, applying a statistical significance threshold (p < 0.001, uncorrected) and an extent threshold, by using a voxel-based statistical parametric analysis. In the image data, the voxels showing significant differences between two conditions are visualized on the brain template. The plot data show the amount of <sup>18</sup>FFDG uptake in the voxels, which was detected by the voxel-based analysis. The insufficient explanation of the data analysis of PET imaging in the initial manuscript may have led to a misunderstanding regarding the activity in the unilateral or bilateral striatal subregions. Therefore, we have revised the explanation for voxel-based statistical parametric analysis, adding a more detailed description of the thresholds in the text (page 7, lines 143–145) and Methods (page 27, lines 672–675).

      Comment 1 (b): From the plots in J, K, and L, it seems that shifts in activity in the different substructures are not unilateral but consistently bilateral, in contrast to what is mentioned in the text. Possibly the text reflects comparisons to the single lever task, and here again, I would emphasize comparing within the same task.

      Please see our response to the first comment (a) regarding our explanation of the consistency in the activity of the unilateral or bilateral striatal subregions between the image and plot data. We have also revised the explanation in the corresponding sections of the manuscript, as described above.

      Comment 2: In Figure 2, the authors present compelling data that chronic excitotoxic lesions with ibotenic acid in the aDLS, pVLS, and DMS produce differential effects on discrimination learning. However, the significant reduction in success rate of performance happens as early as Day 6 in both IBO groups in both aDLS and pVLS mice. This would seem to agree with conclusions drawn about the role of aDLS in the middle stages of learning in Figure 2, but not the pVLS, which only shows an increased activity during the late stages of the behavior.  

      Figure 3 shows the behavioral effects of ibotenic acid injections into striatal subregions in rats. For the aDLS injection, we performed two-way repeated ANOVA, which revealed a significant main effect of group or day and a significant interaction of group × day, and added the simple main effects between the treatments to the figure (Figure 3G). We observed significant differences in the success rate mainly at the middle stage of learning. In contrast, for the pVLS injection there was no significant interaction for group × day, although the main effects of group or day was significant by two-way repeated ANOVA (Figure 3H). Consequently, it was unclear as to when exactly the significant reduction occurred. These results indicate that the aDLS and pVLS are necessary for the acquisition of auditory discrimination, and that the aDLS is mainly required for the middle stage. Similar results were observed in the win-shift-win strategy in the aDLS and pVLS (Figures 3J and 3K).

      Next, we performed temporal inhibition of neuronal activity in striatal subregions by muscimol treatment in order to examine whether the activity in the subregions is linked with learning processes at different stages. In this experiment, muscimol was injected into the aDLS or pVLS at the middle or late stage, and the resultant effects on the success rate were investigated. The success rate in the muscimol-injected groups into the aDLS significantly decreased at the middle stage, but not at the early and late stages (Figure 4C). In contrast, the rate in the muscimol groups into the pVLS significantly decreased at the late stage, but not at the early or middle stages (Figure 4D). The results indicate that the aDLS and pVLS are mainly involved in the processes at the middle and late stages, respectively, and support the PET imaging data showing the activation of two striatal subregions at the various stages.

      We have now provided the results of simple main effects analysis for the aDLS lesion (Figures 3G and 3J) and revised the description of the Results section (page 8, lines 174–178, page 8, lines 186–188, and page 9, line 205-206) and Figure legend (page 44, lines 1000‒1003, and page 44, lines 1010–1013). We have also added the results of simple main effects analysis in Figure 3J.

      Comment 3: In Figure 4, the authors show interesting data with transient inactivation of subregions of the striatum with muscimol, validating their findings that the aDLS mediates the middle and the pVLS the late stages of learning, and the function of each area serves different strategies. However, the inference that aDLS inactivation suppresses the WSW strategy "moderately" is not reflected in the formal statistical value p=0.06. While there still may be a subtle effect, the authors would need to revise their conclusions appropriately to reflect the data. In addition, the authors could try a direct comparison between the success rate during muscimol inhibition in the mid-learning session between the aDLS and pVLS-treated groups in Figure 4C (middle) and 4D (middle). If this comparison is not significant, the authors should be careful to claim that inhibition of these two areas differentially affects behavior.

      In Figure 4E, aDLS inhibition showed a tendency to reduce slightly win-shift-win strategy at the middle stage (t[14] = 2.038, p = 0.061, unpaired Student’s t-test). In accordance with the reviewer’s comment, we changed the word “moderate” to “subtle” (page 12, line 272).

      In the temporal inhibition of the striatal subregions, the aDLS and pVLS experiments (panels C and D, respectively) were conducted separately. Since it is difficult to directly compare the data obtained from different experiments, we did not carry out a direct comparison of the success rate between the aDLS and pVLS injections. 

      Comment 4: The authors have used in vivo electrophysiological techniques to systematically investigate the roles of the aDLS and the pVLS in discriminatory learning, and have done a thorough analysis of responses with each phase of behavior over the course of learning. This is a commendable and extremely informative dataset and is a strength of the study. However, the result could be better organized following the sequence of events of the behavioral task to give the reader an easier structure to follow. Ideally, this would involve an individual figure to compare the responses in both areas to Cue, Lever Press, Reward Sound, and First Lick (in this order).

      We first showed changes in the proportion of event-related neurons during the acquisition phase (Figure S5). Next, we conducted a detailed analysis of the characteristics of aDLS and pVLS neuronal activity. Specifically, we found several types of event-related neurons, including: (1) reward sound-related neurons representing behavioral outcomes in the aDLS; (2) first licking-related neurons showing sustained activity after the reward in the aDLS and pVLS; and (3) cue-onset and cue-response neurons associated with the beginning and ending of a behavior in the pVLS.

      Descriptions of the characteristics of event-related neurons according to the sequence of events in a trial, as the reviewer has suggested, is another way to provide an easy structure for understandings on the electrophysiological data. However, we focused on the characteristics of aDLS neurons at the middle stage and pVLS neurons at the late stage of discrimination learning. Therefore, we explained the electrophysiological data based on the order of learning stages rather than the sequence of events in the trial, as described above.

      Comment 5: An important conceptual point presented in the study is that the aDLS neurons, with learning, show a reduction in firing rates and responsiveness to the first lick as well as the behavioral outcome, and don't play a role in other task-related events such as cue onset. However, the neuroimaging data in Figure 2 seems to suggest a transient enhancement of aDLS activity in the mid-stage of discriminatory learning, that is not reflected in the electrophysiology data. Is there an explanation for this difference?

      In the <sup>18</sup>F-FDG PET imaging study, the brain activity in the aDLS reached a peak at the middle stage of the acquisition phase of auditory discrimination (Figure 2J). In the multi-unit electrophysiological recording experiment, the firing activity of the aDLS neuron subpopulations related to the behavioral outcome showed no significant differences among the three stages (Figure 5E), while the proportion of these subpopulations were gradually reduced through the progress of learning stages (Figure 5F). The extent of the firing activity and length of the firing period of other subpopulations showing sustained activation after the reward appeared to show a learning-dependent decrease (Figures 6B and 6C), although the proportion of these subpopulations indicated no correlation with the progress of the learning (Figure 6D). Patterns of the temporal changes in brain activity in striatal subregions across the learning stages did not match completely the time variation in the property or proportion of specific event-related neurons. In our electrophysiological analysis, we identified well-isolated neurons from the striatal subregions during the auditory discrimination task, focusing on putative medium spiny neurons (Figures S4E–S4G). Based on the combinatorial pattern of the tone instruction cue (high tone/H or low tone /L), and lever press (right/R or left/L), we categorized the electrophysiological data into the four trials, including the HR, LL. LR, and HL. We identified HR or LL type neurons showing significant changes in the firing rate related to specific events, such as cue onset, choice response, reward sound, and first licking compared to the baseline firing rate. These neurons were further divided into two groups with increased or decreased activity relative to the baseline firing (Figures S5A and S5B). In the present study, we focused on event-related neurons with increased activity. Because of the analysis limited to neuronal subpopulations related to specific events with the increased activity, it is difficult to fully explain dynamic shifts in the brain activity of striatal subregions dependent on the progress of learning by the time variation of firing activity of individual event-related neurons. The activity of other subpopulations in the striatum may be involved in the shift in brain activity during the learning processes. In addition, recent studies have reported that the activity of glial cells influences the uptake of <sup>18</sup>FFDG (Zimmer et al., Nat Neurosci., 2017) and that these cells regulate spike timingdependent plasticity (Valtcheva and Venance, Nat Commun, 2016). Changes in glial cellular activity, through the control of synaptic plasticity, may partly contribute to the pattern formation of learning-dependent shifts in brain activity.

      To explain the difference in the time course between the brain activity and the firing activity of specific event-related neurons, we have added the aforementioned information to the Limitations section (pages 21 to 22, lines 512–539). 

      Comment 6: A significant finding of the study is that CO-HR and CO-LL responses are strikingly obvious in the pVLS, but not in the aDLS, in line with the literature that the posterior (sensory) striatum processes sound. This study also shows that responses to the highfrequency tone indicating a correct right-lever choice increase with learning in contrast to the low-frequency tone responses. To further address whether this difference arises from the task contingency, and not from the frequency representation of the pVLS, an important control would be to switch the cue-response association in a separate group of mice, such that high-frequency tones require a left lever press and vice versa. This would also help tease apart task-evoked responses in the aDLS, as I am given to understand all the recording sites were in the left striatum.

      We did not conduct an experiment switching cue-response association in the auditory discrimination task. However, the transient activity of cue onset-related neurons in the pVLS, as the reviewer has suggested, did not appear at the early stage of learning, but was observed in a learning-dependent manner (Figures 7A and S8E). In addition, the cue onset-HR activity showed a slight but notable difference between the HR and LL trials at the middle and late stages (Figure 7B), but there was no difference in activity in the HL and LR incorrect trials at the corresponding stages (Wilcoxon signed rank test; early, p = 0.375, middle, p = 0.931, and late, p = 0.668). These results suggest that the activity of cue onset-related neurons in the pVLS is associated with the stimulus and response association (task contingency) rather than the tone frequency.

      Reviewer #1 (Recommendations For The Authors):

      Minor comment 1: The readability and appeal of this study would be improved by explaining the various neuronal response types, and task-related events in slightly more detail in the results section, and minimizing the use of non-standard abbreviations wherever possible.

      As suggested, we have replaced the abbreviations related to electrophysiological events (CO, CR, RS, and FL) with the original terms, and improved the explanation for neuronal response types and event-related neurons. 

      Minor comment 2: It would be helpful to label DLS and VLS recordings more clearly on the figures instead of only in the figure caption.

      Thank you for pointing this out. The terms “aDLS” and “pVLS” have now been added to the panels showing firing pattern of neurons: “aDLS” in Figures 5D, 6A, S6A, S7A, S8A, S8B. S8C, and S8D; and “pVLS” in Figures 6F, 7A, 7D, S6D, S6E, S7F, S8E, and S8F.

      Minor comment 3: The authors suggest that aDLS HR- and LL- neurons are more sensitive to the behavioral outcome than those in pVLS (Fig 5 and S5). However, their conclusions are based on sample sizes as low as n=3 for each response type.

      We identified event-related neurons from single neurons detected in both the aDLS and pVLS using the same criteria. In the pVLS, we found a small number of neurons that increased their activity during the period when the reward sound is presented (Figures S6D and S6E) (6, 4, and 17 HR type neurons at the early, middle, and late stages, respectively; 3, 5, and 15 LL type neurons at the early, middle, and late stages, respectively). The number of LL type neurons at the early stage was particularly lower, as the reviewer has suggested. However, when we plotted the firing rates of these neurons around the event, their activity did not reflect behavioral outcome. In the aDLS, we detected a large number of reward sound-related neurons representing behavioral outcome (Figures 5 and S6A) (43, 37, and 44 HR type neurons at the early, middle, and late stages, respectively; 49, 62, and 59 LL type neurons at the early, middle, and late stages, respectively). These observations suggest that aDLS neurons are more sensitive to behavioral outcomes than pVLS neurons.

      Minor comment 4: Typo in Figure 4C and D, right plots, y-axis label: "subtracted".

      The typographic errors in Figures 4C–4H have now been corrected to “subtracted”.

      Reviewer #2 (Public Reviews):

      The study by Setogawa et al. aims to understand the role that different striatal subregions belonging to parallel brain circuits have in associative learning and discrimination learning (S-O-R and S-R tasks). Strengths of the study are the use of multiple methodologies to measure and manipulate brain activity in rats, from microPET imaging to excitotoxic lesions and multielectrode recordings across anterior dorsolateral (aDLS), posterior ventral lateral (pVLS)and dorsomedial (DMS) striatum. The main conclusions are that the aDLS promotes stimulus-response association and suppresses response-outcome associations. The pVLS is engaged in the formation and maintenance of the stimulus-response association. There is a lot of work done and some interesting findings however, the manuscript can be improved by clarifying the presentation and reasoning. The inclusion of important controls will enhance the rigor of the data interpretation and conclusions.

      We appreciate the reviewer’s valuable feedback, which has been beneficial in our endeavor to improve our manuscript. In response to the comments, we have revised the description of the experimental methods and underlying rationale, as well as the Results section. We have also provided additional data for some of the experiments that support the conclusions. For more details, please refer to the responses to each comment, included below.

      Reviewer #2 (Recommendations For The Authors):

      Comment 1: Generally, the manuscript is hard to read because of the cumbersome sentence structure, overuse of poorly defined acronyms, and lack of clarity on the methods used.

      According to the following comments (a)–(d), we have revised the corresponding text in the manuscript to clarify the sentence structure, definitions of terms, and methodology. 

      Comment 1 (a): For example, the single lever task used as a control for the auditory discrimination task could be introduced better, explaining the reasoning and the strategy for subtracting it from the images obtained during the discrimination phase at the start of the section.

      We analyzed task-related activity by comparing <sup>18</sup>F-FDG uptake on Days 2, 6, 10, or 24 of auditory discrimination task with that on Day 4 of the single lever press task. This task was used as a control that does not require a decision process based on the auditory stimulus. For clarification, we have provided a more detailed explanation of the flow of the single lever press task used in the PET experiment, including the rationale for employing this task as a control (page 6, lines 129–135). We have also revised the explanation of voxel-based statistical parametric analysis, adding a more detailed description of the thresholds (page 7, lines 143–145).

      Comment 1 (b): Another example is that important methodological information is buried deep in the text and complicates the interpretation of the results.

      We have revised the following sentences in the manuscript in order to provide clearer methodological information.

      (1) As described above, explanations for the single lever task (page 6, lines 129–135) and voxel-based statistical parametric analysis were added (page 7, lines 143–145). 

      (2) Definition of the early, middle, and late stages were described in the initial behavioral experiment (page 6, lines 113–119). 

      (3) Abbreviations related to behavioral strategies (WSW and LSL) and electrophysiological events (CO, CR, RS, and FL) were replaced with the original terms. 

      Comment 1 (c): The specie being studied is not stated in the abstract, nor the introduction, and only in the middle of the result section. Please include the specie in the abstract and the first part of the result also for clarity.

      We included the name of the species (rats) in the Abstract (page 3, line 47), at the end of the Introduction (page 5, lines 87–88) and at the beginning of the Results (page 5, line 109).

      Comment 1 (d): The last part of the intro is copied/pasted from the abstract. Please revise.

      The last part of the Introduction was revised accordingly (page 5, lines 97–104).

      Comment 2: The glucose microPET imaging is carried out 30 mins after the rats performed the task and it is expected to capture activation during the task. Is this correct? This assumption has to be validated with an experiment, which is a control showing a validation of the microPET approach used, and this way can report activation of brain areas during the task completed 20-30 minutes before. For example, V1 or A1 would be a control that we would expect to be activated during the task.

      Our PET experiment was conducted in accordance with previously established methods (Cui et al, Neuroimage, 2015), where rats received intravenous administration of <sup>18</sup>FFDG solution just before the start of the behavioral session, which lasted for 30 min. The <sup>18</sup>F-FDG uptake in the brain starts immediately and reaches the maximum level until 30 min after the administration, and the level is kept at least for 1 h (Mizuma et al., J Nucl Med, 2010). The rats were returned to their home cages, and a 30-min PET scan started 25 min after the session. The start time of the scan was chosen to allow for sufficient reduction of 18F radioactivity in arterial blood to increase the S/N ratio of the radioactivity (Mizuma et al., J Nucl Med, 2010). As shown in Table S1, we confirmed that the brain activity in the medial geniculate body (auditory thalamus) was increased on Days 6 and 10 in the acquisition phase, although the activity in the auditory cortex was not changed, which is consistent with the results of a previous study reporting that the auditory cortex does not show the causality for the pure-tone discrimination task (Gimenez et al., J Neurophysiol., 2015).

      Comment 3: Why are Days 2, 6, 10, and 13 chosen and compared for the behavior? Why aren't these the same days chosen in the other part of the study? It is unclear why authors focused on these days and why the focus changed later.

      We conducted daily training of the discrimination task. The success rate reached a plateau on Day 13 and was maintained until Day 24 (Figure 1B). Based on these results, we categorized the learning processes into the acquisition and learned phases, and then divided the acquisition phase into the early (< 60%), middle (60–80%), and late (> 80%) stages. In the PET experiment, we selected Days 2, 6, and 10 as the representatives of each stage during the acquisition phase. In addition, we also selected Day 24 for the learned phase.  However, no scan was performed on Day 13 due to the transition between the two phases.   

      Comment 4: (A) Is the learning and acquisition of the single lever press and discrimination task completed by day 4? Or are rats still learning? The authors claimed no changes in DMS activity between single lever press & discrimination, and therefore DMS isn't involved in learning. But to make this claim we should have measures that the learning has already happened, which I am not sure have been provided. (B) On this same point, the DMS activity is elevated on Day 4 of a single lever press compared to the aDLS and pVLS. So is it possible that the activity in DMS was already elevated on Day 4 of single lever press training? Especially given that DMS is supposedly involved in goal-directed behavior?

      (A) In the single lever press task, the number of lever presses plateaued on Day 2 (Figure 1C). In addition, we analyzed response time and its variability, which plateaued from Day 3 and Day 2, respectively (see Author response image 1). These results indicate that the learning in the task was completed by Day 4. In the auditory discrimination task, Day 4 corresponded to the transition period from the early-tomiddle stages of the acquisition phase, suggesting that learning was still progressing. 

      In the imaging analysis, we examined task-related activity by comparing <sup>18</sup>F-FDG uptake on either day of the discrimination task with that on Day 4 of the single lever press task, and did not find any changes in the brain activity in the DMS. In addition, we investigated learning-related activity, and the DMS activity did not change during acquisition phase. These results suggest that the DMS is not involved in the acquisition phase of learning. Furthermore, comparisons between Days 10 and Day 24 showed a decrease in DMS activity during the learned phase, suggesting that DMS activity was downregulated during the learned phase. In addition, chronic lesion in the DMS indicated that the success rate in the discrimination task was comparable between the control and lesioned groups (Figure 3I), whereas the response time lengthened throughout the learning in the lesioned group compared to the controls (Figure S1C). These results support our notion that the DMS contributes to the execution, but not learning, of discriminative behavior (Figure 3I and S1C).

      Author response image 1.

      Performance of single lever press task conducted before auditory discrimination task. (A) Number of lever presses. (B) Response time (Kruskal-Wallis test, χ<sup>2</sup> = 38.063, p = 2.7 × 10<sup>-8</sup>, post hoc Tukey–Kramer test, p = 0.047 for Day 1 vs. Day 2; p = 2.3 × 10<sup>-7</sup> for Day 1 vs. Day 3; and p = 4.0 × 10<sup>-6</sup> for Day 1 vs. Day 4; p = 0.019 for Day 2 vs. Day 3; p = 0.082 for Day 2 vs. Day 4; p = 0.951 for Day 3 vs. Day 4). (C) Response time variability (Kruskal-Wallis test, χ<sup>2</sup> = 28.929, p = 2.3 × <sup>-6</sup>, post hoc Tukey–Kramer test, p = 0.077 for Day 1 vs. Day 2; p = 5.7 × 10<sup>-6</sup> for Day 1 vs. Day 3; and p = 1.3 × 10<sup>-4</sup> for Day 1 vs. Day 4; p = 0.060 for Day 2 vs. Day 3; p = 0.253 for Day 2 vs. Day 4; p = 0.912 for Day 3 vs. Day 4). Data obtained from the task shown in Figure 2C are plotted as the median and quartiles with the maximal and minimal values. *p < 0.05, **p < 0.01, and ***p < 0.001.

      (B) We compared <sup>18</sup>F-FDG uptakes among striatal subregions on Day 4 of the single lever press task (334.8 ± 2.86, 299.0 ± 1.71, and 336.8 ± 2.18 for the aDLS, pVLS, and DMS, respectively; one-way ANOVA, F[2,41] = 104.767, p = 2.1 × 10<sup>-16</sup>). The uptake was comparable between the aDLS and DMS (post hoc Tukey-Kramer test, p = 0.058), but it was significantly lower in the pVLS compared to either of the other two subregions (post hoc Tukey-Kramer test, aDLS vs. pVLS, p = 5.1 × 10<sup>-9</sup>, post hoc Tukey-Kramer test, pVLS vs. DMS, p = 5.1 × 10<sup>-9</sup>). However, since we did not measure the brain activity in the single lever task outside of Day 4, it is unclear whether there was an increase in DMS activity during the acquisition of the task. Similarly, since we did not confirm the behavioral modes, which include goal-directed and habitual actions, it is difficult to conclude that the lever presses in the task were controlled by the goaldirected mode. However, our chronic lesion experiment suggests that the DMS is involved in the execution of discrimination behavior (Figure S1C). A clearer understanding of the DMS function in discrimination learning is an important challenge in the future.

      Comment 5: It seems like the procedure of microPET imaging affects performance on the task. The anesthesia used maybe? Figures 2C and D show evidence that the behavior was negatively affected on the days on which microPET imaging was performed after the training. Can the author clarify/comment?

      Isoflurane anesthesia may slightly reduce behavioral performance. We carried out anesthesia (median [interquartile range]: 6 [5–8] min) during the insertion of the catheter for FDG injection, and set a recovery period of at least 2 h until the beginning of the behavioral session, to minimize the impact of anesthesia. The performances in Figure 2E were similar to those in the intact rats (compared to Figures 1C–1F), suggesting that the procedure for PET scans does not affect the acquisition of discrimination. 

      We have added detailed information on the isoflurane anesthesia to the Methods section (page 26, lines 649–653).

      Comment 6: More on clarity. Section 3 of the results (muscimol inactivation) refers a lot to "the behavioral strategies" without really clarifying what these are - are they referring to WSW / LSL (which also could use a better introduction) or goal-directed/habitual or stimulus-response/stimulus-outcome?

      The dorsal striatum is involved in both behavioral strategies based on stimulus-response association and the response-outcome association during instrumental learning. To assess the impact of striatal lesions on the behavioral strategies, we analyzed the proportion of response attributed to two strategies in all responses of each session. One is the “win-shift-win” strategy, which is considered to reflect the behavioral strategy based on the stimulus-response association. In this strategy, after a correct response in the previous trial, the rats press the opposite lever in the current trial in response to a shift of the instruction cue, resulting in the correct response.  Another strategy is the “lose-shift-lose” strategy, which is considered to appear as a consequence of the behavioral strategy based on the response-outcome association. In this strategy, after an error response in the previous trial, the rats press the opposite lever in the current trial despite a shift of the instruction cue, leading to another error response.

      We have revised the explanations of the behavioral strategies in the section of the Results section (page 9, lines 192–201). 

      Comment 7: Related to WSW / LSL needing a better introduction, on lines 192/193 authors describe a result where they saw the WSW and LSL strategies increase and decrease, respectively, in saline-injected mice. Is the change in performance expected or an undesired effect of the saline injection? This is not clear now and it should be clarified.

      The explanations of the win-shift-win and lose-shift-lose strategies have been revised in the Results section on excitotoxic lesion experiment (page 9, lines 192–201) as described in our response to Comment 6. Win-shift-win is an indicator of correct responses, while lose-shift-lose indicates errors. Therefore, win-shift-win is predicted to increase, and lose-shift-lose decrease, as discrimination learning progresses. Indeed, in the results of the behavioral experiments, shown in Figure 1, both indicators change in a similar pattern to those in the results of the lesion experiments (Figure 3).

      We have added the explanation of the proportions of both strategies in intact rats (page 9, lines 203–204) with a supplementary figure (Figure S2) and accompanying legend (page 56, lines 1173–1177).

      Comment 8: Muscimol experiments - two questions/comments. How often do rats receive muscimol?

      In this section, muscimol is given on day 2 and on days after the animals hit a 60% or 80% success rate. Can the authors provide a mean and SEM for when are those injections?

      The first injection was conducted on Day 2 to target the early stage. The second and third injections were conducted on the days after the success rate had reached 60% and 80% for the first time through the training, respectively, to target the middle and late stage. respectively. These conditions are described in the Results (page 10, lines 234– 237) and Methods (page 26, lines 633–636). The mean and s.e.m. of the injection day at the middle and late stages were not significantly different between the saline and muscimol-injected groups into the aDLS (see Author response image 2A) and pVLS (see Author response image 2B).

      Author response image 2.

      Injection days during auditory discrimination learning. Injections with saline (SAL) and muscimol (MUS) into the aDLS (A) or pVLS (B) were performed after the success rate had reached 60% (middle stage) and 80% (late stage) for the first time through the training, respectively (A, Wilcoxon signed rank test, middle, Z = 65, p = 0.772, late, Z = 56.5, p = 0.242 for the aDLS; B, Wilcoxon signed rank test, middle, Z = 39, p = 1.000, late, Z = 43, p = 0.587). Data are indicated as the median and quartiles with the maximal and minimal values. 

      Comment 9: Muscimol experiments. Can the authors comment on the effects on performance vs learning? What happens on the days after Muscimol? Does performance bounce back or is it still impaired?

      We conducted a transient inhibition experiment with muscimol to examine whether the neuronal activity in the striatal subregions is linked with the processes at different stages. In this experiment, to lower the possibility that compensation of learning may occur during a session after the muscimol injection (Day N), we limited the session time to 15 min (45 trials) and evaluated the impact of the injection on the success rate at specific stages. The success rate in the muscimol-injected groups into the aDLS significantly decreased at the middle stage compared to the corresponding salineinjected groups, but not at the early and late stages (Figure 4C), and the rate in the muscimol groups into the pVLS significantly decreased at the late stage compared with the respective saline groups, but not at the early and middle stages (Figure 4D). Our results demonstrated that the aDLS and pVLS mainly function at the middle and late stages of the auditory discrimination task, respectively. 

      In addition, we here reply to comment 10 as for the comparison of success rates before (Day N-1) and after (Day N+1) the injections (see Author response image 3). We focused on two injections into the aDLS at the middle stage and into the pVLS at the late stage, in which the rate was reduced soon after the muscimol injection on Day N. The success rate for the two injections showed no significant main effect regarding group (saline/muscimol) or day (Days N-1/N+1) and no significant interactions for group × day. Moreover, the success rate was not significantly increased on Day N+1 as compared to Day N-1, even in the saline-injected control group, probably because of the limited session time soon after the injection. Therefore, we consider that it was difficult to define the effects of drug injection on the learning of auditory discrimination in our behavioral protocol for the transient inhibition experiment, and that the reduced rates observed in the muscimol-injected group on Day N mostly reflect the impacts of muscimol at least partly on the performance of discriminative behavior. 

      Author response image 3.

      Comparison of success rate between days before (Day N1) and after (Day N+1) the injections into striatal subregions. Success rate in the saline (SAL)- and muscimol (MUS)-injected groups into the aDLS (A) or pVLS (B) at the early, middle, and late stages of auditory discrimination learning (two-way repeated ANOVA; early, day, F[1,14] = 5.266, p = 0.038, group, F[1,14] = 0.276, p = 0.608, day × group, F[1,14] = 0.118, p = 0.736; middle, day, F[1,14] = 4.110, p = 0.062, group, F[1,14] = 0.056, p = 0.816, day × group, F[1,14] = 1.150, p = 0.302; late, day, F[1,14] = 6.408, p = 0.024, group, F[1,14] = 0.229, p = 0.640, day × group, F[1,14] = 1.277, p = 0.278 for the aDLS; and early, day, F[1,10] = 0.115, p = 0.746, group, F[1,10] = 2.414, p = 0.151, day × group, F[1,10] = 0.157, p = 0.700; middle, day, F[1,10] = 0.278, p = 0.610, group, F[1,10] = 0.511, p = 0.491, day × group, F[1,10] = 4.144, p = 0.069; late, day, F[1,10] = 0.151, p = 0.705, group, F[1,10] = 0.719, p = 0.416, day × group, F[1,10] = 0.717, p = 0.417 for the pVLS). Data are indicated as the mean ± s.e.m.

      Comment 10: Muscimol data has a pair before and after, can the authors show this comparison at early, middle, and late training? Not just the subtraction.

      The comparison of success rates before and after drug injection is shown in Author response image 3.

      Comment 11: Ephys recordings. These are complex figures and include a large number of acronyms. It would help to define them again and help the reader through these figures so the reader can focus on understanding the finding more than the figure presentation.

      We replaced the abbreviations related to electrophysiological events (CO, CR, RS, and FL) with the original terms, and improved the explanation in the text and figures. 

      Comment 12: Figure 7B/E - on correct trials, they see a difference in the cue response to high tone / low tone but no difference in the choice. This is the one that seemed like a topography issue.

      The transient activity of cue onset-related neurons in the pVLS did not appear at the early stage of learning, but was observed in a learning-dependent manner (Figures 7A and S8E). In addition, the cue onset-HR activity showed a slight but notable difference between the HR and LL trials at the middle and late stages (Figure 7B), whereas there was no difference between activities in the HL and LR incorrect trials at the corresponding stages (Wilcoxon signed rank test; early, p = 0.375, middle, p = 0.931, and late, p = 0.668). These results suggest that the cue onset-related neurons in the pVLS represents the stimulus and response association (task contingency) rather than the topography of tone frequency.

      Comment 13: Animals were normally trained for 60 minutes but on muscimol days only trained for 15 mins. On PET days only trained for 30 minutes. Ephys sessions were 60 mins. Is this correct? Why?

      We determined the session time for each experiment by considering both technical and behavioral aspects. In the initial behavioral experiment, the session time was set to 60 min per day. Under this condition, the rats acquired the discrimination learning within 13 days. In the imaging experiment, the session without a PET scan was conducted for 60 min, while the session with a PET scan was carried out for 30 min as described previously (Cui et al, Neuroimage, 2015). This time schedule produced a learning curve similar to that of the initial behavioral experiment. In the transient inhibition experiment, the sessions without drug injections lasted for 60 min. As described in our response to the comment 2, the time of the session soon after the injection was limited to 15 min to lower the possibility of compensation of learning during the session. In the chronic lesion and electrophysiological experiments, all sessions were conducted for 60 min, corresponding to the initial experiment. 

      References

      Mizuma, H., Shukuri, M., Hayashi, T., Watanabe, Y. & Onoe, H. Establishment of in vivo brain imaging method in conscious mice. Journal of Nuclear Medicine 51, 10681075 (2010).

      Cui, Y., et al. A voxel-based analysis of brain activity in high-order trigeminal pathway in the rat induced by cortical spreading depression. Neuroimage 108, 17-22 (2015).

      Zimmer, E.R., et al. [18 F] FDG PET signal is driven by astroglial glutamate transport. Nat Neurosci 20, 393-395 (2017).

      Valtcheva, S. & Venance, L. Astrocytes gate Hebbian synaptic plasticity in the striatum. Nature communications 7, 13845 (2016).

      Gimenez T.L., Lorenc M., Jaramillo S. Adaptive categorization of sound frequency does not require the auditory cortex in rats. J Neurophysiol 114:1137-1145 (2015).

    1. Author response:

      The following is the authors’ response to the current reviews.

      Reviewer #1 (Public Review):

      Summary:

      This manuscript explores the impact of serotonin on olfactory coding in the antennal lobe of locusts and odor-evoked behavior. The authors use serotonin injections paired with an odorevoked palp-opening response assay and bath application of serotonin with intracellular recordings of odor-evoked responses from projection neurons (PNs).

      Strengths:

      The authors make several interesting observations, including that serotonin enhances behavioral responses to appetitive odors in starved and fed animals, induces spontaneous bursting in PNs, directly impacts PN excitability, and uniformly enhances PN responses to odors.

      Weaknesses:

      The one remaining issue to be resolved is the theoretical discrepancy between the physiology and the behavior. The authors provide a computational model that could explain this discrepancy and provide the caveat that while the physiological data was collected from the antennal lobe, but there could be other olfactory processing stages involved. Indeed other processing stages could be the sites for the computational functions proposed by the model. There is an additional caveat which is that the physiological data were collected 5-10 minutes after serotonin application whereas the behavioral data were collected 3 hours after serotonin application. It is difficult to link physiological processes induced 5 minutes into serotonin application to behavioral consequences 3 hours subsequent to serotonin application. The discrepancy between physiology and behavior could easily reflect the timing of action of serotonin (i.e. differences between immediate and longer-term impact).

      For our behavioral experiments, we waited 3 hours after serotonin injection to allow serotonin to penetrate through the layers of air sacks and the sheath, and for the locusts to calm down and recover their baseline POR activity levels. For the physiology experiments, we noticed that the quality of the patch decreased over time after serotonin introduction. Hence, it was difficult to hold cells for that long. However, the point raised by the reviewer is well-taken. We have performed additional experiments to show that the changes in POR levels to different odorants are rapid and can be observed within 15 minutes of injecting serotonin (Author response image 2) and that the physiological changes in PNs (bursting spontaneous activity, maintenance of temporal firing patterns, and increase odor-evoked responses) persists when the cells are held for longer duration (i.e. 3 hours akin to our behavioral experiments). It is worth noting that 3-hour in-vivo intracellular recordings are not easily achievable and come with many experimental constraints. So far, we have managed to record from two PNs that were held for this long and add them to this rebuttal to support our conclusions. (Author response image 1).

      Author response image 1.

      Spontaneous and odor-evoked responses in individual PNs remain consistent for three hours after serotonin introduction into the recording chamber/bath. (A) Representative intracellular recording showing membrane potential fluctuations in a projection neuron (PN) in the antennal lobe. Spontaneous and odor-evoked responses to four odorants (pink color bars, 4 s duration) are shown before (control) and after serotonin application (5HT). Voltage traces 30 minutes (30min), 1 hour (1h), 2 hours (2h), and 3 hours (3h) after 5HT application are shown to illustrate the persisting effect of serotonin during spontaneous and odor-evoked activity periods. (B) Rasterized spiking activities in two recorded PNs are shown. Spontaneous and odor-evoked responses are shown in all 5 consecutive trials. Note that the odor-evoked response patterns are maintained, but the spontaneous activity patterns are altered after serotonin introduction.

      Author response image 2.

      Palp-opening response (POR) patterns to different odorants remain consistent following serotonin introduction. The probability of PORs is shown as a bar plot for four different odorants; hexanol (green), benzaldehyde (blue), linalool (red), and ammonium (purple). PORs before serotonin injection (solid bars) are compared against response levels after serotonin injection (striped bars). As can be noted, PORs to the four odorants remain consistent when tested 15 minutes and 3 hours after (5HT) serotonin injection.

      Overall, the study demonstrates the impact of serotonin on odor-evoked responses of PNs and odor-guided behavior in locusts. Serotonin appears to have non-linear effects including changing the firing patterns of PNs from monotonic to bursting and altering behavioral responses in an odor-specific manner, rather than uniformly across all stimuli presented.

      We thank the reviewer for again providing very useful feedback for improving our manuscript.

      Reviewer #2 (Public Review):

      Summary:

      The authors investigate the influence of serotonin on feeding behavior and electrophysiological responses in the antennal lobe of locusts. They find that serotonin injection changes behavior in an odor-specific way. In physiology experiments, they can show that projection neurons in the antennal lobe generally increase their baseline firing and odor responses upon serotonin injection. Using a modeling approach the authors propose a framework on how a general increase in antennal lobe output can lead to odor-specific changes in behavior.

      Strengths:

      This study shows that serotonin affects feeding behavior and odor processing in the antennal lobe of locusts, as serotonin injection increases activity levels of projection neurons. This study provides another piece of evidence that serotonin is a general neuromodulator within the early olfactory processing system across insects and even phyla.

      Weaknesses:

      I still have several concerns regarding the generalizability of the model and interpretation of results. The authors cannot provide evidence that serotonin modulation of projection neurons impacts behavior.

      This is true and likely to be true for any study linking neural responses to behavior. There are multiple circuits and pathways that would get impacted by a neuromodulator like serotonin. What we showed with our physiology is how spontaneous and odor-evoked responses in the very first neural network that receives olfactory sensory neuron input are altered by serotonin. Given the specificity of the changes in behavioral outcomes (i.e. odor-specific increase and decrease in an appetitive behavior) and non-specificity in the changes at the level of individual PNs (general increase in odor-evoked spiking activity), we presented a relatively simple computational model to address the apparent mismatch between neural and behavioral responses. (Author response image 4).

      The authors show that odor identity is maintained after 5-HT injection, however, the authors do not show if PN responses to different odors were differently affected after serotonin exposure.

      The PN responses to different odorants changed in a qualitatively similar fashion. (Author response image 3)

      Author response image 3.

      PN activity before and after 5HT application are compared for different cellodor combinations. As can be noted, the changes are qualitatively similar in all cases. After 5HT application, the baseline activity became more bursty, but the odor-evoked response patterns were robustly maintained for all odorants.

      Regarding the model, the authors show that the model works for odors with non-overlapping PN activation. However, only one appetitive, one neutral, and one aversive odor has been tested and modeled here. Can the fixed-weight model also hold for other appetitive and aversive odors that might share more overlap between active PNs? How could the model generate BZA attraction in 5-HT exposed animals (as seen in behavior data in Figure 1) if the same PNs just get activated more?

      Author response image 4.

      Testing the generality of the proposed computational model. To test the generality of the model proposed we used a published dataset [Chandak and Raman, 2023]: Neural dataset – 89 PN responses to a panel of twenty-two odorants; Behavioral dataset – probability of POR responses to the same twenty-two odorants. We built the model using just the three odorants overlapping between the two datasets: hexanol, benzaldehyde and linalool. The true probability of POR values of the twenty odorants and the POR probability predicted by the model are shown for all twenty-two odorants as a scatter plot. As can be noted, there is a high correlation (0.79) between the true and the predicted values.

      The authors should still not exclude the possibility that serotonin injections could affect behavior via modulation of other cell types than projection neurons. This should still be discussed, serotonin might rather shut down baseline activation of local inhibitory neurons - and thus lead to the interesting bursting phenotypes, which can also be seen in the baseline response, due to local PN-to-LN feedback.

      As we agreed, there could be other cells that are impacted by serotonin release. Our goal in this study was to characterize how spontaneous and odor-evoked responses in the very first neural network that receives olfactory sensory neuron input are altered by serotonin. Within this circuit, there are local inhibitory neurons (LNs), as correctly indicated by this reviewer. Surprisingly, our preliminary data indicates that LNs are not shut down but also have an enhanced odor-evoked neural response. (Author response image 5.) Further data would be needed to verify this observation and determine the mechanism that mediate the changes in PN excitability. Irrespective, since PN activity should incorporate the effects of changes in the local neuron responses and is the sole output from the antennal lobe that drives all downstream odor-evoked activity, we focused on them in this study.

      Author response image 5.

      Representative traces showing intracellular recording from a local neuron in the antennal lobe. Five consecutive trials are shown. Note that LNs in the locust antennal lobe are non-spiking. The LN activity before, during, and after the presentation of benzaldehyde and hexanol (colored bar; 4s) are shown. The Left and Right panels show LN activity before and after the application of 5HT. As can be noted, 5HT did not shut down odor-evoked activity in this local neuron.

      The authors did not fully tone down their claims regarding causality between serotonin and starved state behavioral responses. There is no proof that serotonin injection mimics starved behavioral responses.

      Specific minor issues:<br /> It is still unclear how naturalistic the chosen odor concentrations are. This is especially important as behavioral responses to different concentrations of odors are differently modulated after serotonin injection (Figure 2: Linalool and Ammonium). The new method part does not indicate the concentrations of odors used for electrophysiology.

      All odorants were diluted to 0.01-10% concentration by volume in either mineral oil or distilled water. This information is included in the Methods section. For most odorants used in the study, the lower concentrations only evoked a very weak neural response, and the higher concentrations evoked more robust responses. The POR responses for these odorants at various concentrations chosen are included in Figure 2. Note, that the responses to linalool and ammonium remained weak throughout the concentration changes, compared to hexanol and benzaldehyde.

      Did all tested PNs respond to all odorants?

      No, only a subset of them responses to each odorant. These responses have been well characterized in earlier publications [included refs].

      The authors do not show if PN responses to different odors were differently affected after serotonin exposure. They describe that ON responses were robust, but OFF responses were less consistent after 5-HT injection. Was this true across all odors tested? Example traces are shown, but the odor is not indicated in Figure 4A. Figure 4D shows that many odor-PN combinations did not change their peak spiking activity - was this true across odorants? In Figure 5 - are PNs ordered by odor-type exposure?

      Also, Figure 6A only shows example trajectories for odorants - how does the average look? Regarding the data used for the model - can the new dataset from the 82 odor-PN pairs reproduce the activation pattern of the previously collected dataset of 89 pairs?

      What is shown in Figure 6A is the trial-averaged response trajectory combining activities of all 82 odor-PN pairs. 82 odor-PN pair was collected intracellularly examining the responses to four odorants before and after 5HT application. The second dataset involving 89 PN responses to 22 odorants was collected extracellularly. They have qualitative similarities in each odorant activate a unique subset of those neurons.

      The authors toned down their claims that serotonin injection can mimic the starved state behavioral response. However, some sentences still indicate this finding and should also be toned down:

      last sentence of introduction - "In sum, our results provide a more systems-level view of how a specific neuromodulator (serotonin) alters neural circuits to produce flexible behavioral outcomes."

      We believe we showed this with our computational model, how uniform changes in the neural responses could lead to variable and odor-specific changes in behavioral PORs.

      discussion: "Finally, fed locusts injected with serotonin generated similar appetitive responses to food-related odorants as starved locusts indicating the role of serotonin in hunger statedependent modulation of odor-evoked responses." This claim is not supported.

      Figure 7 shows that the fed locusts had lower POR to hex and bza. The POR responses significantly increased after the 5HT application. However, we have rephrased this sentence to limit our claims to this result. "Finally, fed locusts injected with serotonin generated similar appetitive palp-opening responses to food-related odorants as observed in starved locusts”

      last results: "However, consistent with results from the hungry locusts, the introduction of serotonin increased the appetitive POR responses to HEX and BZA. Intriguingly, the appetitive responses of fed locusts treated with 5HT were comparable or slightly higher than the responses of hungry locusts to the same set of odorants."

      Again this sentence simply describes the result shown in Figure 7.

      In Figure 7 - BZA response seems unchanged in hungry and fed animals and only 5-HT injection enhances the response. There is only one example where 5-HT application and starvation induce the same change in behavior - N=1 is not enough to conclude that serotonin influences food-driven behaviors.

      The reviewer is ignoring the lack of changes to PORs to linalool and ammonium. Taken together, serotonin increased PORs to only two of the four odorants in starved locusts. The responses after 5HT modulation to these four odorants were similar in fed locusts treated with 5HT and starved locusts.

      Also, this seems to be wrongly interpreted in Figure 7: "It is worth noting that responses to LOOL and AMN, non-food related odorants with weaker PORs, remained unchanged in fed locusts treated with 5HT." The authors indicate a significant reduction in POR after 5-HT injection on LOOL response in Figure 7.

      Revised.<br /> It is worth noting that responses to LOOL and AMN, non-food related odorants with weaker PORs, and reduced in fed locusts treated with 5HT."

      Also, the newly added sentence at the end of the discussion does not make sense: "However, since 5HT increased behavioral responses in both fed and hungry locusts, the precise role of 5HT modulation and whether it underlies hunger-state dependent modulation of appetitive behavior still remains to be determined."<br /> The authors did not test 5-HT injection in starved animals

      The results shown in Figure 1 compare the POR responses of starved locusts before and after 5HT introduction.

      We again thank the reviewer for useful feedback to further improve our manuscript.


      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public Review):

      Summary:

      This manuscript explores the impact of serotonin on olfactory coding in the antennal lobe of locusts and odor-evoked behavior. The authors use serotonin injections paired with an odor-evoked palp-opening response assay and bath application of serotonin with intracellular recordings of odor-evoked responses from projection neurons (PNs).

      Strengths:

      The authors make several interesting observations, including that serotonin enhances behavioral responses to appetitive odors in starved and fed animals, induces spontaneous bursting in PNs, and uniformly enhances PN responses to odors. Overall, I had no technical concerns. Weaknesses:

      While there are several interesting observations, the conclusions that serotonin enhanced sensitivity specifically and that serotonin had feeding-state-specific effects, were not supported by the evidence provided. Furthermore, there were other instances in which much more clarification was needed for me to follow the assumptions being made and inadequate statistical testing was reported.

      Major concerns.

      • To enhance olfactory sensitivity, the expected results would be that serotonin causes locusts to perceive each odor as being at a relatively higher concentration. The authors recapitulate a classic olfactory behavioral phenomenon where higher odor concentrations evoke weaker responses which is indicative of the odors becoming aversive. If serotonin enhanced the sensitivity to odors, then the dose-response curve should have shifted to the left, resulting in a more pronounced aversion to high odor concentrations. However, the authors show an increase in response magnitude across all odor concentrations. I don't think the authors can claim that serotonin enhances the behavioral sensitivity to odors because the locusts no longer show concentration-dependent aversion. Instead, I think the authors can claim that serotonin induces increased olfactory arousal.

      The reviewer makes a valid point. Bath application of serotonin increased POR behavioral responses across all odor concentrations, and concentration-dependent aversion was also not observed. Furthermore, the monotonic relationship between projection neuron responses and the intensity of current injection is altered when serotonin is exogenously introduced (see Author response image 1; see below for more explanation). Hence, our data suggests that serotonin alters the dose-response relationship between neural/behavioral responses and odor intensity. As recommended, we have followed what the reviewer has suggested and revised our claim to serotonin inducing increase in olfactory arousal. The new physiology data has been added as Supplementary Figure 3 to the revised manuscript.

      • The authors report that 5-HT causes PNs to change from tonic to bursting and conclude that this stems from a change in excitability. However, excitability tests (such as I/V plots) were not included, so it's difficult to disambiguate excitability changes from changes in synaptic input from other network components.

      To confirm that the PN excitability did indeed change after serotonin application, we performed a new set of current-clamp recordings. In these experiments, we monitored the spiking activities in individual PNs as we injected different levels of current injections (200 – 1000 pico Amperes). Note that locust LNs that provide recurrent inhibition arborize and integrate inputs from a large number of sensory neurons and projection neurons. Therefore, activating a single PN should not activate the local neurons and therefore the antennal lobe network.

      We found that the total spiking activity monotonically increased with the magnitude of the current injection in all four PNs recorded (Author response image 1). However, after serotonin injection, we found that the spiking activity remained relatively stable and did not systematically vary with the magnitude of the current injection. While the changes in odor-evoked responses may incorporate both excitability changes in individual PNs and recurrent feedback inhibition through GABAergic LNs, these results from our current injection experiments unambiguously indicate that there are changes in excitability at the level of individual PNs. We have added this result to the revised manuscript.

      Author response image 1.

      Current-injection induced spiking activity in individual PNs is altered after serotonin application. (A) Representative intracellular recordings showing membrane potential fluctuations as a function of time for one projection neuron (PNs) in the locust antennal lobe. A two-second window when a positive 200-1000pA current was applied is shown. Firing patterns before (left) and after (right) serotonin application are shown for comparison. Note, the spiking activity changes after the 5HT application. The black bar represents the 20mV scale. (B) Dose-response curves showing the average number of action potentials (across 5 trials) during the 2second current pulse before (green) and after (purple) serotonin for each recorded PN. Note that the current intensity was systematically increased from 200 pA to 1000 pA. The (C) The mean number of spikes across the four recorded cells during current injection is shown. The color progression represents the intensity of applied current ranging 200pA (leftmost bar) to 1000pA (rightmost bar). The dose-response trends before (green) and after (purple) 5HT application are shown for comparison. The error bars represent SEM across the four cells.

      • There is another explanation for the theoretical discrepancy between physiology and behavior, which is that odor coding is further processing in higher brain regions (ie. Other than the antennal lobe) not studied in the physiological component of this study. This should at least be discussed.

      This is a valid argument. For our model of neural mapping onto behavior to work, we only need the odorant that evokes or suppresses PORs to activate a distinct set of neurons. Having said that, our extracellular recording results (Fig. 6E) indicate that hexanol (high POR) and linalool (low POR) do activate highly non-overlapping sets of PNs in the antennal lobe. Hence, our results suggest that the segregation of neural activity based on behavioral relevance already begins in the antennal lobe. We have added this clarification to the discussion section.

      • The authors cannot claim that serotonin underlies a hunger state-dependent modulation, only that serotonin impacts responses to appetitive odors. Serotonin enhanced PORs for starved and fed locusts, so the conclusion would be that serotonin enhances responses regardless of the hunger state. If the authors had antagonized 5-HT receptors and shown that feeding no longer impacts POR, then they could make the claim that serotonin underlies this effect. As it stands, these appear to be two independent phenomena.

      This is also a valid point. We have clarified this in the revised manuscript.

      Reviewer #2 (Public Review):

      Summary:

      The authors investigate the influence of serotonin on feeding behavior and electrophysiological responses in the antennal lobe of locusts. They find that serotonin injection changes behavior in an odorspecific way. In physiology experiments, they can show that antennal lobe neurons generally increase their baseline firing and odor responses upon serotonin injection. Using a modeling approach the authors propose a framework on how a general increase in antennal lobe output can lead to odorspecific changes in behavior. The authors finally suggest that serotonin injection can mimic a change in a hunger state.

      Strengths:

      This study shows that serotonin affects feeding behavior and odor processing in the antennal lobe of locusts, as serotonin injection increases activity levels of antennal lobe neurons. This study provides another piece of evidence that serotonin is a general neuromodulator within the early olfactory processing system across insects and even phyla. Weaknesses:

      I have several concerns regarding missing control experiments, unclear data analysis, and interpretation of results.

      A detailed description of the behavioral experiments is lacking. Did the authors also provide a mineral oil control and did they analyze the baseline POR response? Is there an increase in baseline response after serotonin exposure already at the behavioral output level? It is generally unclear how naturalistic the chosen odor concentrations are. This is especially important as behavioral responses to different concentrations of odors are differently modulated after serotonin injection (Figure 2: Linalool and Ammonium).

      POR protocol: Sixth instar locusts (Schistocera americana) of either sex were starved for 24-48 hours before the experiment or taken straight from the colony and fed blades of grass for the satiated condition. Locusts were immobilized by placing them in the plastic tube and securing their body with black electric tape (see Author response image 2). Locusts were given 20 - 30 minutes to acclimatize after placement in the immobilization tube. As can be noted, the head of the locusts along with the antenna and maxillary palps protruded out of this immobilization tube so they can be freely moved by the locusts. Note that the maxillary palps are sensory organs close to the mouth parts that are used to grab food and help with the feeding process.

      It is worth noting that our earlier studies had shown that the presentation of ‘appetitive odorants’ triggers the locust to open their maxillary palps even when no food is presented (Saha et al., 2017; Nizampatnam et al., 2018; Nizampatnam et al., 2022; Chandak and Raman, 2023.) Furthermore, our earlies results indicate that the probability of palp opening varies across different odorants (Chandak and Raman, 2023). We chose four odorants that had a diverse range of palp-opening: supra-median (hexanol), median (benzaldehyde), and sub-median (linaool). Therefore, each locust in our experiments was presented with one concentration of four odorants (hexanol, benzaldehyde, linalool, and ammonium) in a pseudorandomized order. The odorants were chosen based on our physiology results such that they evoked different levels of spiking activities.

      The odor pulse was 4 s in duration and the inter-pulse interval was set to 60 s. The experiments were recorded using a web camera (Microsoft) placed right in front of the locusts. The camera was fully automated with the custom MATLAB script to start recording 2 seconds before the odor pulse and end recording at odor termination. An LED was used to track the stimulus onset/offset. The POR responses were manually scored offline. Responses to each odorant were scored a 0 or 1 depending on if the palps remained closed or opened. A positive POR was defined as a movement of the maxillary palps during the odor presentation time window as shown on the locust schematic (Main Paper Figure 1).

      Author response image 2.

      Pictures showing the behavior experiment setup and representative palp-opening responses in a locust.

      As the reviewer inquired, we performed a new series of POR experiments, where we explored POR responses to mineral oil and hexanol, before and after serotonin injection. For this study, we used 10 locusts that were starved 24-48 hours before the experiment. Note that hexanol was diluted at 1% (v/v) concentration in mineral oil. Our results reveal that locusts PORs to hexanol (~ 50% PORs) were significantly higher than those triggered by mineral oil (~10% PORs). Injection of serotonin increased the POR response rate to hexanol but did not alter the PORs evoked by mineral oil (Author response image 3).

      Author response image 3.

      Serotonin does not alter the palp-opening responses evoked by paraffin oil. The PORs before and after (5HT) serotonin injection are summarized and shown as a bar plot for hexanol and paraffin oil. Striped bars signify the data collected after 5HT injection. Significant differences are identified in the plot (one-tailed paired-sample t-test; (*p<0.05).

      Regarding recordings of potential PNs - the authors do not provide evidence that they did record from projection neurons and not other types of antennal lobe neurons. Thus, these claims should be phrased more carefully.

      In the locust antennal lobe, only the cholinergic projection neurons fire full-blown sodium spikes. The GABAergic local neurons only fire calcium ‘spikelets’ (Laurent, TINS, 1996; Stopfer et al., 2003; see Author response image 4 for an example). Hence, we are pretty confident that we are only recording from PNs. Furthermore, due to the physiological properties of the LNs, their signals being too small, they are also not detected in the extracellular recordings from the locust antennal lobe. Hence, we are confident with our claims and conclusion.

      Author response image 4.

      PN vs LN physiological differences: Left: A representative raw voltage traces recorded from a local neuron before, during, and after a 4-second odor pulse are shown. Note that the local neurons in the locust antennal lobe do not fire full-blown sodium spikes but only fire small calcium spikelets. On the right: A representative raw voltage trace recorded from a representative projection neuron is shown for comparison. Clear sodium spikes are clearly visible during spontaneous and odor-evoked periods. The gray bar represents 4 seconds of odor pulse. The vertical black bar represents the 40mV.

      The presented model suggests labeled lines in the antennal lobe output of locusts. Could the presented model also explain a shift in behavior from aversion to attraction - such as seen in locusts when they switch from a solitarious to a gregarious state? The authors might want to discuss other possible scenarios, such as that odor evaluation and decision-making take place in higher brain regions, or that other neuromodulators might affect behavioral output. Serotonin injections could affect behavior via modulation of other cell types than antennal lobe neurons. This should also be discussed - the same is true for potential PNs - serotonin might not directly affect this cell type, but might rather shut down local inhibitory neurons.

      There are multiple questions here. First, regarding solitary vs. gregarious states, we are currently repeating these experiments on solitary locusts. Our preliminary results (not included in the manuscript) indicate that the solitary animals have increased olfactory arousal and respond with a higher POR but are less selective and respond similarly to multiple odorants. We are examining the physiology to determine whether the model for mapping neural responses onto behavior could also explain observations in solitary animals.

      Second, this reviewer makes the point raised by Reviewer 1. We agree that odor evaluation and decisionmaking might take place in higher brain regions. All we could conclude based on our data is that a segregation of neural activity based on behavioral relevance might provide the simplest approach to map non-specific increase in stimulus-evoked neural responses onto odor-specific changes in behavioral outcome. Furthermore, our results indicate that hexanol and linalool, two odorants that had an increase and decrease in PORs after serotonin injection, had only minimal neural response overlap in the antennal lobe. These results suggest that the formatting of neural activity to support varying behavioral outcomes might already begin in the antennal lobe. We have added this to our discussion.

      Third, regarding serotonin impacting PNs, we performed a new set of current-clamp experiments to examine this issue (Author response image 1). Our results clearly show that projection neuron activity in response to current injections (that should not incorporate feedback inhibition through local neurons) was altered after serotonin injection. Therefore, the observed changes in the odor-evoked neural ensemble activity should incorporate modulation at both individual PN level and at the network level. We have added this to our discussion as well.

      Finally, the authors claim that serotonin injection can mimic the starved state behavioral response. However, this is only shown for one of the four odors that are tested for behavior (HEX), thus the data does not support this claim.

      We note that Hex is the only appetitive odorant in the panel. But, as reviewer 1 has also brought up a similar point, we have toned down our claims and will investigate this carefully in a future study.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      • Was the POR of the locusts towards linalool and ammonium higher than towards a blank odor cartridge? I ask because the locusts appear to be less likely to respond to these odors and so I am concerned that this assay is not relevant to the ecological context of these odors. In other words, perhaps serotonin did not enhance the responses to these odors in this assay, because this is not a context in which locusts would normally respond to these odors.

      The POR response to linalool and ammonium is lower and comparable to that of paraffin oil. Serotonin does not increase POR responses to paraffin oil but does increase response to hexanol (an appetitive odorant). We have clarified this using new data (Author response image 5).

      • It seems to me that Figure 5C is the crux for understanding the potential impact of 5-HT on odor coding, but it is somewhat confusing and underutilized. Is the implication that 5-HT decorrelates spontaneous activity such that when an odor stimulus arrives, the odor-evoked activity deviates to a greater degree? The authors make claims about this figure that require the reader to guess as to the aspect of the figure to which they are referring.

      The reviewer makes an astute observation. Yes, the spontaneous activity in the antennal lobe network before serotonin introduction is not correlated with the ensemble spontaneous activity after serotonin bath application. Remarkably, the odor-evoked responses were highly similar, both in the reduced PCA space and when assayed using high-dimensional ensemble neural activity vectors. Whether the changes in network spontaneous activity have a function in odor detection and recognition is not fully understood and cannot be convincingly answered using our data. But this is something that we had pondered.

      • The modeling component summarized in Figure 6 needs clarification and more detail. Perhaps example traces associated with positive weighting within neural ensemble 1 relative to neural ensemble 2? I struggled to understand conceptually how the model resolved the theoretical discrepancy between physiology and behavior.

      As recommended, here is a plot showing the responses of four PNs that had positive weights to hexanol and linalool. As can be expected, each PN in this group had higher responses to hexanol and no response to linalool. Further, the four PNs that received negative weights had response only to linalool.

      Author response image 5.

      Odor-evoked responses of four PNs that received positive weights in the model (top panel), and four PNs that were assigned negative weights in the model (bottom).

      • Was there a significant difference between the PORs of hungry vs. fed locusts? The authors state that they differ and provide statistics for the comparisons to locusts injected with 5-HT, but then don't provide any statistical analyses of hungry vs. fed animals.

      The POR responses to HEX (an appetitive odorant) were significantly different between the hungry and starved locusts.

      Author response image 6.

      A bar plot summarizing PORs to all four odors for satiated locust (highlighted with stripes), before (dark shade), and after 5HT injection (lighter shade). To allow comparison before 5HT injection for starved locust plotted as well (without stripes). The significance was determined using a one-tailed paired-sample ttest(*p<0.05).

      • Were any of the effects of 5-HT on odor-evoked PN responses significant? No statistics are provided.

      We examined the distribution of odor-evoked responses in PNs before and after 5HT introduction. We found that the overall distribution was not significantly different between the two (one-tailed pairedsample t-test; p = 0.93).

      Author response image 7.

      Comparison of the distribution of odor-evoked PN responses before (green) and after (purple) 5HT introduction. One-tailed paired sample t-test was used to compare the two distributions.

      • The authors interchangeably use "serotonin", "5HT" and "5-HT" throughout the manuscript, but this should be consistent.

      This has been fixed in the revised manuscript.

      • On page 2 the authors provide an ecological relevance for linalool as being an additive in pesticides, however, linalool is a common floral volatile chemical. Is the implication that locusts have learned to associate linalool with pesticides?

      Linalool is a terpenoid alcohol that has a floral odor but has also been used as a pesticide and insect repellent [Beier et al., 2014]. As shown in Author response image 2, it evoked the least POR responses amongst a diverse panel of 22 odorants that were tested. We have clarified how we chose odorants based on the prior dataset in the Methods section.

      • In Figure 1, there should be a legend in the figure itself indicating that the black box indicates the absence of POR and the white box indicates presence, rather than just having it in the legend text.

      Done.

      • In Figure 2, the raw data from each animal can be moved to the supplements. The way it is presented is overwhelming and the order of comparisons is difficult to follow.

      Done.

      • For the induction of bursting in PNs by the application of 5-HT, were there any other metrics observed such as period, duration of bursts, or peak burst frequency? The authors rely on ISI, but there are other bursting metrics that could also be included to understand the nature of this observation. In particular, whether the bursts are likely due to changes in intrinsic biophysical properties of the PNs or polysynaptic effects.

      We could use other metrics as the reviewer suggests. Our main point is that the spontaneous activity of individual PNs changed. We have added a new current-injection experiments to show that the PNs output to square pulses of current becomes different after serotonin application (Author response image 1)

      • Were 4-vinyl anisole, 1-nonanol, and octanoic acid selected as additional odors because they had particular ecological relevance, or was it for the diversity of chemical structure?

      These odorants were selected based on both, chemical structure and ecological relevance. The logic behind this was to have a very diverse odor panel that consisted of food odorant – Hexanol, aggregation pheromone – 4-vinyl anisole, sex pheromone – benzaldehyde, acid – octanoic acid, base – ammonium, and alcohol – 1-nonanol. Additionally, we selected these odors based on previous neural and behavioral data on these odorants (Chandak and Raman, 2023, Traner and Raman, 2023, Nizampatnam et al, 2022 & 2018; Saha et al., 2017 & 2013).

      Reviewer #2 (Recommendations For The Authors):

      The electrophysiology dataset combines all performed experiments across all tested different PN-odor pairs. How many odors have been tested in a single PN and how many PNs have been tested for a single odor? This information is not present in the current manuscript. Can the authors exclude that there are odor-specific modulations?

      In total, our dataset includes recordings from 19 PNs. Seven PNs were tested on a panel of seven odorants (4-vinyl anisole, 1-nonanol, octanoic acid, Hex, Bza, Lool, and Amn), and the remaining twelve were tested with the four main odorants used in the study (Hex, Bza, Lool, and Amn). This information has been added to the Methods section

      How did the authors choose the concentrations of serotonin injections and bath applications - is this a naturalistic amount?

      The serotonin concentration for ephys experiments was chosen based on trial-error experiments:

      0.01mM was the highest concentration that did not cause cell death. For the behavioral experiments, we increased the concentration (0.1 M) due to the presence of anatomical structures in the locust's head such as air sacks, sheath as well as hemolymph which causes some degree of dilution that we cannot control.

      Behavior experiments were performed 3 hours after injection - ephys experiments 5-10 minutes following bath application. Can the authors exclude that serotonin affects neural processing differently on these different timescales?

      We cannot exclude this possibility. We did ePhys experiments 5-10 minutes after bath application as it would be extremely hard to hold cells for that long.

      A longer delay was required for our behavioral experiments as the locusts tended to be a bit more agitated with larger spontaneous movements of palps as well as exhibited unprompted vomiting. A 3hour period allowed the locust to regain its baseline level movements after 5HT introduction. [This information has been added to the methods section of the revised manuscript]

      Concerning the analysis of electrophysiological data. The authors should correct for changes in the baseline before performing PCA analysis. And how much of the variance is explained by PC1 and PC2?

      We did not correct for baseline changes or subtract baseline as we wanted to show that the odor-evoked neural responses still robustly encoded information about the identity of the odorant.

      The authors should perform dye injections after recordings to visualize the cell type they recorded from. Serotonin might affect also other cell types in the antennal lobe.

      As mentioned above, in the locust antennal lobe only PNs fire full-blown sodium spikes, and LNs only fire calcium spikelets (Author response image 4). Since these signals are small, they will be buried under the noise floor when using extracellular recording electrodes for monitoring responses in the AL antennal lobe.

      Hence we are pretty certain what type of cells we are recording from.

      There were several typos in the manuscript, please check again.

      We have fixed many of the grammatical errors and typos in the revised version.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public Review):

      Summary:

      The Notch signaling pathway plays an important role in many developmental and disease processes. Although well-studied there remain many puzzling aspects. One is the fact that as well as activating the receptor through trans-activation, the transmembrane ligands can interact with receptors present in the same cell. These cis-interactions are usually inhibitory, but in some cases, as in the assays used here, they may also be activating. With a total of 6 ligands and 4 receptors, there is potentially a wide array of possible outcomes when different combinations are co-expressed in vivo. Here the authors set out to make a systematic analysis of the qualitative and quantitative differences in the signaling output from different receptor-ligand combinations, generating sets of "signaling" (ligand expressing) and "receiving" (receptor +/- ligand expressing cells).

      The readout of pathway activity is transcriptional, relying on the fusion of GAL4 in the intracellular part of the receptor. Positive ligand interactions result in the proteolytic release of Gal4 that turns on the expression of H2B-citrine. As an indicator of ligand and receptor expression levels, they are linked via TA to H2B mCherry and H2B mTurq expression respectively. The authors also manipulate the expression of the glycosyltransferase Lunatic-Fringe (LFng) that modifies the EGF repeats in the extracellular domains impacting their interactions. The testing of multiple ligand-receptor combinations at varying expression levels is a tour de force, with over 50 stable cell lines generated, and yields valuable insights although as a whole, the results are quite complex.

      Strengths:

      Taking a reductionist approach to testing systematically differences in the signaling strength, binding strength, and cis-interactions from the different ligands in the context of the Notch1 and Notch 2 receptors (they justify well the choice of players to test via this approach) produces a baseline understanding of the different properties and leads to some unexpected and interesting findings. Notably:

      -                Jag1 ligand expressing cells failed to activate Notch1 receptor although were capable of activating Notch2. Conversely, Jag2 cells elicited the strongest activation of both receptors. The results with

      Jag1 are surprising also because it exhibits some of the strongest binding to plate-bound ligands. The failure to activate Notch1 has major functional significance and it will be important in the future to understand the mechanistic basis.

      -                Jagged ligands have the strongest cis-inhibitory effects and the receptors differ in their sensitivity to cis-inhibition by Dll ligands. These observations are in keeping with earlier in vivo and cell culture studies. More referencing of those would better place the work in context but it nicely supports and extends previous studies that were conducted in different ways.

      -                Responses to most trans-activating ligands showed a degree of ultrasensitivity but this was not the case for cis-interactions where effects were more linear. This has implications for the way the two mechanisms operate and for how the signaling levels will be impacted by ligand expression levels.

      -                Qualitatively similar results are obtained in a second cell line, suggesting they reflect fundamental properties of the ligands/receptors.

      We appreciate the positive and constructive feedback.

      Weaknesses:

      One weakness is that the methods used to quantify the expression of ligands and receptors rely on the co-translation of tagged nuclear H2B proteins. These may not accurately capture surface levels/correctly modified transmembrane proteins. In general, the multiple conditions tested partly compensate for the concerns - for example, as Jag1 cells do activate Notch2 even if they do not activate Notch1 some Jag1 must be getting to the surface. But even with Notch2, Jag1 activities are on the lower side, making it important to clarify, especially given the different outcomes with the plated ligands. Similarly, is the fact that all ligands "signalled strongest to Notch2" an inherent property or due to differences in surface levels of Notch 2 compared to Notch1? The results would be considerably strengthened by calibration of the ligand/receptor levels (and ideally their sub-cellular localizations). Assessing the membrane protein levels would be relatively straightforward to perform on some of the basic conditions because their ligand constructs contain Flag tags, making it plausible to relate surface protein to H2B, and there are antibodies available for Notch1 and Notch2.

      We agree that mCherry fluorescence does not provide a direct readout of active surface ligand levels. As the reviewer points out, the ability of Jag1 to activate Notch2 demonstrates that expressed Jag1 is competent for signaling. Further, in some cases, Jag1-Notch2 activation can be comparable to Dll1-Notch2 activation (Figure 2A). Following the reviewer’s suggestion, we performed a Western blot for multiple expression levels for each of three surface ligands (Dll1, Dll4, Jag1) (Figure 2—figure supplement 2). This blot revealed a signal for surface expression of Jag1. Interpretation is complicated by the expected dependence of the efficiency of surface protein purification on the number of primary amines in the protein, which varies among these ligands, and qualitatively correlates with the staining intensity. While this makes quantitative interpretation difficult, this result further supports the notion that Jag1 is present on the cell surface. Finally, we note that high signaling activity need not, in general, directly correlate with surface expression levels. In fact, one study showed an example in which increased ligand activity occurred with decreased basal ligand surface levels (Antfolk et al., 2017). While one would ideally like to know all parameters of the system, including surface protein levels, rates of recycling, etc. the perspective taken here is that the net effect of these many post-translational processing steps can be subsumed into the overall relationship between the expression of the protein (which, in our case, is read out by the co-translational reporter) and its activity, which is relevant for the behavior of developmental circuits, among other systems. To address this comment, we now explicitly mention the limitation of mCherry as a proxy for surface protein, and add a reference to previous work highlighting the relationship between surface levels and ligand activity.

      In terms of the dependence of signaling on Notch levels, the metric of signaling activity used here is explicitly normalized by the mTurquoise co-translational reporter of Notch expression to account for differences in receptor expression across receiver clones. We have added a new figure to show the variation in expression (Figure 1—figure supplement 1A) and to demonstrate this normalization (Figure 1—figure supplement 5). Having said that, as the reviewer correctly points out, we cannot directly address the dependence on surface receptor levels with mTurquoise alone. To address this comment, we have added a figure that shows cotranslational and surface receptor expression for a subset of our receiver clones (Figure 1—figure supplement 1B). Although antibody binding strengths may vary, it appears unlikely that higher surface levels could explain most ligands’ preferential activation of Notch2 over Notch1, since Notch2 levels were lower than Notch1 levels in both surface expression and cotranslational expression.

      Cis-activation as a mode of signaling has only emerged from these synthetic cell culture assays raising questions about its physiological relevance. Cis-activation is only seen at the higher ligand (Dll1, Dll4) levels, how physiological are the expression levels of the ligands/receptors in these assays? Is it likely that this would make a major contribution in vivo? Is it possible that the cells convert themselves into "signaling" and "receiving" sub-populations within the culture by post-translational mechanism? Again some analysis of the ligand/receptors in the cultures would be a valuable addition to show whether or not there are major heterogeneities.

      The cis-activation results in this paper are, as the reviewer points out, conducted in synthetic cell culture assays. Cis-activation is observed across a large dynamic range of ligand expression, possibly including non-physiologically high levels. However, our previous work (Nandagopal et al, eLife 2019) showed that cis-activation does not require over-expression, as it occurred in unmodified Caco-2 and NMuMG cells with their endogenous ligand and receptor expression levels. As shown here in Figure 4B, cis-activation for Notch2 increases monotonically and is substantial even at intermediate ligand concentrations. In other cases, cis-activation is maximal at intermediate concentrations. We agree that the in vivo role remains unclear, and is difficult to determine due to the typical close contacts among cells in tissues. Therefore, these assays do not speak to in vivo relevance. Note that we can, however, rule out the possibility of trans signaling between well-mixed cell populations at these densities (Figure 4A).

      It is hard to appreciate how much cell-to-cell variability in the "output" there is. For example, low "outputs" could arise from fewer cells becoming activated or from all cells being activated less. As presented, only the latter is considered. That may be already evident in their data, but not easy for the reader to distinguish from the way they are presented. For example, in many of the graphs, data have been processed through multiple steps of normalization. Some discussion/consideration of this point is needed.

      We agree that in different experiments changes in a mean response can reflect changes in fraction of activated cells, or level of activation or some combination of both. In this work, most assays were conducted by flow cytometry, which provides a full distribution of cellular responses. We provided distributions for some experiments in the supplementary figures (i.e., Figure 4—figure supplement 1, and Figure 5—figure supplement 4). The sheer number of experiments and samples prevents us from displaying all underlying histograms. Therefore, we have provided all flow data sets in an extensive archive that is publicly available on data.caltech.edu (https://doi.org/10.22002/gjjkn-wrj28).

      Impact:

      Overall, cataloging the outcomes from the different ligand-receptor combinations, both in cis and trans, yields a valuable baseline for those investigating their functional roles in different contexts. There is still a long way to go before it will be possible to make a predictive model for outcomes based on expression levels, but this work gives an idea about the landscape and the complexities. This is especially important now that signaling relationships are frequently hypothesized based on single-cell transcriptomic data. The results presented here demonstrate that the relationships are not straightforward when multiple players are involved.

      We appreciate this concise impact summary, and agree with its conclusions.

      Reviewer #2 (Public Review):

      Summary:

      In this manuscript, the authors extend their previous studies on trans-activation, cis-inhibition (PMID: 25255098), and cis-activation (PMID: 30628888) of the Notch pathway. Here they create a large number of cell lines using CHO-K1 and C2C12 cells expressing either Notch1-Gal4 or Notch2-Gal4 receptors which express a fluorescent protein upon receptor activation (receiver cells). For cis-inhibition and cis-activation assays, these cells were engineered to express one of the four canonical Notch ligands (Dll1, Dll4, Jag1, Jag2) under tetracycline control. Some of the receiver cells were also transfected with a Lunatic fringe (Lfng) plasmid to produce cells with a range of Lfng expression levels. Sender cells expressing all of the canonical ligands were also produced. Cells were mixed in a variety of co-culture assays to highlight trans-activation, cis-activation, and cis-inhibition. All four ligands were able to trans-activate Notch1 and Notch 2, except Jag1 did not transactivate Notch1. Lfng enhanced trans-activation of both Notch receptors by Dll1 and Dll2, and inhibited Notch1 activation by Jag2 and Notch2 activation by both Jag 1 and Jag2. Cis-expression of all four ligands was predominantly inhibitory, but Dll1 and Dll4 showed strong cis-activation of Notch2. Interestingly, cis-ligands preferentially inhibited trans-activation by the same ligand, with varying effects on other trans-ligands.

      Strengths:

      This represents the most comprehensive and rigorous analysis of the effects of canonical ligands on cis- and trans-activation, and cis-inhibition, of Notch1 and Notch2 in the presence or absence of Lfng so far. Studying cis-inhibition and cis-activation is difficult in vivo due to the presence of multiple Notch ligands and receptors (and Fringes) that often occur in single cells. The methods described here are a step towards generating cells expressing more complex arrays of ligands, receptors, and Fringes to better mimic in vivo effects on Notch function.

      In addition, the fact that their transactivation results with most ligands on Notch1 and 2 in the presence or absence of Lfng were largely consistent with previous publications provides confidence that the author's assays are working properly.

      We appreciate the thoughtful comments and feedback.

      Weaknesses:

      It was unusual that the engineered CHO cells expressing Notch1-Gal4 were not activated at all by co-culture with Jag1-expressing CHO cells. Many previous reports have shown that Jag1 can activate Notch1 in co-culture assays, including when Notch1 was expressed in CHO cells. Interestingly, when the authors used Jag1-Fc in a plate coating assay, it did activate Notch1 and could be inhibited by the expression of Lfng.

      In our assays, we do in fact also see some signaling of Jag1 to Notch1, especially when dLfng is coexpressed (Figure 2—figure supplement 4, formerly Figure 2—figure supplement 3). While these levels are lower than those observed for other ligand-receptor combinations, they are significantly elevated compared to baseline. In specific natural contexts, it will be important to determine whether the weak but non-zero Jag1-Notch1 signaling acts negatively to suppress signaling from other ligands, or provides weak but potentially functionally important levels of signaling. Evidence for both modes exists in the literature. To address this, we have expanded the discussion of Jag1-Notch1 signaling and added references to other work on Jag1-Notch1 signaling to the Discussion section.

      The cell surface level of the ligands was determined by flow cytometry of a co-translated fluorescent protein. Some calibration of the actual cell surface levels with the fluorescent protein would strengthen the results.

      This issue was also raised by Reviewers #1 and #3. Please see responses to Reviewer #1, above.

      Reviewer #3 (Public Review):

      Summary:

      This manuscript reports a comprehensive analysis of Notch-Delta/Jagged signaling inclusive of the human Notch1 and Notch2 receptors and DLL1, DLL4, JAG1, and JAG2 ligands. Measurements

      encompassed signaling activity for ligand trans-activation, cis-activation, cis-inhibition, and activity modulation by Lfng. The most striking observations of the study are that JAG1 has no detectable activity as a Notch1 ligand when presented on a cell (though it does have activity when immobilized on a surface), even though it is an effective cis-inhibitor of Notch1 signaling by other ligands, and that DLL1 and DLL4 exhibit cis-activating activity for Notch1 and especially for Notch2. Notwithstanding the artificiality of the system and some of its shortcomings, the results should nevertheless be a valuable resource for the Notch signaling community.

      Strengths:

      (1)  The work is systematic and comprehensive, addressing questions that are of importance to the community of researchers investigating mammalian Notch proteins, their activation by ligands, and the modulation of ligand activity by LFng.

      (2)  A quantitative and thorough analysis of the data is presented.

      Weaknesses:

      (1) The manuscript is primarily descriptive and does not delve into the underlying, mechanistic origin or source of the different ligand activities.

      We agree that the goals of this paper were largely to discover the range of signaling modes that occur. A mechanistic analysis would be beyond the scope of this work, but we agree it is an important next step.

      (2) The amount of ligand or receptor expressed is inferred from the flow cytometry signal of a co-translated fluorescent protein-histone fusion, and is not directly measured. The work would be more compelling if the amount of ligand present on the cell surface were directly measured with anti-ligand antibodies, rather than inferred from measurements of the fluorescent protein-histone fusion.

      This issue was also raised by Reviewers #1 and #2. Please see responses to Reviewer #1, above.

      (3) It would be helpful to see plots of the raw activity data before transformation and normalization, because the plots present data after several processing steps, and it is not clear how the processed data relate to the original values determined in each measurement.

      We included examples showing how raw data is processed in Figure 4—figure supplement 1 and Figure 5—figure supplement 4. The sheer number of experiments precludes including similar figures for all data sets. However, all raw and processed data and data analysis code is publicly available at (https://doi.org/10.22002/gjjkn-wrj28).

      (4) The authors use sparse plating of engineered cells with parental (no ligand or receptor-expressing cell to measure cis activation). However, the cells divide within the cultured period of 22-24 h and can potentially trans-activate each other.

      If measured cis-activation signal arises solely from trans-activation, then the measured cis-activation signal per cell should increase with cell density, since trans-activation per cell does depend on cell density (Figure 4A). However, for the strongest cis-activators (Dll1- and Dll4-Notch2), signaling magnitude is similar when these cells are cultured sparsely or at confluence, which would otherwise allow efficient trans signaling (Figure 5A). Thus, for Dll1- and Dll4-Notch2 receivers, total signaling strength per cell depends little or not at all on the opportunity to signal intercellularly. Moreover, cis-activation signal for the Dll1- and Dll4-Notch2 combinations exceeded the maximum trans-signaling levels we could achieve for the same receivers when cis-ligand was suppressed (Figure 4B). These results argue that cis interactions dominate signaling in this context. However, we have not ruled out the possibility that trans-signaling between sister cells after division contributes to the comparatively weak cis-activation observed for Notch1 receivers.

      Reviewer #1 (Recommendations For The Authors):

      As outlined in the public review, there is a question of whether the nuclear H2B accurately reflects the surface levels of the transmembrane proteins (ligand and receptor). Clearly, it would not be feasible to check levels in all of the experimental conditions, but some baseline conditions should be analyzed.

      We addressed this above.

      Reviewer #2 (Recommendations For The Authors):

      (1)  As mentioned above, it was unusual that Jag1 did not activate Notch1 in co-culture assays, but did activate Notch1 in plate-coating assays. The authors should add some text to the Discussion to explain why they think this is happening in their engineered cells. One possibility is that the CHO cells express Manic fringe (Mfng) which is known to reduce Jag1-Notch1 activation. Data for Mfng levels in CHO cells were not included in Supplemental Table 2. Knocking down all three Fringes in CHO cells might increase Jag1-Notch1 activation.

      This is already addressed in a sentence in the results: “Strikingly, while Jag1 sender cells failed to activate Notch1 receivers above background (Figure 2D), plate-bound Jag1-ext-Fc activated Notch1 only ~3-fold less efficiently than it activated Notch2 (Figure 3B-D). This suggests that the natural endocytic activation mechanism, or potential differences in tertiary structure between the expressed and recombinant Jag1 extracellular domains, could play roles in preventing Jag1-Notch1 signaling in coculture.” Regarding the point about Mfng, we added a note to Supplementary Table about other CHO-K1 expression data.

      (2) Figure 1-supplemental figure 1: Both the Notch1-Jag1 and Notch1-Jag2 cells show high expression of Jag1 in low 4epi, but any higher concentration reduces to control levels. How much of a problem is this for interpreting your data?

      This was not the ideal behavior, but by binning cells by co-translational reporters for ligand expression, we were able to obtain enough cells in intermediate bins. (Note: Figure 1—figure supplement 1 is now Figure 1—figure supplement 2.)

      (3)  Figure 1C legend: Are these stably-expressing cells or Tet-off cells? Please state in legend.

      The figure legend has been updated.

      (4)  Figure 1E: How long is the knockdown of Rfng and Lfng effective? Does it affect the expression of Lfng later?

      siRNA effects generally last for at least 72-96 hours, so we do not anticipate this being an issue.

      (5) Page 9: "Lfng significantly decreased trans-activation of both receptors by Jag1 (>2.5-fold)". If there is no Jag1-Notch1 activation, how can Lfng decrease trans-activation?

      We added a note in the main text to clarify that while Jag1-Notch1 signaling is relatively low, it can still be detectably decreased.

      (6) Figure 4A legend: Please define what "2.5k ea senders and Rec" means. In the text, it says "To focus on cis-interactions alone, we then cultured receiver cells at low density, amid an excess of wildtype CHO-K1 cells" (page 14).

      This was clarified in the text.

      (7)  Page 14: "By contrast, Notch2 was cis-activated by both Dll1 and Dll4, to levels exceeding those produced by trans-activation by high-Dll1 senders (Figure 4B, lower left)." Where is the trans-activation data? 4B, lower right?

      We updated this reference in the main text.

      (8)  Page 16: "For Notch2-Dll1 and Notch2-Dll4, single cell reporter activities correlated with cis-ligand expression, regardless of whether cells were pre-induced at a high or low culture density (Figure 4D)." It appears that Notch2-Dll1 has lower Notch activation at sparse culture than confluent.

      We agree that the level signaling is lower in sparse compared to confluent on average. This is explained by the sensitivity of the Tet-OFF promoter to culture density (Figure 4—figure supplement 2). However, the key point of this experiment is the positive correlation, which is consistent with cis-activation, and inconsistent with the pre-generation of NEXT hypothesis diagrammed in Figure 4C, which would not be expected to produce such a correlation.

      (9a) For the creation of the C2C12-Nkd cells: Has genomic sequencing been done to confirm editing of Notch2 and Jag1 loci?

      We confirmed the knockdown but did not do genomic sequencing.

      (9b) The gel in Figure 7-Supplement 1C is not adequate for showing loss of Jag1. It should be repeated.

      In this case, we have only the single gel. We added a note in figure legend that no duplicate was performed.

      (10) Figure 7A: Which Fringes are expressed in C2C12 cells? You should provide a rationale for knocking down just Rfng.

      Figure 7—figure supplement 1A shows the levels of expression in C2C12. Note that Mfng is not highlighted because its levels were undetectable.

      (11) Figure 7-Supplement 1D: This is confusing. Notch2 levels are not reduced in the left panel, and Notch1 and Notch2 levels are not reduced in the right panel?

      C2C12-Nkd cells exhibit reduced levels of Notch1 and Notch3. This can be seen in Figure 7—figure supplement 1A. Panel D presents the results of additional siRNA knockdown, performed to prevent subsequent up-regulation of Notch1 and Notch3 during the assay. These knockdown results were variable, as shown. The Notch2 siRNA knockdown was not essential for these experiments, but performed despite very low levels of Notch2 to begin with. In the revision, we have added this note to the Methods.

      Reviewer #3 (Recommendations For The Authors):

      (1) The results section of the manuscript is very dense and difficult to follow, as are the figure legends.

      We appreciate the criticism, and regret that it is not easier to read in its current form.

      (2) The authors could emphasize areas of concordance with published results (where available) to place their artificial, engineered system into a better biological context. Are there any examples of studies in whole organisms where cis-activation plays a role?

      We are not aware of examples of cis-activation in whole organisms at this point.

      (3) How do the authors rationalize the different responses of Notch1 to cell-presented Jag1 as opposed to immobilized Jag1, where its signal strength is second in rank order on a molar basis?

      This comment was addressed above in response to the first recommendation from Reviewer #2.

      It is also difficult to understand Figure 2_—_figure Supplement 3B, in which it appears that Jag1 induces a Notch1 reporter response when LFng is knocked down (dLfng), and how those data relate to the inactive response to Jag1 shown in the main figures.

      The issue here is a difference of normalization. Figure 2A in the main text is normalized to the sender expression level, i.e. relative signaling strength. By contrast, Figure 2—figure supplement 4B (previously Figure 2—figure supplement 3B) shows absolute signaling activity, which can appear higher because it does not normalize for ligand expression. For Jag1-Notch1 signaling in particular, substantial signaling required very high levels of Jag1. We have added a new figure to demonstrate these two types of normalization (Figure 2—figure supplement 1A).

      See the Authr response image 1 below for a direct comparison of these two normalization modes using data from both Figure 2A and Figure 2—figure supplement 4B. Note how the Jag1-Notch1 signaling activities that are nonzero in the top plot go to zero in the bottom plot as a result of normalizing the values to ligand expression.

      Author response image 1. Comparison of normalization modes in Figure 2A and Figure 2—figure supplement 4B (formerly 3B). Normalized trans-activation signaling activities for different ligand-receptor combinations (with dLfng only), either with further normalization to ligand expression (bottom row) or without further normalization (top row). Normalized signaling activity is defined as reporter activity (mCitrine, A.U.) divided by cotranslational receptor expression (mTurq2, A.U.), normalized to the strongest biological replicate-averaged signaling activity across all ligand-receptor-Lfng combinations in this experiment. Saturated data points, defined here as those with normalized signaling activity over 0.75 in both dLfng and Lfng conditions, were excluded. Colors indicate the identity of the trans-ligand expressed by cocultured sender cells. Error bars denote bootstrapped 95% confidence intervals (Methods), in this case sampled from the number of biological replicates given in the legend—n1 (for Notch1) or n2 (for Notch2). See Methods and Figure 2A caption for more details. Note that the only difference between this figure and the new Figure 2—figure supplement 1A is that this figure additionally includes the Jag1-high data from Figure 2—figure supplement 4B.

    1. Author Response

      The following is the authors’ response to the original reviews.

      eLife assessment

      This fundamental study evaluates the evolutionary significance of variations in the accuracy of the intron-splicing process across vertebrates and insects. Using a powerful combination of comparative and population genomics approaches, the authors present convincing evidence that species with lower effective population size tend to exhibit higher rates of alternative splicing, a key prediction of the drift-barrier hypothesis. The analysis is carefully conducted and all observations fit with this hypothesis, but focusing on a greater diversity of metazoan lineages would make these results even more broadly relevant. This study will strongly appeal to anyone interested in the evolution of genome architecture and the optimisation of genetic systems.

      Public Reviews):

      Reviewer #1 (Public Review:

      Summary:

      Functionally important alternative isoforms are gold nuggets found in a swamp of errors produced by the splicing machinery.

      The architecture of eukaryotic genomes, when compared with prokaryotes, is characterised by a preponderance of introns. These elements, which are still present within transcripts, are rapidly removed during the splicing of messenger RNA (mRNA), thus not contributing to the final protein. The extreme rarity of introns in prokaryotes, and the elimination of these introns from mRNAs before translation into protein, raises questions about the function of introns in genomes. One explanation comes from functional biology: introns are thought to be involved in post-transcriptional regulation and in the production of translational variants. The latter function is possible when the positions of the edges of the spliced intron vary. While some light has been shed on specific examples of the functional role of alternative splicing, to what extent are they representative of all introns in metazoans?

      In this study, the hypothesis of a functional role for alternative splicing, and therefore to a certain extent for introns, is evaluated against another explanation coming from evolutionary biology: isoforms are above all errors of imprecision by the molecular machinery at work during splicing. This hypothesis is based on a principle established by Motoo Kimura, which has become central to population genetics, explaining that the evolutionary trajectory of a mutation with a given effect is intimately linked to the effective population size (Ne) where this mutation emerges. Thus, the probability of fixation of a weakly deleterious mutation increases when Ne decreases, and the probability of fixation of a weakly advantageous mutation increases when Ne increases. The genomes of populations with low Ne are therefore expected to accumulate more weakly deleterious mutations and fewer weakly advantageous mutations than populations with high Ne. In this framework, if splicing errors have only small effects on the fitness of individuals, then natural selection cannot increase the precision of the splicing machinery, allowing tolerance for the production of alternative isoforms.

      In the past, the debate opposed one-off observations of effectively functional isoforms on the one hand, to global genomic quantities describing patterns without the possibility of interpreting them in detail. The authors here propose an elegant quantitative approach in line with the expected continuous variation in the effectiveness of selection, both between species and within genomes. The result describing the inter-specific pattern on a large scale confirms what was already known (there is a negative relationship between effective size and average alternative splicing rate). The essential novelty of this study lies in 1) the quantification, for each intron studied, of the relative abundance of each isoform, and 2) the analysis of a relationship between this abundance and the evolutionary constraints acting on these isoforms.

      What is striking is the light shed on the general very low abundance of alternative isoforms. Depending on the species, 60% to 96% of cases of alternatively spliced introns lead to an isoform whose abundance is less than 5% of the total variants for a given intron.

      In addition to the fact that 60 %-96% of the total isoforms are more than 20 times less abundant than their majority form, this large proportion of alternative isoforms exhibit coding-phase shift at rates similar to what would be expected by chance, i.e. for a third of them, which reinforces the idea that there is no particular constraint on these isoforms.

      The remaining 4%-40% of isoforms see their coding-phase shift rate decrease as their relative abundance increases. This result represents a major step forward in our understanding of alternative splicing and makes it possible to establish a quantitative model directly linking the relative abundance of an isoform with a putative functional role concerning only those isoforms produced in abundance. Only the (rare) isoforms which are abundantly produced are thought to be involved in a biological function.

      Within the same genome, the authors show that only highly expressed genes, i.e. those that tend to be more constrained on average, are also the genes with the lowest alternative splicing rates on average.

      The comparison between species in this study reveals that the smaller the effective size of a species, the more its genome produces isoforms that are low in abundance and low in constraint. Conversely, species with a large effective size relatively reduce rare isoforms, and increase stress on abundant isoforms. To sum up:

      • the higher the effective size of a species, the fewer introns are spliced.

      • highly expressed genes are spliced less.

      • when splicing occurs, it is mainly to produce low-abundance isoforms.

      • low-abundance isoforms are also less constrained.

      Taken together, these results reinforce a quantitative view of the evolution of alternative splicing as being mainly the product of imprecision in the splicing machinery, generating a great deal of molecular noise. Then, out of all this noise, a few functional gold nuggets can sometimes emerge. From the point of view of the reviewer, the evolutionary dynamics of genomes are depressing. The small effective population sizes are responsible for the accumulation of multiple slightly deleterious introns. Admittedly, metazoan genomes try to get rid of these introns during RNA maturation, but this mechanism is itself rendered imprecise by population sizes.

      Strengths:

      • The authors simultaneously study the effects of effective population size, isoform abundance, and gene expression levels on the evolutionary constraints acting on isoforms. Within this framework, they clearly show that an isoform becomes functionally important only under certain rare conditions.

      • The authors rule out an effect putatively linked to variations in expression between different organs which could have biased comparisons between different species.

      Weaknesses:

      • While the longevity of organisms as a measure of effective size seems to work overall, it may not be relevant for discriminating within a clade. For example, within Hymenoptera, we might expect them to have the same overall longevity, but that effective size would be influenced more by the degree of sociality: solitary bees/ants/wasps versus eusocial. I am therefore certain that the relationship shown in Figure 4D is currently not significant because the measure of effective size is not relevant for Hymenoptera. The article would have been even more convincing by contrasting the rates of alternative splicing between solitary versus social hymenopterans.

      As suggested by the reviewer, we investigated the degree of sociality for the 18 hymenopterans included in our study. We observed that the average dN/dS of the 12 eusocial species (4 bees, 6 ants, 2 wasps) is significantly higher than that of the 6 solitary species (p=2.1x10-3; Fig. R1A), consistent with a lower effective population size in eusocial species compared to solitary ones.

      However, the AS rate does not differ significantly between these two groups, neither for the full set of major-isoform introns (Author response image 1B), nor for the subsets of low-AS or high-AS major-isoform introns (Author response image 1C,D). Given the limited sample size (12 eusocial species, 6 solitary species), it is possible that some uncontrolled variables affecting the AS rate hide the impact of Ne.

      Author response image 1.

      Comparison of solitary (N=6) and eusocial hymenopterans (N=12). A: dN/dS ratio. B: AS rate (all major-isoform introns). C: AS rate (low-AS major-isoform introns). D: AS rate (high-AS major-isoform introns). The means of the two group were compared with a Wilcoxon test.

      • When functionalist biologists emphasise the role of the complexity of living things, I'm not sure they're thinking of the comparison between "drosophila" and "homo sapiens", but rather of a broader evolutionary scale. Which gives the impression of an exaggeration of the debate in the introduction.

      We disagree with the referee: in fact, all the debate regarding the paradox of the absence of relationship between the number of genes and organismal complexity arose from the comparative analysis of gene repertoires across metazoans. This debate started in the early 2000’s, when the sequencing of the human genome revealed that it contains only ~20,000 protein-coding genes (far less than the ~100,000 genes that were expected at that time). This came as a big surprise because it showed that the gene repertoire of mammals is not larger than that of invertebrates such as Caenorhabditis elegans (19,000 genes) or Drosophila melanogaster (14,000 genes) . We cite below several articles that illustrate how this paradox has been perceived by the scientific community:

      Graveley BR 2001 Alternative splicing: increasing diversity in the proteomic world. Trends in Genetics 17 : 100–107. https://doi.org/10.1016/S0168-9525(00)02176-4

      “ How can the genome of Drosophila melanogaster contain fewer genes than the undoubtedly simpler organism Caenorhabditis elegans? ”

      Ewing B and Green P 2000 Analysis of expressed sequence tags indicates 35,000 human genes. Nature Genetics 25: 232–234. https://doi.org/10.1038/76115

      “ the invertebrates Caenorhabditis elegans and Drosophila melanogaster having 19,000 and 13,600 genes, respectively. Here we estimate the number of human genes […] approximately 35,000 genes, substantially lower than most previous estimates. Evolution of the increased physiological complexity of vertebrates may therefore have depended more on the combinatorial diversification of regulatory networks or alternative splicing than on a substantial increase in gene number. ”

      Kim E, Magen A and Ast G 2007 Different levels of alternative splicing among eukaryotes. Nucleic Acids Research 35: 125–131. https://doi.org/10.1093/nar/gkl924

      “we reveal that the percentage of genes and exons undergoing alternative splicing is higher in vertebrates compared with invertebrates. […] The difference in the level of alternative splicing suggests that alternative splicing may contribute greatly to the mammal higher level of phenotypic complexity,”

      Nilsen TW and Graveley BR 2010 Expansion of the eukaryotic proteome by alternative splicing. Nature 463 : 457–463. https://doi.org/10.1038/nature08909

      “ It is noteworthy that Caenorhabditis elegans, D. melanogaster and mammals have about 20,000 (ref. 68), 14,000 (ref. 69) and 20,000 (ref. 70) genes, respectively, but mammals are clearly much more complex than nematodes or flies.”

      Reviewer #2 (Public Review):

      Summary:

      Two hypotheses could explain the observation that genes of more complex organisms tend to undergo more alternative splicing. On one hand, alternative splicing could be adaptive since it provides the functional diversity required for complexity. On the other hand, increased rates of alternative splicing could result through nonadaptive processes since more complex organisms tend to have smaller effective population sizes and are thus more prone to deleterious mutations resulting in more spurious splicing events (drift-barrier hypothesis). To evaluate the latter, Bénitière et al. analyzed transcriptome sequencing data across 53 metazoan species. They show that proxies for effective population size and alternative splicing rates are negatively correlated. Furthermore, the authors find that rare, nonfunctional (and likely erroneous) isoforms occur more frequently in more complex species. Additionally, they show evidence that the strength of selection on splice sites increases with increasing effective population size and that the abundance of rare splice variants decreases with increased gene expression. All of these findings are consistent with the drift-barrier hypothesis.

      This study conducts a comprehensive set of separate analyses that all converge on the same overall result and the manuscript is well organized. Furthermore, this study is useful in that it provides a modified null hypothesis that can be used for future tests of adaptive explanations for variation in alternative splicing.

      Strengths:

      The major strength of this study lies in its complementary approach combining comparative and population genomics. Comparing evolutionary trends across phylogenetic diversity is a powerful way to test hypotheses about the origins of genome complexity. This approach alone reveals several convincing lines of evidence in support of the drift-barrier hypothesis. However, the authors also provide evidence from a population genetics perspective (using resequencing data for humans and fruit flies), making results even more convincing.

      The authors are forward about the study's limitations and explain them in detail. They elaborate on possible confounding factors as well as the issues with data quality (e.g. proxies for Ne, inadequacies of short reads, heterogeneity in RNA-sequencing data).

      Weaknesses:

      The authors primarily consider insects and mammals in their study. This only represents a small fraction of metazoan diversity. Sampling from a greater diversity of metazoan lineages would make these results and their relevance to broader metazoans substantially more convincing. Although the authors are careful about their tone, it is challenging to reconcile these results with trends across greater metazoans when the underlying dataset exhibits ascertainment bias and represents samples from only a few phylogenetic groups. Relatedly, some trends (such as Figure 1B-C) seem to be driven primarily by non-insect species, raising the question of whether some results may be primarily explained by specific phylogenetic groups ( although the authors do correct for phylogeny in their statistics). How might results look if insects and mammals (or vertebrates) are considered independently?

      Following the referee’s suggestion, we investigated the relationship between AS rate and proxies of Ne, separately for insects and vertebrates (Supplementary Fig. 11) . We observed that the relationship was consistent in vertebrates and insects: linear regressions show a positive correlation, significant (p<0.05) in all cases, except for body length in vertebrates. We added a sentence (line 166) to mention this point.

      Note that for these analyses we have smaller sample sizes, so we have a weaker power to detect signal. We therefore prefer to present the combined analyses, using PGLS to account for phylogenetic inertia.

      Throughout the manuscript, the authors refer to infrequently spliced ( mode <5%) introns as "minor introns" and frequently spliced (mode >95%) as "major introns". This is extremely confusing since "minor introns" typically represent introns spliced by the U12 spliceosome, whereas "major introns" are those spliced by the U2 spliceosome.

      To avoid any confusion, we modified the terminology: we now refer to infrequently spliced introns as " minor-isoform introns" and frequently spliced as "major -isoform introns" (see line 135-137) . The entire manuscript (including the figures) has been modified accordingly.

      Furthermore, it remains unclear whether the study only considers major introns or both major and minor introns. Minor introns typically have AT-AC splice sites whereas major introns usually have GT/GC-AG splice sites, although in rare cases the U2 can recognize AT-AC (see Wu and Krainer 1997 for example).

      We modified the text (line 148-150) to clearly state that we studied all introns, both U2-type and U12-type.

      The authors also note that some introns show noncanonical AT-AC splice sites while these are actually canonical splice sites for minor introns.

      This is corrected (line 148).

      Recommendations for the authors:

      Reviewer #2 (Recommendations For The Authors):

      Figures 1, 3, and 4: I suggest that authors add regression lines.

      We added the regression lines with the “pgls” function from the R package “caper” (in Fig. 1, 3 and 4, and also in all other figures where we present correlations).

      Figure 2: As previously mentioned, the terms "minor introns" and "major introns" are extremely confusing. I strongly suggest the authors use different naming conventions.

      We changed the terminology:

      minor introns -> minor-isoform introns

      major introns -> major-isoform introns

      Figure 5: Intron-exon boundaries and splice site annotations are shown at the bottom of B, C, and D but not A. I suggest removing the annotation beneath B for consistency and since A+C and B+D are aligned on the x-axis.

      Corrected, it was a mistake.

      Figure 7: The yellow dotted line is very challenging to see in A.

      Corrected, the line has been widened.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:  

      Reviewer #1 (Public Review): 

      Summary: 

      In their manuscript entitled 'The domesticated transposon protein L1TD1 associates with its ancestor L1 ORF1p to promote LINE-1 retrotransposition', Kavaklıoğlu and colleagues delve into the role of L1TD1, an RNA binding protein (RBP) derived from a LINE1 transposon. L1TD1 proves crucial for maintaining pluripotency in embryonic stem cells and is linked to cancer progression in germ cell tumors, yet its precise molecular function remains elusive. Here, the authors uncover an intriguing interaction between L1TD1 and its ancestral LINE-1 retrotransposon. 

      The authors delete the DNA methyltransferase DNMT1 in a haploid human cell line (HAP1), inducing widespread DNA hypo-methylation. This hypomethylation prompts abnormal expression of L1TD1. To scrutinize L1TD1's function in a DNMT1 knock-out setting, the authors create DNMT1/L1TD1 double knock-out cell lines (DKO). Curiously, while the loss of global DNA methylation doesn't impede proliferation, additional depletion of L1TD1 leads to DNA damage and apoptosis.  

      To unravel the molecular mechanism underpinning L1TD1's protective role in the absence of DNA methylation, the authors dissect L1TD1 complexes in terms of protein and RNA composition. They unveil an association with the LINE-1 transposon protein L1-ORF1 and LINE-1 transcripts, among others.  

      Surprisingly, the authors note fewer LINE-1 retro-transposition events in DKO cells than in DNMT1 KO alone.  

      Strengths: 

      The authors present compelling data suggesting the interplay of a transposon-derived human RNA binding protein with its ancestral transposable element. Their findings spur interesting questions for cancer types, where LINE1 and L1TD1 are aberrantly expressed.  

      Weaknesses: 

      Suggestions for refinement:  

      The initial experiment, inducing global hypo-methylation by eliminating DNMT1 in HAP1 cells, is intriguing and warrants a more detailed description. How many genes experience misregulation or aberrant expression? What phenotypic changes occur in these cells? 

      This is an excellent suggestion. We have gene expression data on WT versus DNMT1 KO HAP1 cells and have included them now as Suppl. Figure S1. The  transcriptome analysis of DNMT1 KO cells showed hundreds of deregulated genes upon DNMT1 ablation. As expected, the majority were up-regulated and gene ontology analysis revealed that among the strongest up-regulated genes were gene clusters with functions in “regulation of transcription from RNA polymerase II promoter” and “cell differentiation” and genes encoding proteins with KRAB domains. In addition, the de novo methyltransferases DNMT3A and DNMT3B were up-regulated in DNMT1 KO cells suggesting the set-up of compensatory mechanisms in these cells. 

      Why did the authors focus on L1TD1? Providing some of this data would be helpful to understand the rationale behind the thorough analysis of L1TD1. 

      We have previously discovered that conditional deletion of the maintenance DNA methyltransferase DNMT1 in the murine epidermis results not only in the up-regulation of mobile elements, such as IAPs but also the induced expression of L1TD1 ([1], Suppl. Table 1 and Author response image 1). Similary, L1TD1 expression was induced by treatment of primary human keratinocytes or squamous cell carcinoma cells with the DNMT inhibitor azadeoxycytidine (Author response images 2 and 3). These findings are in accordance with the observation  that inhibition of DNA methyltransferase activity by aza-deoxycytidine in human non-small cell lung cancer cells (NSCLCs) results in up-regulation of L1TD1 [2]. Our interest in L1TD1 was further fueled by reports on a potential function of L1TD1 as prognostic tumor marker. We have included this information in the last paragraph of the Introduction in the revised manuscript.

      Author response image 1. RT-qPCR of L1TD1 expression in cultured murine control and Dnmt1 Δ/Δker keratinocytes. mRNA levels of L1td1 were analyzed in keratinocytes isolated at P5 from conditional Dnmt1 knockout mice [1]. Hprt expression was used for normalization of mRNA levels and wildtype control was set to 1. Data represent means ±s.d. with n=4. **P < 0.01 (paired t-test). 

      Author response image 2. RT-qPCR analysis of L1TD1 expression in primary human keratinocytes. Cells were treated with 5-aza-2-deoxycidine for 24 hours or 48 hours, with PBS for 48 hours or were left untreated. 18S rRNA expression was used for normalization of mRNA levels and PBS control was set to 1. Data represent means ±s.d. with n=3. **P < 0.01 (paired t-test).

      Author response image 3. Induced L1TD1 expression upon DNMT inhibition in squamous cell carcinoma cell lines SCC9 and SCCO12. Cells were treated with 5-aza-2-deoxycidine for 24 hours, 48 hours or 6 days. (A) Western blot analysis of L1TD1 protein levels using beta-actin as loading control. (B) Indirect immunofluorescence microscopy analysis of L1TD1 expression in SCC9 cells. Nuclear DNA was stained with DAPI. Scale bar: 10 µm. (C)  RT-qPCR analysis of L1TD1 expression in primary human keratinocytes. Cells were treated with 5-aza-2deoxycidine for 24 hours or 48 hours, with PBS for 48 hours or were left untreated. 18S rRNA expression was used for normalization of mRNA levels and PBS control was set to 1. Data represent means ±s.d. with n=3. *P < 0.05, **P < 0.01 (paired t-test).

      The finding that L1TD1/DNMT1 DKO cells exhibit increased apoptosis and DNA damage but decreased L1 retro-transposition is unexpected. Considering the DNA damage associated with retro-transposition and the DNA damage and apoptosis observed in L1TD1/DNMT1 DKO cells, one would anticipate the opposite outcome. Could it be that the observation of fewer transposition-positive colonies stems from the demise of the most transposition-positive colonies? Further exploration of this phenomenon would be intriguing. 

      This is an important point and we were aware of this potential problem. Therefore, we calibrated the retrotransposition assay by transfection with a blasticidin resistance gene vector to take into account potential differences in cell viability and blasticidin sensitivity. Thus, the observed reduction in L1 retrotransposition efficiency is not an indirect effect of reduced cell viability. We have added a corresponding clarification in the Results section on page 8, last paragraph. 

      Based on previous studies with hESCs and germ cell tumors [3], it is likely that, in addition to its role in retrotransposition, L1TD1 has further functions in the regulation of cell proliferation and differentiation. L1TD1 might therefore attenuate the effect of DNMT1 loss in KO cells generating an intermediate phenotype (as pointed out by Reviewer 2) and simultaneous loss of both L1TD1 and DNMT1 results in more pronounced effects on cell viability. This is in agreement with the observation that a subset of L1TD1 associated transcripts encode proteins involved in the control of cell division and cell cycle. It is possible that subtle changes in the expression of these protein that were not detected in our mass spectrometry approach contribute to the antiproliferative effect of L1TD1 depletion as discussed in the Discussion section of the revised manuscript. 

      Reviewer #2 (Public Review):           

      In this study, Kavaklıoğlu et al. investigated and presented evidence for the role of domesticated transposon protein L1TD1 in enabling its ancestral relative, L1 ORF1p, to retrotranspose in HAP1 human tumor cells. The authors provided insight into the molecular function of L1TD1 and shed some clarifying light on previous studies that showed somewhat contradictory outcomes surrounding L1TD1 expression. Here, L1TD1 expression was correlated with L1 activation in a hypomethylation-dependent manner, due to DNMT1 deletion in the HAP1 cell line. The authors then identified L1TD1-associated RNAs using RIP-Seq, which displays a disconnect between transcript and protein abundance (via Tandem Mass Tag multiplex mass spectrometry analysis). The one exception was for L1TD1 itself, which is consistent with a model in which the RNA transcripts associated with L1TD1 are not directly regulated at the translation level. Instead, the authors found the L1TD1 protein associated with L1-RNPs, and this interaction is associated with increased L1 retrotransposition, at least in the contexts of HAP1 cells. Overall, these results support a model in which L1TD1 is restrained by DNA methylation, but in the absence of this repressive mark, L1TD1 is expressed and collaborates with L1 ORF1p (either directly or through interaction with L1 RNA, which remains unclear based on current results), leads to enhances L1 retrotransposition. These results establish the feasibility of this relationship existing in vivo in either development, disease, or both.   

      Recommendations for the authors:

      Reviewer #2 (Recommendations For The Authors):        

      Major 

      (1) The study only used one knockout (KO) cell line generated by CRISPR/Cas9. Considering the possibility of an off-target effect, I suggest the authors attempt one or both of these suggestions. 

      A) Generate or acquire a similar DMNT1 deletion that uses distinct sgRNAs, so that the likelihood of off-targets is negligible. A few simple experiments such as qRT-PCR would be sufficient to suggest the same phenotype.  

      B) Confirm the DNMT1 depletion also by siRNA/ASO KD to phenocopy the KO effect.  (2) In addition to the strategies to demonstrate reproducibility, a rescue experiment restoring DNMT1 to the KO or KD cells would be more convincing. (Partial rescue would suffice in this case, as exact endogenous expression levels may be hard to replicate). 

      We have undertook several approaches to study the effect of DNMT1 loss or inactivation: As described above, we have generated a conditional KO mouse with ablation of DNMT1 in the epidermis. DNMT1-deficient keratinocytes isolated from these mice show a significant increase in L1TD1 expression.  In addition, treatment of primary human keratinocytes and two squamous cell carcinoma cell lines with the DNMT inhibitor aza-deoxycytidine led to upregulation of L1TD1 expression. Thus, the derepression of L1TD1 upon loss of DNMT1 expression or activity is not a clonal effect. Also, the spectrum of RNAs identified in RIP experiments as L1TD1-associated transcripts in HAP1 DNMT1 KO cells showed a strong overlap with the RNAs isolated by a related yet different method in human embryonic stem cells. When it comes to the effect of L1TD1 on L1-1 retrotranspostion, a recent study has reported a similar effect of L1TD1 upon overexpression in HeLa cells [4].  

      All of these points together help to convince us that our findings with HAP1 DNMT KO are in agreement with results obtained in various other cell systems and are therefore not due to off-target effects. With that in mind, we would pursue the suggestion of Reviewer 1 to analyze the effects of DNA hypomethylation upon DNMT1 ablation.

      (3) As stated in the introduction, L1TD1 and ORF1p share "sequence resemblance" (Martin 2006). Is the L1TD1 antibody specific or do we see L1 ORF1p if Fig 1C were uncropped?  (6) Is it possible the L1TD1 antibody binds L1 ORF1p? This could make Figure 2D somewhat difficult to interpret. Some validation of the specificity of the L1TD1 antibody would remove this concern (see minor concern below).  

      This is a relevant question. We are convinced that the L1TD1 antibody does not crossreact with L1 ORF1p for the following reasons: Firstly, the antibody does not recognize L1 ORF1p (40 kDa) in the  uncropped Western blot for Figure 1C (Author response image 4A). Secondly, the L1TD1 antibody gives only background signals in DKO cells in the  indirect immunofluorescence experiment shown in Figure 1E of the manuscript. 

      Thirdly, the immunogene sequence of L1TD1 that determines the specificity of the antibody was checked in the antibody data sheet from Sigma Aldrich. The corresponding epitope is not present in the L1 ORF1p sequence. Finally, we have shown that the ORF1p antibody does not cross-react with L1TD1 (Author response image 4B).

      Author response image 4. (A) Uncropped L1TD1 Western blot shown in Figure 1C. An unspecific band is indicated by an asterisk. (B) Westernblot analysis of WT, KO and DKO cells with L1 ORF1p antibody.

      (4) In abstract (P2), the authors mentioned that L1TD1 works as an RNA chaperone, but in the result section (P13), they showed that L1TD1 associates with L1 ORF1p in an RNAindependent manner. Those conclusions appear contradictory. Clarification or revision is required. 

      Our findings that both proteins bind L1 RNA, and that L1TD1 interacts with ORF1p are compatible with a scenario where L1TD1/ORF1p heteromultimers bind to L1 RNA. The additional presence of L1TD1 might thereby enhance the RNA chaperone function of ORF1p. This model is visualized now in Suppl. Figure S7C. 

      (5) Figure 2C fold enrichment for L1TD1 and ARMC1 is a bit difficult to fully appreciate. A 100 to 200-fold enrichment does not seem physiological. This appears to be a "divide by zero" type of result, as the CT for these genes was likely near 40 or undetectable. Another qRT-PCRbased approach (absolute quantification) would be a more revealing experiment. 

      This is the validation of the RIP experiments and the presentation mode is specifically developed for quantification of RIP assays (Sigma Aldrich RIP-qRT-PCR: Data Analysis Calculation Shell). The unspecific binding of the transcript in the absence of L1TD1 in DNMT1/L1TD1 DKO cells is set to 1 and the value in KO cells represents the specific binding relative the unspecific binding. The calculation also corrects for potential differences in the abundance of the respective transcript in the two cell lines. This is not a physiological value but the quantification of specific binding of transcripts to L1TD1. GAPDH as negative control shows no enrichment, whereas specifically associated transcripts show strong enrichement. We have explained the details of RIPqRT-PCR evaluation in Materials and Methods (page 14) and the legend of Figure 2C in the revised manuscript.       

      (6) Is it possible the L1TD1 antibody binds L1 ORF1p? This could make Figure 2D somewhat difficult to interpret. Some validation of the specificity of the L1TD1 antibody would remove this concern (see minor concern below).            

      See response to (3).  

      (7) Figure S4A and S4B: There appear to be a few unusual aspects of these figures that should be pointed out and addressed. First, there doesn't seem to be any ORF1p in the Input (if there is, the exposure is too low). Second, there might be some L1TD1 in the DKO (lane 2) and lane 3. This could be non-specific, but the size is concerning. Overexposure would help see this.

      The ORF1p IP gives rise to strong ORF1p signals in the immunoprecipitated complexes even after short exposure. Under these contions ORF1p is hardly detectable in the input. Regarding the faint band in DKO HAP1 cells, this might be due to a technical problem during Western blot loading. Therefore, the input samples were loaded again on a Western blot and analyzed for the presence of ORF1p, L1TD1 and beta-actin (as loading control) and shown as separate panel in Suppl. Figure S4A. 

      (8) Figure S4C: This is related to our previous concerns involving antibody cross-reactivity. Figure 3E partially addresses this, where it looks like the L1TD1 "speckles" outnumber the ORF1p puncta, but overlap with all of them. This might be consistent with the antibody crossreacting. The western blot (Figure 3C) suggests an upregulation of ORF1p by at least 2-3x in the DKO, but the IF image in 3E is hard to tell if this is the case (slightly more signal, but fewer foci). Can you return to the images and confirm the contrast are comparable? Can you massively overexpose the red channel in 3E to see if there is residual overlap? 

      In Figure 3E the L1TD1 antibody gives no signal in DNMT1/L1TD1 DKO cells confirming that it does not recognize ORF1p. In agreement with the Western blot in Figure 3C the L1 ORF1p signal in Figure 3E is stronger in DKO cells. In DNMT1 KO cells the L1 ORF1p antibody does not recognize all L1TD1 speckles. This result is in agreement with the Western blot shown above in Figure R4B and indicates that the L1 ORF1p antibody does not recognize the L1TD1 protein. The contrast is comparable and after overexposure there are still L1TD1 specific speckles. This might be due to differences in abundance of the two proteins.

      (9) The choice of ARMC1 and YY2 is unclear. What are the criteria for the selection?

      ARMC1 was one of the top hits in a pilot RIP-seq experiment (IP versus input and IP versus  IgG IP). In the actual RIP-seq experiment with DKO HAP1 cells instead of IgG IP as a negative control, we found ARMC1 as an enriched hit, although it was not among the top 5 hits. The results from the 2nd RIP-seq further confirmed the validity of ARMC1 as an L1TD1-interacting transcript. YY2 was of potential biological relevance as an L1TD1 target due to the fact that it is a processed pseudogene originating from YY1 mRNA as a result of retrotransposition. This is mentioned on page 6 of the revised manuscript.

      (10) (P16) L1 is the only protein-coding transposon that is active in humans. This is perhaps too generalized of a statement as written. Other examples are readily found in the literature. Please clarify.  

      We will tone down this statement in the revised manuscript. 

      (11) In both the abstract and last sentence in the discussion section (P17), embryogenesis is mentioned, but this is not addressed at all in the manuscript. Please refrain from implying normal biological functions based on the results of this study unless appropriate samples are used to support them.

      Much of the published data on L1TD1 function are related to embryonic stem cells [3-7]. Therefore, it is important to discuss our findings in the context of previous reports.

      (12) Figure 3E: The format of Figures 1A and 3E are internally inconsistent. Please present similar data/images in a cohesive way throughout the manuscript.  

      We show now consistent IF Figures in the revised manuscript.

      Minor: 

      (1) Intro:           

      - Is L1Td1 in mice and Humans? How "conserved" is it and does this suggest function?  

      Murine and human L1TD1 proteins share 44% identity on the amino acid level and it was suggested that the corresponding genes were under positive selection during evolution with functions in transposon control and maintenance of pluripotency [8].  

      - Why HAP1? (Haploid?) The importance of this cell line is not clear.          

      HAP1 is a nearly haploid human cancer cell line derived from the KBM-7 chronic myelogenous leukemia (CML) cell line [9, 10]. Due to its haploidy is perfectly suited and widely used for loss-of-function screens and gene editing. After gene editing  cells can be used in the nearly haploid or in the diploid state. We usually perform all experiments with diploid HAP1 cell lines.  Importantly, in contrast to other human tumor cell lines, this cell line tolerates ablation of DNMT1. We have included a corresponding explanation in the revised manuscript on page 5, first paragraph.

      - Global methylation status in DNMT1 KO? (Methylations near L1 insertions, for example?) 

      The HAP1 DNMT1 KO cell line with a 20 bp deletion in exon 4 used in our study was validated in the study by Smits et al. [11]. The authors report a significant reduction in overall DNA methylation. However, we are not aware of a DNA methylome study on this cell line. We show now data on the methylation of L1 elements in HAP1 cells and upon DNMT1 deletion in the revised manuscript in Suppl. Figure S1B.

      (2) Figure 1:  

      - Figure 1C. Why is LMNB used instead of Actin (Fig1D)?  

      We show now beta-actin as loading control in the revised manuscript.  

      - Figure 1G shows increased Caspase 3 in KO, while the matching sentence in the result section skips over this. It might be more accurate to mention this and suggest that the single KO has perhaps an intermediate phenotype (Figure 1F shows a slight but not significant trend). 

      We fully agree with the reviewer and have changed the sentence on page 6, 2nd paragraph accordingly.  

      - Would 96 hrs trend closer to significance? An interpretation is that L1TD1 loss could speed up this negative consequence. 

      We thank the reviewer for the suggestion. We have performed a time course experiment with 6 biological replicas for each time point up to 96 hours and found significant changes in the viability upon loss of DNMT1 and again significant reduction in viability upon additional loss of L1TD1 (shown in Figure 1F). These data suggest that as expexted loss of DNMT1 leads to significant reduction viability and that additional ablation of L1TD1 further enhances this effect.

      - What are the "stringent conditions" used to remove non-specific binders and artifacts (negative control subtraction?) 

      Yes, we considered only hits from both analyses, L1TD1 IP in KO versus input and L1TD1 IP in KO versus L1TD1 IP in DKO. This is now explained in more detail in the revised manuscript on page 6, 3rd paragraph.  

      (3) Figure 2:  

      - Figure 2A is a bit too small to read when printed. 

      We have changed this in the revised manuscript.

      - Since WT and DKO lack detectable L1TD1, would you expect any difference in RIP-Seq results between these two?

      Due to the lack of DNMT1 and the resulting DNA hypomethylation, DKO cells are more similar to KO cells than WT cells with respect to the expressed transcripts.

      - Legend says selected dots are in green (it appears blue to me). 

      We have changed this in the revised manuscript.           

      - Would you recover L1 ORF1p and its binding partners in the KO? (Is the antibody specific in the absence of L1TD1 or can it recognize L1?) I noticed an increase in ORF1p in the KO in Figure 3C.  

      Thank you for the suggestion. Yes, L1 ORF1p shows slightly increased expression in the proteome analysis and we have marked the corresponding dot in the Volcano plot (Figure 3A).

      - Should the figure panel reference near the (Rosspopoff & Trono) reference instead be Sup S1C as well? Otherwise, I don't think S1C is mentioned at all. 

      - What are the red vs. green dots in 2D? Can you highlight ERV and ALU with different colors? 

      We added the reference to Suppl. Figure S1C (now S3C) in the revised manuscript. In Figure 2D L1 elements are highlighted in green, ERV elements in yellow, and other associated transposon transcripts in red.     

      - Which L1 subfamily from Figure 2D is represented in the qRT-PCR in 2E "LINE-1"? Do the primers match a specific L1 subfamily? If so, which? 

      We used primers specific for the human L1.2 subfamily. 

      - Pulling down SINE element transcripts makes some sense, as many insertions "borrow" L1 sequences for non-autonomous retro transposition, but can you speculate as to why ERVs are recovered? There should be essentially no overlap in sequence. 

      In the L1TD1 evolution paper [8], a potential link between L1TD1 and ERV elements was discussed: 

      "Alternatively, L1TD1 in sigmodonts could play a role in genome defense against another element active in these genomes. Indeed, the sigmodontine rodents have a highly active family of ERVs, the mysTR elements [46]. Expansion of this family preceded the death of L1s, but these elements are very active, with 3500 to 7000 species-specific insertions in the L1-extinct species examined [47]. This recent ERV amplification in Sigmodontinae contrasts with the megabats (where L1TD1 has been lost in many species); there are apparently no highly active DNA or RNA elements in megabats [48]. If L1TD1 can suppress retroelements other than L1s, this could explain why the gene is retained in sigmodontine rodents but not in megabats." 

      Furthermore, Jin et al. report the binding of L1TD1 to repetitive sequences in transcripts [12]. It is possible that some of these sequences are also present in ERV RNAs.

      - Is S2B a screenshot? (the red underline). 

      No, it is a Powerpoint figure, and we have removed the red underline.

      (4) Figure 3: 

      - Text refers to Figure 3B as a western blot. Figure 3B shows a volcano plot. This is likely 3C but would still be out of order (3A>3C>3B referencing). I think this error is repeated in the last result section. 

      - Figure and legends fail to mention what gene was used for ddCT method (actin, gapdh, etc.). 

      - In general, the supplemental legends feel underwritten and could benefit from additional explanations. (Main figures are appropriate but please double-check that all statistical tests have been mentioned correctly).

      Thank you for pointing this out. We have corrected these errors in the revised manuscript.

      (5) Discussion: 

      -Aluy connection is interesting. Is there an "Alu retrotransposition reporter assay" to test whether L1TD1 enhances this as well? 

      Thank you for the suggestion. There is indeed an Alu retrotransposition reporter assay reported be Dewannieux et al. [13]. The assay is based on a Neo selection marker. We have previously tested a Neo selection-based L1 retrotransposition reporter assay, but this system failed to properly work in HAP1 cells, therefore we switched to a blasticidinbased L1 retrotransposition reporter assay. A corresponding blasticidin-based Alu retrotransposition reporter assay might be interesting for future studies (mentioned in the Discussion, page 11 paragraph 4 of the revised manuscript.

      (6) Material and Methods       : 

      - The number of typos in the materials and methods is too numerous to list. Instead, please refer to the next section that broadly describes the issues seen throughout the manuscript. 

      Writing style  

      (1) Keep a consistent style throughout the manuscript: for example, L1 or LINE-1 (also L1 ORF1p or LINE-1 ORF1p); per or "/"; knockout or knock-out; min or minute; 3 times or three times; media or medium. Additionally, as TE naming conventions are not uniform, it is important to maintain internal consistency so as to not accidentally establish an imprecise version. 

      (2) There's a period between "et al" and the comma, and "et al." should be italic. 

      (3) The authors should explain what the key jargon is when it is first used in the manuscript, such as "retrotransposon" and "retrotransposition".    

      (4) The authors should show the full spelling of some acronyms when they use it for the first time, such as RNA Immunoprecipitation (RIP).  

      (5) Use a space between numbers and alphabets, such as 5 µg.  

      (6) 2.0 × 105 cells, that's not an "x".  

      (7) Numbers in the reference section are lacking (hard to parse).  

      (8) In general, there are a significant number of typos in this draft which at times becomes distracting. For example, (P3) Introduction: Yet, co-option of TEs thorough (not thorough, it should be through) evolution has created so-called domesticated genes beneficial to the gene network in a wide range of organisms. Please carefully revise the entire manuscript for these minor issues that collectively erode the quality of this submission.  

      Thank you for pointing out these mistakes. We have corrected them in the revised manuscript. A native speaker from our research group has carefully checked the paper. In summary, we have added Supplementary Figure S7C and have changed Figures 1C, 1E, 1F, 2A, 2D, 3A, 4B, S3A-D, S4B and S6A based on these comments. 

      REFERENCES

      (1) Beck, M.A., et al., DNA hypomethylation leads to cGAS-induced autoinflammation in the epidermis. EMBO J, 2021. 40(22): p. e108234.

      (2) Altenberger, C., et al., SPAG6 and L1TD1 are transcriptionally regulated by DNA methylation in non-small cell lung cancers. Mol Cancer, 2017. 16(1): p. 1.

      (3) Narva, E., et al., RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells, 2012. 30(3): p. 452-60.

      (4) Jin, S.W., et al., Dissolution of ribonucleoprotein condensates by the embryonic stem cell protein L1TD1. Nucleic Acids Res, 2024. 52(6): p. 3310-3326.

      (5) Emani, M.R., et al., The L1TD1 protein interactome reveals the importance of posttranscriptional regulation in human pluripotency. Stem Cell Reports, 2015. 4(3): p. 519-28.

      (6) Santos, M.C., et al., Embryonic Stem Cell-Related Protein L1TD1 Is Required for Cell Viability, Neurosphere Formation, and Chemoresistance in Medulloblastoma. Stem Cells Dev, 2015. 24(22): p. 2700-8.

      (7) Wong, R.C., et al., L1TD1 is a marker for undifferentiated human embryonic stem cells. PLoS One, 2011. 6(4): p. e19355.

      (8) McLaughlin, R.N., Jr., et al., Positive selection and multiple losses of the LINE-1-derived L1TD1 gene in mammals suggest a dual role in genome defense and pluripotency. PLoS Genet, 2014. 10(9): p. e1004531.

      (9) Andersson, B.S., et al., Ph-positive chronic myeloid leukemia with near-haploid conversion in vivo and establishment of a continuously growing cell line with similar cytogenetic pattern. Cancer Genet Cytogenet, 1987. 24(2): p. 335-43.

      (10) Carette, J.E., et al., Ebola virus entry requires the cholesterol transporter Niemann-Pick C1. Nature, 2011. 477(7364): p. 340-3.

      (11) Smits, A.H., et al., Biological plasticity rescues target activity in CRISPR knock outs. Nat Methods, 2019. 16(11): p. 1087-1093.

      (12) Jin, S.W., et al., Dissolution of ribonucleoprotein condensates by the embryonic stem cell protein L1TD1. Nucleic Acids Res, 2024.

      (13) Dewannieux, M., C. Esnault, and T. Heidmann, LINE-mediated retrotransposition of marked Alu sequences. Nat Genet, 2003. 35(1): p. 41-8.

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Reviewer #1 (Public Review):

      Summary:

      In this study, the authors provide a new computational platform called Vermouth to automate topology generation, a crucial step that any biomolecular simulation starts with. Given a wide arrange of chemical structures that need to be simulated, varying qualities of structural models as inputs obtained from various sources, and diverse force fields and molecular dynamics engines employed for simulations, automation of this fundamental step is challenging, especially for complex systems and in case that there is a need to conduct high-throughput simulations in the application of computer-aided drug design (CADD). To overcome this challenge, the authors develop a programing library composed of components that carry out various types of fundamental functionalities that are commonly encountered in topological generation. These components are intended to be general for any type of molecules and not to depend on any specific force field and MD engines. To demonstrate the applicability of this library, the authors employ those components to re-assemble a pipeline called Martinize2 used in topology generation for simulations with a widely used coarse-grained model (CG) MARTINI. This pipeline can fully recapitulate the functionality of its original version Martinize but exhibit greatly enhanced generality, as confirmed by the ability of the pipeline to faithfully generate topologies for two high-complexity benchmarking sets of proteins.

      Strengths:

      The main strength of this work is the use of concepts and algorithms associated with induced subgraph in graph theory to automate several key but non-trivial steps of topology generation such as the identification of monomer residue units (MRU), the repair of input structures with missing atoms, the mapping of topologies between different resolutions, and the generation of parameters needed for describing interactions between MRUs. In addition, the documentation website provided by the authors is very informative, allowing users to get quickly started with Vermouth.

      Weaknesses:

      Although the Vermouth library is designed as a general tool for topology generation for molecular simulations, only its applications with MARTINI have been demonstrated in the current study. Thus, the claimed generality of Vermouth remains to be exmained. The authors may consider to point out this in their manuscript.

      In order to demonstrate generality of the here proposed concepts for generating topologies for molecular dynamics simulations, we have now implemented and tested a workflow that will produce topologies for the popular CHARMM36 all-atom force field. To facilitate generation of all-atom topologies with Martinize2 a .rtp reader was introduced, which allows users to provide .rtp files that are the native GROMACS topology files for proteins instead of .ff files. These .rtp files exist for all major atomic protein forcefields. In addition, for CHARMM36 we also included modification files, which describe non-standard pH amino acids, histidine tautomers, and end terminal modifications. Thus, the current implementation unlocks all features available at the CG Martini level also for CHARMM36. We note that users must add the modifications files for other all-atom force fields e.g. AMBER.

      We have added a new item in the main manuscript (p28) briefly describing this proof-of-concept implementation. However, we like to point out that there are many specialized tools for the various force fields adopted by the respective communities. Thus, an exhaustive discussion on the capabilities of Martinize2 for all-atom force fields seemed out of place.

      Reviewer #2 (Public Review):

      This work introduces a Vermouth library framework to enhance software development within the Martini community. Specifically, it presents a Vermouth-powered program, Martinize2, for generating coarse-grained structures and topologies from atomistic structures. In addition to introducing the Vermouth library and the Martinize2 program, this paper illustrates how Martinize2 identifies atoms, maps them to the Martini model, generates topology files, and identifies protonation states or post-translational modifications. Compared with the prior version, the authors provide a new figure to show that Martinize2 can be applied to various molecules, such as proteins, cofactors, and lipids. To demonstrate the general application, Martinize2 was used for converting 73% of 87,084 protein structures from the template library, with failed cases primarily blamed on missing coordinates.

      I was hoping to see some fundamental changes in the resubmitted version. To my disappointment, the manuscript remains largely unchanged (even the typo I pointed out previously was not fixed). I do not doubt that Martinize2 and Vermouth are useful to the Martini community, and this paper will have some impact. The manuscript is very technical and limited to the Martini community. The scientific insight for the general coarse-grained modeling community is unclear. The goal of the work is ambitious (such as high-throughput simulations and whole-cell modeling), but the results show just a validation of Martinize2. This version does not reverse my previous impression that it is incremental. As I pointed out in my previous review (and no response from the authors), all the issues associated with the Martini model are still there, e.g. the need for ENM. In this shape, I feel this manuscript is suitable for a specialized journal in computational biophysics or stays as part of the GitHub repository.

      We apologize for not fixing the typo; it was fixed but unfortunately got reintroduced in the final resubmitted version. We politely disagree that the goal of the work itself is high-throughput simulations and whole-cell modeling, but the Martinize2 tool is certainly an important element in our ambitions to achieve this. Given the broad interest in these goals by the modeling community in general, we believe this work has a much wider impact beyond the (already large) group of Martini users. Addressing limitations of the Martini model itself, which are certainly there, is clearly not the scope of the current work.

      Reviewer #3 (Public Review):

      The manuscript Kroon et al. described two algorithms, which when combined achieve high throughput automation of "martinizing" protein structures with selected protonation states and post-translational modifications. After the revisions provided by the authors, I recommend minor revision.

      The authors have addressed most of my concerns provided previously. Specifically, showcasing the capability of coarse-graining other types of molecules (Figure 7) is a useful addition, especially for the booming field of therapeutic macrocycles. My only additional concern is that to justify Martinize2 and Vermouth as a "high-throughput" method, the speed of these tools needs to be addressed in some form in the manuscript as a guideline to users.

      We have added some benchmark timings in the manuscript SI and pointed to the data in the discussion part, which addresses the timing. Martinize2 is certainly slower than martinize version 1 as we already pointed out in the previous versions. However, even for larger proteins (> 2000 residues) we are able to generate topologies in about 60s. As Martinize2 runs on a single core, it can be massively parallelized. Keeping this in mind the topology file generation is likely to take up only a fraction in a high-throughput pipeline compared to the more costly simulations themselves.

    1. Author Response:

      The following is the authors' response to the original reviews.

      Reply to Public Reviews:

      Reply to Reviewer #1:

      This is a carefully performed and well-documented study to indicate that the FUS protein interacts with the GGGGCC repeat sequence in Drosophila fly models, and the mechanism appears to include modulating the repeat structure and mitigating RAN translation. They suggest FUS, as well as a number of other G-quadruplex binding RNA proteins, are RNA chaperones, meaning they can alter the structure of the expanded repeat sequence to modulate its biological activities.

      Response: We would like to thank the reviewer for her/his time for evaluating our manuscript. We are very happy to see the reviewer for highly appreciating our manuscript.

      1. Overall this is a nicely done study with nice quantitation. It remains somewhat unclear from the data and discussions in exactly what way the authors mean that FUS is an RNA chaperone: is FUS changing the structure of the repeat or does FUS binding prevent it from folding into alternative in vivo structure?

      Response: We appreciate the reviewer’s constructive comments. Indeed, we showed that FUS changes the higher-order structures of GGGGCC [G4C2] repeat RNA in vitro, and that FUS suppresses G4C2 RNA foci formation in vivo. According to the established definition of RNA chaperone, RNA chaperones are proteins changing the structures of misfolded RNAs without ATP use, resulting in the maintenance of proper RNAs folding (Rajkowitsich et al., 2007). Thus, we consider that FUS is classified into RNA chaperone. To clarify these interpretations, we revised the manuscript as follows.

      (1) On page 10, line 215-219, the sentence “These results were in good agreement with our previous study on SCA31 showing the suppressive effects of FUS and other RBPs on RNA foci formation of UGGAA repeat RNA as RNA chaperones …” was changed to “These results were in good agreement with … RNA foci formation of UGGAA repeat RNA through altering RNA structures and preventing aggregation of misfolded repeat RNA as RNA chaperones …”.

      (2) On page 17, line 363-366, the sentence “FUS directly binds to G4C2 repeat RNA and modulates its G-quadruplex structure, as evident by CD and NMR analyses (Figure 5), suggesting its functional role as an RNA chaperone.” was changed to “FUS directly binds to G4C2 repeat RNA and modulates its G-quadruplex structure as evident by CD and NMR analyses (Figure 5, Figure 5—figure supplement 2), and suppresses RNA foci formation in vivo (Figures 3A and 3B), suggesting its functional role as an RNA chaperone.”

      Reply to Reviewer #2:

      Fuijino et al. provide interesting data describing the RNA-binding protein, FUS, for its ability to bind the RNA produced from the hexanucleotide repeat expansion of GGGGCC (G4C2). This binding correlates with reductions in the production of toxic dipeptides and reductions in toxic phenotypes seen in (G4C2)30+ expressing Drosophila. Both FUS and G4C2 repeats of >25 are associated with ALS/FTD spectrum disorders. Thus, these data are important for increasing our understanding of potential interactions between multiple disease genes. However, further validation of some aspects of the provided data is needed, especially the expression data.

      Response: We would like to thank the reviewer for her/his time for evaluating our manuscript and also for her/his important comments that helped to strengthen our manuscript.

      Some points to consider when reading the work:

      1. The broadly expressed GMR-GAL4 driver leads to variable tissue loss in different genotypes, potentially confounding downstream analyses dependent on viable tissue/mRNA levels.

      Response: We thank the reviewer for this constructive comment. In the RT-qPCR experiments (Figures 1E, 3C, 4G, 6D and Figure 1—figure supplement 1C), the amounts of G4C2 repeat transcripts were normalized to those of gal4 transcripts expressed in the same tissue, to avoid potential confounding derived from the difference in tissue viability between genotypes, as the reviewer pointed out. To clarify this process, we have made the following change to the revised manuscript.

      (1) On page 30, line 548-550, the sentence “The amounts of G4C2 repeat transcripts were normalized to those of gal4 transcripts in the same sample” was changed to “The amounts of G4C2 repeat transcripts were normalized to those of gal4 transcripts expressed in the same tissue to avoid potential confounding derived from the difference in tissue viability between genotypes”.

      2. The relationship between FUS and foci formation is unclear and should be interpreted carefully.

      Response: We appreciate the reviewer’s important comment. We apologize for the lack of clarity. We showed the relationship between FUS and RNA foci formation in our C9-ALS/FTD fly, that is, FUS suppresses RNA foci formation (Figures 3A and 3B), and knockdown of endogenous caz, a Drosophila homologue of FUS, enhanced it conversely (Figures 4E and 4F). We consider that FUS suppresses RNA foci formation through altering RNA structures and preventing aggregation of misfolded G4C2 repeat RNA as an RNA chaperone. To clarify these interpretations, we revised the manuscript as follows.

      (1) On page 10, line 215-219, the sentence “These results were in good agreement with our previous study on SCA31 showing the suppressive effects of FUS and other RBPs on RNA foci formation of UGGAA repeat RNA as RNA chaperones …” was changed to “These results were in good agreement with … RNA foci formation of UGGAA repeat RNA through altering RNA structures and preventing aggregation of misfolded repeat RNA as RNA chaperones …”.

      (2) On page 17, line 363-366, the sentence “FUS directly binds to G4C2 repeat RNA and modulates its G-quadruplex structure, as evident by CD and NMR analyses (Figure 5), suggesting its functional role as an RNA chaperone.” was changed to “FUS directly binds to G4C2 repeat RNA and modulates its G-quadruplex structure as evident by CD and NMR analyses (Figure 5, Figure 5—figure supplement 2), and suppresses RNA foci formation in vivo (Figures 3A and 3B), suggesting its functional role as an RNA chaperone.”

      Reply to Reviewer #3:

      In this manuscript Fujino and colleagues used C9-ALS/FTD fly models to demonstrate that FUS modulates the structure of (G4C2) repeat RNA as an RNA chaperone, and regulates RAN translation, resulting in the suppression of neurodegeneration in C9-ALS/FTD. They also confirmed that FUS preferentially binds to and modulates the G-quadruplex structure of (G4C2) repeat RNA, followed by the suppression of RAN translation. The potential significance of these findings is high since C9ORF72 repeat expansion is the most common genetic cause of ALS/FTD, especially in Caucasian populations and the DPR proteins have been considered the major cause of the neurodegenerations.

      Response: We would like to thank the reviewer for her/his time for evaluating our manuscript. We are grateful to the reviewer for the insightful comments, which were very helpful for us to improve the manuscript.

      1. While the effect of RBP as an RNA chaperone on (G4C2) repeat expansion is supposed to be dose-dependent according to (G4C2)n RNA expression, the first experiment of the screening for RBPs in C9-ALS/FTD flies lacks this concept. It is uncertain if the RBPs of the groups "suppression (weak)" and "no effect" were less or no ability of RNA chaperone or if the expression of the RBP was not sufficient, and if the RBPs of the group "enhancement" exacerbated the toxicity derived from (G4C2)89 RNA or the expression of the RBP was excessive. The optimal dose of any RBPs that bind to (G4C2) repeats may be able to neutralize the toxicity without the reduction of (G4C2)n RNA.

      Response: We appreciate the reviewer’s constructive comments. We employed the site-directed transgenesis for the establishment of RBP fly lines, to ensure the equivalent expression levels of the inserted transgenes. We also evaluated the toxic effects of overexpressed RBPs themselves by crossbreeding with control EGFP flies, showing in Figure 1A. To clarify them, we have made the following changes to the revised manuscript.

      (1) On page 8, line 166-168, the sentence “The variation in the effects of these G4C2 repeat-binding RBPs on G4C2 repeat-induced toxicity may be due to their different binding affinities to G4C2 repeat RNA, and their different roles in RNA metabolism.” was changed to “The variation in the effects of these G4C2 repeat-binding RBPs on G4C2 repeat-induced toxicity may be due to their different binding affinities to G4C2 repeat RNA, and the different toxicity of overexpressed RBPs themselves.”.

      (2) On page 29, line 519-522, the sentence “By employing site-specific transgenesis using the pUASTattB vector, each transgene was inserted into the same locus of the genome, and was expected to be expressed at the equivalent levels.” was added.

      2. In relation to issue 1, the rescue effect of FUS on the fly expressing (G4C2)89 (FUS-4) in Figure 4-figure supplement 1 seems weaker than the other flies expressing both FUS and (G4C2)89 in Figure 1 and Figure 1-figure supplement 2. The expression level of both FUS protein and (G4C2)89 RNA in each line is important from the viewpoint of therapeutic strategy for C9-ALS/FTD.

      Response: We appreciate the reviewer’s important comment. The FUS-4 transgene is expected to be expressed at the equivalent level to the FUS-3 transgene, since they are inserted into the same locus of the genome by the site-directed transgenesis. Thus, we suppose that the weaker suppressive effect of FUS-4 coexpression on G4C2 repeat-induced eye degeneration can be attributed to the C-terminal FLAG tag that is fused to FUS protein expressed in FUS-4 fly line. Since the caz fly expresses caz protein also fused to FLAG tag at the C-terminus, we used this FUS-4 fly line to directly compare the effect of caz on G4C2 repeat-induced toxicity to that of FUS.

      3. While hallmarks of C9ORF72 are the presence of DPRs and the repeat-containing RNA foci, the loss of function of C9ORF72 is also considered to somehow contribute to neurodegeneration. It is unclear if FUS reduces not only the DPRs but also the protein expression of C9ORF72 itself.

      Response: We thank the reviewer for this comment. We agree that not only DPRs, but also toxic repeat RNA and the loss-of-function of C9ORF72 jointly contribute to the pathomechanisms of C9-ALS/FTD. Since Drosophila has no homolog corresponding to the human C9orf72 gene, the effect of FUS on C9orf72 expression cannot be assessed. Our fly models are useful for evaluating gain-of-toxic pathomechanisms such as RNA foci formation and RAN translation, and the association between FUS and loss-of function of C9ORF72 is beyond the scope of this study.

      4. In Figure 5E-F, it cannot be distinguished whether FUS binds to GGGGCC repeats or the 5' flanking region. The same experiment should be done by using FUS-RRMmut to elucidate whether FUS binding is the major mechanism for this translational control. Authors should show that FUS binding to long GGGGCC repeats is important for RAN translation.

      Response: We would like to thank the reviewer for these insightful comments. Following the reviewer’s suggestion, we perform in vitro translation assay again using FUS-RRMmut, which loses the binding ability to G4C2 repeat RNA as evident by the filter binding assay (Figure 5A), instead of BSA. The results are shown in the figures of Western blot analysis below. The addition of FUS to the translation system suppressed the expression levels of GA-Myc efficiently, whereas that of FUS-RRMmut did not. FUS decreased the expression level of GA-Myc at as low as 10nM, and nearly eliminated RAN translation activity at 100nM. At 400nM, FUS-RRMmut weakly suppressed the GA-Myc expression levels probably because of the residual RNA-binding activity. These results suggest that FUS suppresses RAN translation in vitro through direct interactions with G4C2 repeat RNA.

      Unfortunately, RAN translation from short G4C2 repeat RNA was not investigated in our translation system, although the previous study reported the low efficacy of RAN translation from short G4C2 repeat RNA (Green et al., 2017).

      Author response image 1.

      (A) Western blot analysis of the GA-Myc protein in the samples from in vitro translation. (B) Quantification of the GA-Myc protein levels.

      We have made the following changes to the revised manuscript.

      (1) Figure 5F was replaced to new Figures 5F and 5G.

      (2) On page 14-15, line 326-330, the sentence “Notably, the addition of FUS to this system decreased the expression level of GA-Myc in a dose-dependent manner, whereas the addition of the control bovine serum albumin (BSA) did not (Figure 5F).” was changed to “Notably, upon the addition to this translation system, FUS suppressed RAN translation efficiently, whereas FUS-RRMmut did not. FUS decreased the expression levels of GA-Myc at as low as 10nM, and nearly eliminated RAN translation activity at 100nM. At 400nM, FUS-RRMmut weakly suppressed the GA-Myc expression levels probably because of the residual RNA-binding activity (Figure 5F and 5G).”.

      (3) On page 15, line 330-332, the sentence “Taken together, these results indicate that FUS suppresses RAN translation from G4C2 repeat RNA in vitro as an RNA chaperone.” was changed to “Taken together, these results indicate that FUS suppresses RAN translation in vitro through direct interactions with G4C2 repeat RNA as an RNA chaperone.”.

      (4) On page 37, line 720-723, the sentence “For preparation of the FUS protein, the human FUS (WT) gene flanked at the 5¢ end with an Nde_I recognition site and at the 3¢ end with a _Xho_I recognition site was amplified by PCR from pUAST-_FUS.” was changed to “For preparation of the FUS proteins, the human FUS (WT) and FUS-RRMmut genes flanked at the 5¢ end with an Nde_I recognition site and at the 3¢ end with a _Xho_I recognition site was amplified by PCR from pUAST-_FUS and pUAST- FUS-RRMmut, respectively.”.

      (5) On page 41, line 816-819, the sentence “FUS or BSA at each concentration (10, 100, and 1,000 nM) was added for translation in the lysate.” was changed to “FUS or FUS-RRMmut at each concentration (10, 100, 200, 400, and 1,000 nM) was preincubated with mRNA for 10 min to facilitate the interaction between FUS protein and G4C2 repeat RNA, and added for translation in the lysate.”.

      5. It is not possible to conclude, as the authors have, that G-quadruplex-targeting RBPs are generally important for RAN translation (Figure 6), without showing whether RBPs that do not affect (G4C2)89 RNA levels lead to decreased DPR protein level or RNA foci.

      Response: We appreciate the reviewer’s critical comment. Following the suggestion by the reviewer, we evaluate the effect of these G-quadruplex-targeting RBPs on RAN translation. We additionally performed immunohistochemistry of the eye imaginal discs of fly larvae expressing (G4C2)89 and these G-quadruplex-targeting RBPs. As shown in the figures of immunohistochemistry below, we found that coexpression of EWSR1, DDX3X, DDX5, and DDX17 significantly decreased the number of poly(GA) aggregates. The results suggest that these G-quadruplex-targeting RBPs regulate RAN translation as well as FUS.

      Author response image 2.

      (A) Immunohistochemistry of poly(GA) in the eye imaginal discs of fly larvae expressing (G4C2)89 and the indicated G-quadruplex-targeting RBPs. (B) Quantification of the number of poly(GA) aggregates.

      We have made the following changes to the revised manuscript.

      (1) Figures 6E and 6F were added.

      (2) On page 6-7, line 135-137, the sentence “In addition, other G-quadruplex-targeting RBPs also suppressed G4C2 repeat-induced toxicity in our C9-ALS/FTD flies.” was changed to “In addition, other G-quadruplex-targeting RBPs also suppressed RAN translation and G4C2 repeat-induced toxicity in our C9-ALS/FTD flies.”.

      (3) On page 15, line 344-346, the sentence “As expected, these RBPs also decreased the number of poly(GA) aggregates in the eye imaginal discs (Figures 6E and 6F).” was added.

      (4) On page 15, line 346-347, the sentence “Their effects on G4C2 repeat-induced toxicity and repeat RNA expression were consistent with those of FUS.” was changed to “Their effects on G4C2 repeat-induced toxicity, repeat RNA expression, and RAN translation were consistent with those of FUS.”

      (5) On page 16, line 355-357, the sentence “Thus, some G-quadruplex-targeting RBPs regulate G4C2 repeat-induced toxicity by binding to and possibly by modulating the G-quadruplex structure of G4C2 repeat RNA.” was changed to “Thus, some G-quadruplex-targeting RBPs regulate RAN translation and G4C2 repeat-induced toxicity by binding to and possibly by modulating the G-quadruplex structure of G4C2 repeat RNA.”

      (6) On page 19, line 417-421, the sentence “We further found that G-quadruplex-targeting RNA helicases, including DDX3X, DDX5, and DDX17, which are known to bind to G4C2 repeat RNA (Cooper-Knock et al., 2014; Haeusler et al., 2014; Mori et al., 2013a; Xu et al., 2013), also alleviate G4C2 repeat-induced toxicity without altering the expression levels of G4C2 repeat RNA in our Drosophila models.” was changed to “We further found that G-quadruplex-targeting RNA helicases, … ,also suppress RAN translation and G4C2 repeat-induced toxicity without altering the expression levels of G4C2 repeat RNA in our Drosophila models.”.

      Reply to Recommendations For The Authors:

      1) It is not clear from the start that the flies they generated with the repeat have an artificial vs human intronic sequence ahead of the repeat. It would be nice if they presented somewhere the entire sequence of the insert. The reason being that it seems they also tested flies with the human intronic sequence, and the effect may not be as strong (line 234). In any case, in the future, with a new understanding of RAN translation, it would be nice to compare different transgenes, and so as much transparency as possible would be helpful regarding sequences. Can they include these data?

      Response: We thank the editors and reviewers for this comment. We apologize for the lack of clarity. We used artificially synthesized G4C2 repeat sequences when generating constructs for (G4C2)n transgenic flies, so these constructs do not contain human intronic sequence ahead of the G4C2 repeat in the C9orf72 gene, as explained in the Materials and Methods section. To clarify the difference between our C9-ALS/FTD fly models and LDS-(G4C2)44GR-GFP fly model (Goodman et al., 2019), we have made the following change to the revised manuscript.

      (1) Schema of the LDS-(G4C2)44GR-GFP construct was presented in Figure 3—figure supplement 1.

      Furthermore, to maintain transparency of the study, we have provided the entire sequence of the insert as the following source file.

      (2) The artificial sequences inserted in the pUAST vector for generation of the (G4C2)n flies were presented in Figure 1—figure supplement 1—source data 1.

      2) It is really nice how they quantitated everything and showed individual data points.

      Response: We thank the editors and reviewers for appreciating our data analysis method. All individual data points and statistical analyses are summarized in source data files.

      3) So when they call FUS an RNA chaperone, are they simply meaning it is changing the structure of the repeat, or could it just be interacting with the repeat to coat the repeat and prevent it from folding into whatever in vivo structures? Can they speculate on why some RNA chaperones lead to presumed decay of the repeat and others do not? Can they discuss these points in the discussion? Detailed mechanistic understanding of RNA chaperones that ultimately promote decay of the repeat might be of highly significant therapeutic benefit.

      Response: We appreciate these critical comments. Indeed, we showed that FUS changes the higher-order structures of G4C2 repeat RNA in vitro, and that FUS suppresses G4C2 RNA foci formation. According to the established definition of RNA chaperone, RNA chaperones are proteins changing the structures of misfolded RNAs without ATP use, resulting in the maintenance of proper RNAs folding (Rajkowitsich et al., 2007). Thus, we consider that FUS is classified into RNA chaperone. To clarify these interpretations, we revised the manuscript as follows.

      (1) On page 10, line 215-219, the sentence “These results were in good agreement with our previous study on SCA31 showing the suppressive effects of FUS and other RBPs on RNA foci formation of UGGAA repeat RNA as RNA chaperones …” was changed to “These results were in good agreement with … RNA foci formation of UGGAA repeat RNA through altering RNA structures and preventing aggregation of misfolded repeat RNA as RNA chaperones …”.

      (2) On page 17, line 363-366, the sentence “FUS directly binds to G4C2 repeat RNA and modulates its G-quadruplex structure, as evident by CD and NMR analyses (Figure 5), suggesting its functional role as an RNA chaperone.” was changed to “FUS directly binds to G4C2 repeat RNA and modulates its G-quadruplex structure as evident by CD and NMR analyses (Figure 5, Figure 5—figure supplement 2), and suppresses RNA foci formation in vivo (Figures 3A and 3B), suggesting its functional role as an RNA chaperone.”

      Besides these RNA chaperones, we observed the expression of IGF2BP1, hnRNPA2B1, DHX9, and DHX36 decreased G4C2 repeat RNA expression levels. In addition, we recently reported that hnRNPA3 reduces G4C2 repeat RNA expression levels, leading to the suppression of neurodegeneration in C9-ALS/FTD fly models (Taminato et al., 2023). We speculate these RBPs could be involved in RNA decay pathways as components of the P-body or interactors with the RNA deadenylation machinery (Tran et al., 2004; Katahira et al., 2008; Geissler et al., 2016; Hubstenberger et al., 2017), possibly contributing to the reduced expression levels of G4C2 repeat RNA. To clarify these interpretations, we revised the manuscript as follows.

      (3) On page 18, line 392-398, the sentences “Similarly, we recently reported that hnRNPA3 reduces G4C2 repeat RNA expression levels, leading to the suppression of neurodegeneration in C9-ALS/FTD fly models (Taminato et al., 2023). Interestingly, these RBPs have been reported to be involved in RNA decay pathways as components of the P-body or interactors with the RNA deadenylation machinery (Tran et al., 2004; Katahira et al., 2008; Geissler et al., 2016; Hubstenberger et al., 2017), possibly contributing to the reduced expression levels of G4C2 repeat RNA.” was added.

      4) What is the level of the G4C2 repeat when they knock down caz? Is it possible that knockdown impacts the expression level of the repeat? Can they show this (or did they and I miss it)?

      Response: We thank the editors and reviewers for this comment. The expression levels of G4C2 repeat RNA in (G4C2)89 flies were not altered by the knockdown of caz, as shown in Figure 4G.

      5) A puzzling point is that FUS is supposed to be nuclear, so where is FUS in the brain in their lines? They suggest it modulates RAN translation, and presumably, that is in the cytoplasm. Is FUS when overexpressed now in part in the cytoplasm? Is the repeat dragging it into the cytoplasm? Can they address this in the discussion? If FUS is never found in vivo in the cytoplasm, then it raises the point that the impact they find of FUS on RAN translation might not reflect an in vivo situation with normal levels of FUS.

      Response: We appreciate these important comments. We agree with the editors and reviewers that FUS is mainly localized in the nucleus. However, FUS is known as a nucleocytoplasmic shuttling RBP that can transport RNA into the cytoplasm. Indeed, FUS is reported to facilitate transport of actin-stabilizing protein mRNAs to function in the cytoplasm (Fujii et al., 2005). Thus, we consider that FUS binds to G4C2 repeat RNA in the cytoplasm and suppresses RAN translation in this study.

      6) When they are using 2 copies of the driver and repeat, are they also using 2 copies of FUS? These are quite high levels of transgenes.

      Response: We thank the editors and reviewers for this comment. We used only 1 copy of FUS when using 2 copies of GMR-Gal4 driver. Full genotypes of the fly lines used in all experiments are described in Supplementary file 1.

      7) In Figure5-S1, FUS colocalizing with (G4C2)RNA is not clear. High-magnification images are recommended.

      Response: We appreciate this constructive comment on the figure. Following the suggestion, high-magnification images are added in Figure 5—figure supplement 1.

      8) I also suggest that the last sentence of the Discussion be revised as follows: Thus, our findings contribute not only to the elucidation of C9-ALS/FTD, but also to the elucidation of the repeat-associated pathogenic mechanisms underlying a broader range of neurodegenerative and neuropsychiatric disorders than previously thought, and it will advance the development of potential therapies for these diseases.

      Response: We appreciate this recommendation. We have made the following change based on the suggested sentence.

      (1) On page 20-21, line 455-459, “Thus, our findings contribute not only towards the elucidation of repeat-associated pathogenic mechanisms underlying a wider range of neuropsychiatric diseases than previously thought, but also towards the development of potential therapies for these diseases.” was changed to “Thus, our findings contribute to the elucidation of the repeat-associated pathogenic mechanisms underlying not only C9-ALS/FTD, but also a broader range of neuromuscular and neuropsychiatric diseases than previously thought, and will advance the development of potential therapies for these diseases.”.

      Authors’ comment on previous eLife assessment:

      We thank the editors and reviewers for appreciating our study. We mainly evaluated the function of human FUS protein on RAN translation and G4C2 repeat-induced toxicity using Drosophila expressing human FUS in vivo, and the recombinant human FUS protein in vitro. To validate that FUS functions as an endogenous regulator of RAN translation, we additionally evaluated the function of Drosophila caz protein as well. We are afraid that the first sentence of the eLife assessment, that is, “This important study demonstrates that the Drosophila FUS protein, the human homolog of which is implicated in amyotrophic lateral sclerosis (ALS) and related conditions, …” is somewhat misleading. We would be happy if you modify this sentence like “This important study demonstrates that the human FUS protein, which is implicated in amyotrophic lateral sclerosis (ALS) and related conditions, …”.

    1. Author Response:

      The following is the authors' response to the original reviews.

      Reviewer #1 (Public Review):

      The authors investigated state-dependent changes in evoked brain activity, using electrical stimulation combined with multisite neural activity across wakefulness and anesthesia. The approach is novel, and the results are compelling. The study benefits from an in-depth sophisticated analysis of neural signals. The effects of behavioral state on brain responses to stimulation are generally convincing.

      It is possible that the authors' use of "an average reference montage that removed signals common to all EEG electrodes" could also remove useful components of the signal, which are common across EEG electrodes, especially during deep anesthesia. For example, it is possible (in fact from my experience I would be surprised if it is not the case) that under isoflurane anesthesia, electrical stimulation induces a generalized slow wave or a burst of activity across the brain. Subtracting the average signal will simply remove that from all channels. This does not only result in signals under anesthesia being affected more by the referencing procedure than during waking but also will have different effects on different channels, e.g. depending on how strong the response is in a specific channel.

      We thank the reviewer for the positive comments and for raising this point. We do not believe that the average reference montage is obscuring an evoked slow wave in the isoflurane-anesthetized mice. Electrical stimulation did elicit a brief activation in nearby neurons that was followed by roughly 200 ms of quiescence, but no significant changes in firing in the other regions we recorded from (Author response image 1).

      Author response image 1

      ERP and evoked population activity during isoflurane anesthesia do not show evidence of global responses. (Top). ERP (-0.2 to +0.8 s around stimulus onset) with all EEG electrode traces superimposed. Data represented is the same: red traces have been processed with the average reference montage, black traces have not. (Bottom) Population mean firing rates from the areas of interest from the same experiment as above.

      We are familiar with the work from Dasilva et al. (2021), a study similar to ours because they also performed cortical electrical stimulation in mice anesthetized with isoflurane. They show widespread evoked multi-unit activity (derived from LFP) in isoflurane-anesthetized mice in response to electrical stimulation, but critical experimental differences may underlie the conflicting results presented in our study. Both works use similar levels of isoflurane to maintain anesthesia (we use a level roughly equivalent to their “deep” level). However, our experiments use only isoflurane, whereas Dasilva et al. induced anesthesia with ketamine and medetomidine followed by isoflurane. It has been shown that isoflurane and ketamine have different effects on neural dynamics (Sorrenti et al., 2021). Typically, isoflurane causes reduced spontaneous firing rates and decreased evoked response amplitudes compared to wakefulness, whereas ketamine has been shown to increase firing rates and evoked response amplitudes (Aasebø et al., 2017; Michelson & Kozai, 2018). Perhaps a more relevant difference are the electrical stimulation parameters used to perturb the brain. Dasilva et al. used 1 ms pulses of 500 μA, which would have a much larger effect than the stimulation used in this work, 0.2 ms pulses of 10-100 μA.

      Additionally, we would like to clarify that the average reference montage is not impacting the main findings of this work. As the reviewer correctly pointed out, the average reference montage does change the appearance of the ERP in the butterfly plots (Top panel in Author response image 1). However, all the quantitative analyses of the EEG-ERPs are performed on the global field power, computed by taking the standard deviation across all EEG channels, which is not affected by the average reference montage.

      Reviewer #2 (Public Review):

      […] The conclusions regarding the thalamic contributions to the ERP components are strongly supported by the data.

      The spatiotemporal complexity is almost a side point compared to what seems to be the most important point of the paper: showing the contribution of thalamic activity to some components of the cortical ERP. Scalp ERPs have long been regarded as purely cortical phenomena, just like most EEGs, and this study shows convincing evidence to the contrary.

      The data presented seemingly contradicts the results presented by Histed et al. (2009), who assert that cortical microstimulation only affects passing fibers near the tip of the electrodes, and results in distant, sparse, and somewhat random neural activation. In this study, it is clear that the maximum effect happens near the electrodes, decays with distance, and is not sparse at all, suggesting that not only passing fibers are activated but that also neuronal elements might be activated by antidromic propagation from the axonal hillock. This appears to offer proof that microstimulation might be much more effective than it was thought after the publication of Histed 2009, as the uber-successful use of DBS to treat Parkinson's disease has also shown.

      We thank the reviewer for their positive comments and thoughtful suggestions. We appreciate and agree with the reviewer’s perspective that the thalamic contribution to the cortical ERP is one of the key points of this study. We also thank the reviewer for their comment on the apparently contradictory results reported by Histed et al. (2009). This gives us the opportunity to further highlight the important contribution of our study to the field.

      First, we would like to highlight some key experimental differences between the two studies. In our study we used single pulse stimulation with currents between 10 and 100 μA, whereas Histed et al. used trains of pulses (100 ms in duration at 250 Hz) with lower current intensities (between 2 and 50 μA). We varied the depth of stimulation, targeting superficial and deep cortical layers; Histed et al. exclusively stimulated superficial cortical layers. In addition, the two studies used recording methods that are orthogonal in nature. We used Neuropixels probes that record from neurons that span all cortical layers depth-wise while Histed et al. used two-photon calcium imaging to record from a horizontal plane of neurons (again, in the superficial cortical layers).

      Because of these important methodological differences, it is more appropriate to compare the Histed et al. results to our results from superficial stimulation at comparable current intensities. In this case, we believe the two studies show similar results: stimulation activated a small fraction of neurons even hundreds of microns away from the stimulating electrode (see Figure 4A from our manuscript). However, our study adds an important observation pointing to the critical role of the depth of the stimulating electrode. We observe significant excitation of local cortical neurons (Figure 4D) and trans-synaptic activation of the thalamus only when we delivered deep stimulation (Figure5A). This effect is likely mediated by activation of large, myelinated cortico-thalamic fibers, which are thought to be more excitable that non-myelinated horizontal fibers (Tehovnik & Slocum, 2013).

      To summarize, Histed et al. (2009) concluded that microstimulation causes a sparse activation of a distributed set of neurons with little evidence of synaptically driven activation. Instead, we showed that microstimulation can robustly activate local neurons and trans-synaptically activate distant neurons when stronger stimuli are directed to deep cortical layers. Based on this, we conclude that electrical stimulation is indeed highly effective, and is a valid tool that can be used to probe and characterize the cortico-thalamo-cortical network of any behavioral state.

      ----------

      Reviewer #1 (Recommendations for the authors):

      1. I am not clear how "putative pyramidal" or RS and "putative inhibitory" fast-spiking neurons were identified. Please provide some further details on that, including average spike wave shapes, and distribution of firing rates, and it would be interesting to know the proportion of "putative" RS and FS neurons in your recorded population. Obviously, caution is warranted here because, without further work, you cannot be sure that those are indeed pyramidal cells or interneurons! Is this subdivision necessary at all?

      We added details regarding the cell-type classification to the Results (lines 136-140) and the Methods section. This classification is common practice in cortical extracellular electrophysiology recordings given that cell-type specific analyses can reveal important differences between the two putative populations (Barthó et al., 2004; Bortone et al., 2014; Bruno & Simons, 2002; Jia et al., 2016; Niell & Stryker, 2008; Sirota et al., 2008). Based on our findings that the two populations respond to electrical stimulation in similar ways (excitation followed by a period of quiescence and rebound excitation), we agree the subdivision is not necessary to support our conclusions. However, we believe that some readers will appreciate seeing the two putative populations presented separately.

      2. I wonder how the authors know whether the animals were awake, specifically when they were not running. Did you observe animals falling asleep when head-fixed? Providing some analyses of spontaneous EEG/LFP signals in each state could add some reassurance that only wakefulness was included, as intended.

      While we cannot conclusively rule out that mice were asleep during the “quiet wakefulness” periods we analyzed, we believe they are likely to be awake for two main reasons: 1) all the experiments are performed during the dark phase of the light/dark cycle, when the mice are less likely to enter a sleep state (Franken et al., 1999); 2) the animals are not undergoing specific training to promote drowsiness or sleep. Indeed, many sleep-focused studies in head-fixed mice are performed during the light phase of the animal’s cycle to maximize the likelihood of capturing sleep states (Kobayashi et al., 2023; Turner et al., 2020; Yüzgeç et al., 2018; Zhang et al., 2022). We have added this note to the Discussion section (lines 402-406).

      Because we do not specifically record during sleep states and our recording does not include electromyography, which is commonly used in conjunction with EEG to classify sleep stages, we cannot accurately perform spectral comparison between “quiet wakefulness” and sleep states in our recordings.

      3. I was unsure about the meaning of some of the terminology, specifically "rebound", "rebound spiking", "rebound excitation" etc. Why do you call it "rebound"?

      “Rebound” is a term often used to describe a period of enhanced spiking following a period of prolonged silence or inhibition (Guido & Weyand, 1995; Roux et al., 2014). Grenier et al. list “postinhibitory rebound excitation” as an intrinsic property of cortical and thalamic neurons (1998). We added this description to the text (lines 79-80).

      Reviewer #2 (Recommendations For The Authors):

      Regarding analysis, I would make three main points:

      Regarding the CSD analysis, I think the authors have done a good job of circumventing several of the known issues of this technique, especially by using ERPs rather than ongoing activity. However, although I do not immediately have access to the literature to back up this claim, I've heard that many assumptions behind CSD require a laminar structure with electrodes positioned perpendicular to these layers. In Figure 1B it seems like the neuropixels probe is not really perpendicular to the cortical layers, and I wonder if this might be an issue. I am also wondering how to interpret the thalamic CSD, as this structure is not laminar, lacks the mass of neatly stacked neuronal dipoles present in the cortex, and does not have an orderly array of synaptic inputs and outputs. I understand that CSD analysis helps minimize the contributions of volume conduction, but in this case, I also wonder if the thalamic CSD is even necessary to back up the paper's claims.

      One-dimensional CSD is computed assuming that the electrode is inserted perpendicular to cortex. This is mainly important for the interpretation of sinks and sources, since CSD can be also computed on radial voltages (e.g., EEG [Tenke & Kayser, 2012]). In general, our Neuropixels probes do not significantly deviate from perpendicular (mean deviation from perpendicular 15.3 degrees, minimum 5.2 degrees, and maximum 36.6 degrees). The probe represented in Figure 1B deviates from perpendicular by 31.2 degrees, which is an outlier compared to the rest of the insertions. Any deviation from perpendicular would result in the “effective” cortical thickness being larger by a factor of 1/cos(angle deviation from perpendicular) and thus would not affect the relative location of sources and sinks. We have added a statement to clarify this in the text (lines 126 and 454-456).

      We agree with the statement regarding CSD analysis in the thalamus. We originally included the CSD for the thalamus in Figure 2F for completeness. As the reviewer pointed out, thalamic CSD was not used to perform any subsequent analysis and is, therefore, not necessary to back up any claims. As such, we have removed CSD plot from Figure 2F to avoid any confusion and made a comment to this effect in the legend (lines 1175-1177).

      On the merits of using the z-score normalization for spike rates vs. other strategies like standardizing to maximum firing, I am aware that both procedures have limitations, but the z-score changes the range of the firing rate from [0, +Inf] to [-Inf, +Inf]. This does not seem correct considering that negative spiking rates do not exist. The standardization to maximum rate keeps the range within [0, 1], not creating negative rates. Another point that it will be worth discussing is the reported values of the z-scored values. For example, what does it mean to be 54 standard deviations away from the mean? 6 standard deviations is already a big distance from the mean.

      For Figure 2, we chose to represent the neural firing rates as z-scores because we found it important to report the magnitude of both the increase and decrease of the evoked firing rates in the post-stimulus period relative to the pre-stimulus rate. The normalization we used helps to visualize the magnitude of the effects of electrical stimulation in neuronal activity for both directions, which is an important result of the study. Despite the differences between the two normalization methods, the normalization based on the maximum firing does not significantly change the qualitative interpretation of Figure 2 in the manuscript (Author response image 2).

      Author response image 2

      Evoked firing rates for neurons in the areas of interest in response to deep stimulation in MO during the awake state. (Left) Firing rates of all neurons normalized by the average, pre-stimulus firing rate. (Right) Firing rates of all neurons normalized by the maximum post-stimulus firing rate.

      Regarding Figure 3 and the associated text, we would like to clarify that the magnitude metric is not simply a z-score value (with units of s.d.) but rather it is the integrated area under the z-scored response over the response window (with units of s.d.∙seconds). This can help explain why we see values of ~50 s.d.∙s. We chose to z-score firing rates, LFP, and CSD to normalize across the different signals and magnitudes of the evoked responses. We often observed the largest responses in the LFP (see Figure 3A), which may be partly due to the signal naturally having a larger dynamic range than the measured neural firing rates. Then we integrated the z-score response time series to capture the dynamic of the signal over the response window, rather than a static value such as the mean or maximum z-score. After performing a thorough literature search, we found no other ways to capture and compare the magnitudes of the different signals. We have added language to clarify the magnitude metric (lines 155-156) and added the appropriate units.

      In reporting the p-values, I recommend increasing the number of significant digits to four because the p-value seems to be the same for different tests in several places (e.g.: lines 207 to 218), which seems odd. I also wonder whether this could be an artifact of the z-scoring procedure. In the figures, I would like to advise the use of 1 asterisk to denote "weak evidence to reject the null hypothesis (0.05 > p > 0.01)" and two asterisks to denote "strong evidence to reject the null hypothesis (0.01 > p)", and make a note of it accordingly in the manuscript and/or figure legends.

      According to the reviewer’s suggestion, we have changed the statistics language to “* weak evidence to reject null hypothesis (0.05 > p > 0.01), ** strong evidence to reject null hypothesis (0.01 > p > 0.001), *** very strong evidence to reject null hypothesis (0.001 > p)” throughout the manuscript.

      We have also increased the number of significant digits to four throughout the manuscript. It is true that some of the p-values reported for Figure 3 (lines 169-180) are the same for different tests. This is not an artifact of the z-scoring, but rather a consequence of performing the Wilcoxon signed-rank test (an ordinal statistical test) with small sample numbers. Because the p-value depends only on the relative ordering, not the continuous distribution of values, the small sample size (N=6-14) increases the likelihood of obtaining the exact same p-value if the relative ordering of samples is the same.

      Line 202: If the magnitude corresponds to z-score data, please add "s.d." after the number, as z-scored values are expressed in standard deviation units. Please update this throughout the paper.

      As stated above the magnitude metric is the integrated area under the z-scored response over the response window (with units of s.d.∙seconds). We have added the correct units in all places.

      Line 214: Please report how the multiple comparisons correction was performed

      We have added the test used for multiple comparisons in line 169 (formerly line 214) and in the Methods section (line 770).

      Line 462: please replace "Neuropixels activity" with "LFP and single-unit activity".

      We changed the wording to specify “LFP, and single neuron responses…” (now line 337).

      Line 475: a short explanation of the bi-stability phenomena will be helpful for the reader.

      We added the following description: “a state characterized by spontaneous alternation between bouts of activity and periods of silence” (lines 350-351).

      Line 601: It is asserted that "Electrical stimulation directly activates local cells and axons that run near the stimulation site via activation of the axon initial segment" and the paper by Histed et al. 2009 is cited. This does not seem like an appropriate citation, as Histed et al. explicitly state that electrical microstimulation does not activate local neuronal bodies near the electrode tip. See my comment above.

      Upon further reading, we believe we are seeing evidence of direct axonal activation and subsequent antidromic activation of local cell bodies, as you suggested in your above comment and has been proposed by many including Histed et al. (2009) and Nowak and Bullier (1998). We edited our sentence accordingly, kept the Histed et al. citation, and added other relevant citations (lines 487-490).

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    1. Author response:

      Public Review

      Joint Public Review:

      This manuscript presents an algorithm for identifying network topologies that exhibit a desired qualitative behaviour, with a particular focus on oscillations. The approach is first demonstrated on 3-node networks, where results can be validated through exhaustive search, and then extended to 5-node networks, where the search space becomes intractable. Network topologies are represented as directed graphs, and their dynamical behaviour is classified using stochastic simulations based on the Gillespie algorithm. To efficiently explore the large design space, the authors employ reinforcement learning via Monte Carlo Tree Search (MCTS), framing circuit design as a sequential decision-making process.

      This work meaningfully extends the range of systems that can be explored in silico to uncover non-linear dynamics and represents a valuable methodological advance for the fields of systems and synthetic biology.

      Strengths

      The evidence presented is strong and compelling. The authors validate their results for 3-node networks through exhaustive search, and the findings for 5-node networks are consistent with previously reported motifs, lending credibility to the approach. The use of reinforcement learning to navigate the vast space of possible topologies is both original and effective, and represents a novel contribution to the field. The algorithm demonstrates convincing efficiency, and the ability to identify robust oscillatory topologies is particularly valuable. Expanding the scale of systems that can be systematically explored in silico marks a significant advance for the study of complex gene regulatory networks.

      Weaknesses

      The principal weakness of the manuscript lies in the interpretation of biological robustness. The authors identify network topologies that sustain oscillatory behaviour despite perturbations to the system or parameters. However, in many cases, this persistence is due to the presence of partially redundant oscillatory motifs within the network. While this observation is interesting and of clear value for circuit design, framing it as evidence of evolutionary robustness may be misleading. The "mutant" systems frequently exhibit altered oscillatory properties, such as changes in frequency or amplitude. From a functional cellular perspective, mere oscillation is insufficient - preservation of specific oscillation characteristics is often essential. This is particularly true in systems like circadian clocks, where misalignment with environmental cycles can have deleterious effects. Robustness, from an evolutionary standpoint, should therefore be framed as the capacity to maintain the functional phenotype, not merely the qualitative behaviour.

      A secondary limitation is that, despite the methodological advances, the scale of the systems explored remains modest. While moving from 3- to 5-node systems is non-trivial, five elements still represent a relatively small network. It is somewhat surprising that the algorithm does not scale further, particularly when considering the performance of MCTS in other domains - for instance, modern chess engines routinely explore far larger decision trees. A discussion on current performance bottlenecks and potential avenues for improving scalability would be valuable.

      Finally, it is worth noting that the emergence of oscillations in a model often depends not only on the topology but also critically on parameter choices and the nature of the nonlinearities. The use of Hill functions and high Hill coefficients is a common strategy to induce oscillatory dynamics. Thus, the reported results should be interpreted within the context of the modelling assumptions and parameter regimes employed in the simulations.

      We thank the reviewers for their careful consideration of our work and for the interesting feedback and scientific discussion. We are working on a revised text based on their recommendations, which will include some of the discussion below.

      This work meaningfully extends the range of systems that can be explored in silico to uncover non-linear dynamics and represents a valuable methodological advance for the fields of systems and synthetic biology.

      We thank the reviewers for their positive assessment of our work’s impact!

      The use of reinforcement learning to navigate the vast space of possible topologies is both original and effective, and represents a novel contribution to the field. The algorithm demonstrates convincing efficiency, and the ability to identify robust oscillatory topologies is particularly valuable. Expanding the scale of systems that can be systematically explored in silico marks a significant advance for the study of complex gene regulatory networks.

      We appreciate these kind comments about our work’s merits. We are excited to share our reinforcement learning (RL) based method with the fields of systems and synthetic biology, and we consider it a valuable tool for the systematic analysis and design of larger-scale regulatory networks!

      The principal weakness of the manuscript lies in the interpretation of biological robustness. The authors identify network topologies that sustain oscillatory behaviour despite perturbations to the system or parameters… [However, these] "mutant" systems frequently exhibit altered oscillatory properties, such as changes in frequency or amplitude. From a functional cellular perspective, mere oscillation is insufficient - preservation of specific oscillation characteristics is often essential. This is particularly true in systems like circadian clocks, where misalignment with environmental cycles can have deleterious effects. Robustness, from an evolutionary standpoint, should therefore be framed as the capacity to maintain the functional phenotype, not merely the qualitative behaviour.

      We thank the reviewers for their attention to this point. In the large-scale circuit search, summarized in Figures 4A and 4B, we ran a search for 5-component oscillators that can spontaneously oscillate even when subjected to the deletion of a random gene. Some of the best performing circuits under these conditions exhibited a design feature we call “motif multiplexing,” in which multiple smaller motifs are interleaved in a way that makes oscillation possible under many different mutational scenarios. Interestingly, despite not selecting for preservation of frequency, the 3Ai+3Rep circuit (a 5-gene circuit highlighted in Figure 5) anecdotally appears to have a natural frequency that is robust to partial gene knockdowns, although not to complete gene deletions. As shown in Figure 5C, this circuit has a natural frequency of 6 cycles/hr (with one particular parameterization), and it can sustain a knockdown of any of its 5 genes to 50% of the wild-type transcription rate without altering the natural frequency by more than 20%.

      However, we agree that there are salient differences between this training scenario and natural evolution. The revised text will clarify that these differences limit what conclusions can be drawn about biological evolution by analogy. As the reviewers point out, we use the presence of spontaneous oscillations (with or without the deletion) as a measure of fitness, regardless of frequency, so as to screen for designs with promising behavior. Also, the deletion mutations introduced during training likely represent larger perturbations to the system than a typical mutation encountered during genome replication (for example, a point mutation in a response element leading to a moderate change in binding affinity). Finally, we do not introduce any entrainment. Real circadian oscillators are aligned to a 24-hour period (“entrained”) by environmental inputs such as light and temperature. For this reason, natural circadian clocks may have natural frequencies that are slightly shorter or longer than 24 hours, although a close proximity to the 24-hour period does seem to be an important selective factor [1].

      ...despite the methodological advances, the scale of the systems explored remains modest. While moving from 3- to 5-node systems is non-trivial, five elements still represent a relatively small network. It is somewhat surprising that the algorithm does not scale further, particularly when considering the performance of MCTS in other domains - for instance, modern chess engines routinely explore far larger decision trees. A discussion on current performance bottlenecks and potential avenues for improving scalability would be valuable.

      We thank the reviewers for their attention to this point. The main limitation we encountered to exploring circuits with more than 5 nodes in this work was the poor computational scaling of the Gillespie stochastic simulation algorithm, rather than a limitation of MCTS itself. While the average runtime of a 3-node circuit simulation was roughly 7 seconds, this number increased to 18-20 seconds with 5-node circuits. For this reason, we limited the search to topologies with ≤15 interaction arrows (15 sec/simulation). In general, the simulation time was proportional to the square of the number of transcription factors (TFs). We will revise the text to include the reason for stopping at 5 nodes, which is significant for understanding CircuiTree’s scaling properties.

      With regards to scaling, an important advantage of CircuiTree is its ability to generate useful candidate designs after exploring only a portion of the search space. Like exhaustive search, given enough time, MCTS will comprehensively explore the search space and find all possible solutions. However, for large search spaces, RL-based agents are generally given a finite number of simulations (or time) to learn as much as possible.

      Across machine learning (ML) applications [2] and particularly with RL models [3], this training time tends to obey a power law with respect to the underlying complexity of the problem. Thus we can use the complexity of the 3-node and 5-node searches to infer the current scaling limits of CircuiTree. The first oscillator topology was discovered after 2,280 simulations for the 3-node search, and in the 5-node search, the first oscillator using 5 nodes appeared at ~8e5 simulations, resulting in a power law of Y ~ 84.4 X<sup>0.333</sup>. Thus, useful candidate designs may be found for 6-node and 7-node searches after 4.5e7 and 5.26e9 simulations, respectively, even though these spaces contain 1.5e17 and 2.5e23 topologies, respectively. Thus, running a 7-node search with the current implementation of CircuiTree would require resources close to the current boundaries of computation, requiring roughly 1.8 million CPU-hours, or 2 weeks on 5,000 CPUs, assuming a 1-second simulation. These points will be incorporated into both the results and discussion sections in our revised text.

      However, we are optimistic about CircuiTree’s potential to scale to much larger circuits with modifications to its algorithm. CircuiTree uses the original (so-called “vanilla”) implementation of MCTS, which has not been used in professional game-playing AIs in over a decade. Contemporary RL-based game-playing engines leverage deep neural networks to dramatically reduce the training time, using value networks to identify game-winning positions and policy networks to find game-winning moves. AlphaZero, developed by Google DeepMind to learn games by self-play and without domain knowledge, outperformed all other chess AIs after 44 million training games, much smaller than the 10^43 possible chess states [4]. Similarly, the game of go has 10<sup>170</sup> possible states, but AlphaZero outperformed other AIs after only 140 million games [4]. Large circuits live in similarly large search spaces; for example, 19-node and 20-node circuits represent spaces of 10<sup>172</sup> and 10<sup>190</sup> possible topologies. The revised text will include this discussion and identify value and policy networks, as well as more scalable simulation paradigms such as ODEs and neural ODEs, as our future directions for improving CircuiTree’s scalability.

      Finally, our revised discussion will note some important differences between game-playing and biological circuit design. Unlike deterministic games like chess, the final value of a circuit topology is determined stochastically, by running a simulation whose fitness depends on the parameter set and initial conditions. Thus, state-for-state, it is possible that training an agent for circuit design may inherently require more simulations to achieve the same level of certainty compared to classical games. Additionally, while we often possess a priori knowledge about a game such as its overall difficulty or certain known strategies, we lack this frame of reference when searching for circuit designs. Thus, it remains challenging to know if and when a large space of designs has been “satisfactorily” or “comprehensively” searched, since the answer depends on data that are unknown, namely the quantity, quality, and location of solutions residing in the search space.

      Not accounting for redundancy due to structural symmetries

      Finally, it is worth noting that the emergence of oscillations in a model often depends not only on the topology but also critically on parameter choices and the nature of the nonlinearities. The use of Hill functions and high Hill coefficients is a common strategy to induce oscillatory dynamics. Thus, the reported results should be interpreted within the context of the modelling assumptions and parameter regimes employed in the simulations.

      In our dynamical modeling of transcription factor (TF) networks, we do not rely on continuum assumptions about promoter occupancy such as Hill functions. Rather, we model each reaction - transcription, translation, TF binding/unbinding, and degradation - explicitly, and individual molecules appear and disappear via stochastic birth and death events. Many natural TFs are homodimers that bind cooperatively to regulate transcription; similarly, we assume that pairs of TFs bind more stably to their response element than individual TFs. Thus, our model has similar cooperativity to a Hill function, and it can be shown that in the continuum limit, the effective Hill coefficient is always ≤2. Our revision will clarify this aspect of the modeling and include a derivation of this property. Currently, the parameter values used in the figures are shown in Table 2. In the revised text, these will be displayed in the body of the text as well for clarity.

      Bibliography (1) Spoelstra, K., Wikelski, M., Daan, S., Loudon, A. S. I., & Hau, M. (2015). Natural selection against a circadian clock gene mutation in mice. PNAS, 113(3), 686–691. https://doi.org/https://doi.org/10.1073/pnas.1516442113<br /> (2) Neumann, O., & Gros, C. (2023). Scaling Laws for a Multi-Agent Reinforcement Learning Model. The Eleventh International Conference on Learning Representations. Retrieved from https://openreview.net/forum?id=ZrEbzL9eQ3W (3) Jones, A. L. (2021). Scaling Scaling Laws with Board Games. arXiv [Cs.LG]. Retrieved from http://arxiv.org/abs/2104.03113 (4) Silver, D., Hubert, T., Schrittwieser, J., Antonoglou, I., Lai, M., Guez, A., Lanctot, M., Sifre, L., Kumaran, D., Graepel, T., Lillicrap, T., Simonyan, K., & Hassabis, D. (2018). A general reinforcement learning algorithm that Masters Chess, Shogi, and go through self-play. Science, 362(6419), 1140–1144. https://doi.org/10.1126/science.aar6404

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife Assessment

      This valuable study investigates how the neural representation of individual finger movements changes during the early period of sequence learning. By combining a new method for extracting features from human magnetoencephalography data and decoding analyses, the authors provide incomplete evidence of an early, swift change in the brain regions correlated with sequence learning, including a set of previously unreported frontal cortical regions. The addition of more control analyses to rule out that head movement artefacts influence the findings, and to further explain the proposal of offline contextualization during short rest periods as the basis for improvement performance would strengthen the manuscript.

      We appreciate the Editorial assessment on our paper’s strengths and novelty. We have implemented additional control analyses to show that neither task-related eye movements nor increasing overlap of finger movements during learning account for our findings, which are that contextualized neural representations in a network of bilateral frontoparietal brain regions actively contribute to skill learning. Importantly, we carried out additional analyses showing that contextualization develops predominantly during rest intervals.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study addresses the issue of rapid skill learning and whether individual sequence elements (here: finger presses) are differentially represented in human MEG data. The authors use a decoding approach to classify individual finger elements and accomplish an accuracy of around 94%. A relevant finding is that the neural representations of individual finger elements dynamically change over the course of learning. This would be highly relevant for any attempts to develop better brain machine interfaces - one now can decode individual elements within a sequence with high precision, but these representations are not static but develop over the course of learning.

      Strengths:

      The work follows a large body of work from the same group on the behavioural and neural foundations of sequence learning. The behavioural task is well established and neatly designed to allow for tracking learning and how individual sequence elements contribute. The inclusion of short offline rest periods between learning epochs has been influential because it has revealed that a lot, if not most of the gains in behaviour (ie speed of finger movements) occur in these socalled micro-offline rest periods. The authors use a range of new decoding techniques, and exhaustively interrogate their data in different ways, using different decoding approaches. Regardless of the approach, impressively high decoding accuracies are observed, but when using a hybrid approach that combines the MEG data in different ways, the authors observe decoding accuracies of individual sequence elements from the MEG data of up to 94%.

      We have previously showed that neural replay of MEG activity representing the practiced skill was prominent during rest intervals of early learning, and that the replay density correlated with micro-offline gains (Buch et al., 2021). These findings are consistent with recent reports (from two different research groups) that hippocampal ripple density increases during these inter-practice rest periods, and predict offline learning gains (Chen et al., 2024; Sjøgård et al., 2024). However, decoder performance in our earlier work (Buch et al., 2021) left room for improvement. Here, we reported a strategy to improve decoding accuracy that could benefit future studies of neural replay or BCI using MEG.

      Weaknesses:

      There are a few concerns which the authors may well be able to resolve. These are not weaknesses as such, but factors that would be helpful to address as these concern potential contributions to the results that one would like to rule out. Regarding the decoding results shown in Figure 2 etc, a concern is that within individual frequency bands, the highest accuracy seems to be within frequencies that match the rate of keypresses. This is a general concern when relating movement to brain activity, so is not specific to decoding as done here. As far as reported, there was no specific restraint to the arm or shoulder, and even then it is conceivable that small head movements would correlate highly with the vigor of individual finger movements. This concern is supported by the highest contribution in decoding accuracy being in middle frontal regions - midline structures that would be specifically sensitive to movement artefacts and don't seem to come to mind as key structures for very simple sequential keypress tasks such as this - and the overall pattern is remarkably symmetrical (despite being a unimanual finger task) and spatially broad. This issue may well be matching the time course of learning, as the vigor and speed of finger presses will also influence the degree to which the arm/shoulder and head move. This is not to say that useful information is contained within either of the frequencies or broadband data. But it raises the question of whether a lot is dominated by movement "artefacts" and one may get a more specific answer if removing any such contributions.

      Reviewer #1 expresses concern that the combination of the low-frequency narrow-band decoder results, and the bilateral middle frontal regions displaying the highest average intra-parcel decoding performance across subjects is suggestive that the decoding results could be driven by head movement or other artefacts.

      Head movement artefacts are highly unlikely to contribute meaningfully to our results for the following reasons. First, in addition to ICA denoising, all “recordings were visually inspected and marked to denoise segments containing other large amplitude artifacts due to movements” (see Methods). Second, the response pad was positioned in a manner that minimized wrist, arm or more proximal body movements during the task. Third, while online monitoring of head position was not performed for this study, it was assessed at the beginning and at the end of each recording. The head was restrained with an inflatable air bladder, and head movement between the beginning and end of each scan did not exceed 5mm for all participants included in the study.

      The Reviewer states a concern that “it is conceivable that small head movements would correlate highly with the vigor of individual finger movements”. We agree that despite the steps taken above, it is possible that minor head movements could still contribute to some remaining variance in the MEG data in our study. However, such correlations between small head movements and finger movements could only meaningfully contribute to decoding performance if: (A) they were consistent and pervasive throughout the recording (which might not be the case if the head movements were related to movement vigor and vigor changed over time); and (B) they systematically varied between different finger movements, and also between the same finger movement performed at different sequence locations (see 5-class decoding performance in Figure 4B). The possibility of any head movement artefacts meeting all these conditions is unlikely. Alternatively, for this task design a much more likely confound could be the contribution of eye movement artefacts to the decoder performance (an issue raised by Reviewer #3 in the comments below).

      Remember from Figure 1A in the manuscript that an asterisk marks the current position in the sequence and is updated at each keypress. Since participants make very few performance errors, the position of the asterisk on the display is highly correlated with the keypress being made in the sequence. Thus, it is possible that if participants are attending to the visual feedback provided on the display, they may generate eye movements that are systematically related to the task. Since we did record eye movements simultaneously with the MEG recordings (EyeLink 1000 Plus; Fs = 600 Hz), we were able to perform a control analysis to address this question. For each keypress event during trials in which no errors occurred (which is the same time-point that the asterisk position is updated), we extracted three features related to eye movements: 1) the gaze position at the time of asterisk position update (triggered by a KeyDown event), 2) the gaze position 150ms later, and 3) the peak velocity of the eye movement between the two positions. We then constructed a classifier from these features with the aim of predicting the location of the asterisk (ordinal positions 1-5) on the display. As shown in the confusion matrix below (Author response image 1), the classifier failed to perform above chance levels (overall cross-validated accuracy = 0.21817):

      Author response image 1.

      Confusion matrix showing that three eye movement features fail to predict asterisk position on the task display above chance levels (Fold 1 test accuracy = 0.21718; Fold 2 test accuracy = 0.22023; Fold 3 test accuracy = 0.21859; Fold 4 test accuracy = 0.22113; Fold 5 test accuracy = 0.21373; Overall cross-validated accuracy = 0.2181). Since the ordinal position of the asterisk on the display is highly correlated with the ordinal position of individual keypresses in the sequence, this analysis provides strong evidence that keypress decoding performance from MEG features is not explained by systematic relationships between finger movement behavior and eye movements (i.e. – behavioral artefacts) (end of figure legend).

      Remember that the task display does not provide explicit feedback related to performance, only information about the present position in the sequence. Thus, it is possible that participants did not actively attend to the feedback. In fact, inspection of the eye position data revealed that on majority of trials, participants displayed random-walk-like gaze patterns around a central fixation point located near the center of the screen. Thus, participants did not attend to the asterisk position on the display, but instead intrinsically generated the action sequence. A similar realworld example would be manually inputting a long password into a secure online application. In this case, one intrinsically generates the sequence from memory and receives similar feedback about the password sequence position (also provided as asterisks) as provided in the study task – feedback which is typically ignored by the user.

      The minimal participant engagement with the visual task display observed in this study highlights another important point – that the behavior in explicit sequence learning motor tasks is highly generative in nature rather than reactive to stimulus cues as in the serial reaction time task (SRTT). This is a crucial difference that must be carefully considered when designing investigations and comparing findings across studies.

      We observed that initial keypress decoding accuracy was predominantly driven by contralateral primary sensorimotor cortex in the initial practice trials before transitioning to bilateral frontoparietal regions by trials 11 or 12 as performance gains plateaued. The contribution of contralateral primary sensorimotor areas to early skill learning has been extensively reported in humans and non-human animals.(Buch et al., 2021; Classen et al., 1998; Karni et al., 1995; Kleim et al., 1998) Similarly, the increased involvement of bilateral frontal and parietal regions to decoding during early skill learning in the non-dominant hand is well known. Enhanced bilateral activation in both frontal and parietal cortex during skill learning has been extensively reported (Doyon et al., 2002; Grafton et al., 1992; Hardwick et al., 2013; Kennerley et al., 2004; Shadmehr & Holcomb, 1997; Toni, Ramnani, et al., 2001), and appears to be even more prominent during early fine motor skill learning in the non-dominant hand (Lee et al., 2019; Sawamura et al., 2019). The frontal regions identified in these studies are known to play crucial roles in executive control (Battaglia-Mayer & Caminiti, 2019), motor planning (Toni, Thoenissen, et al., 2001), and working memory (Andersen & Buneo, 2002; Buneo & Andersen, 2006; Shadmehr & Holcomb, 1997; Toni, Ramnani, et al., 2001; Wolpert et al., 1998) processes, while the same parietal regions are known to integrate multimodal sensory feedback and support visuomotor transformations (Andersen & Buneo, 2002; Buneo & Andersen, 2006; Shadmehr & Holcomb, 1997; Toni, Ramnani, et al., 2001; Wolpert et al., 1998), in addition to working memory (Grover et al., 2022). Thus, it is not surprising that these regions increasingly contribute to decoding as subjects internalize the sequential task. We now include a statement reflecting these considerations in the revised Discussion.

      A somewhat related point is this: when combining voxel and parcel space, a concern is whether a degree of circularity may have contributed to the improved accuracy of the combined data, because it seems to use the same MEG signals twice - the voxels most contributing are also those contributing most to a parcel being identified as relevant, as parcels reflect the average of voxels within a boundary. In this context, I struggled to understand the explanation given, ie that the improved accuracy of the hybrid model may be due to "lower spatially resolved whole-brain and higher spatially resolved regional activity patterns".

      We disagree with the Reviewer’s assertion that the construction of the hybrid-space decoder is circular for the following reasons. First, the base feature set for the hybrid-space decoder constructed for all participants includes whole-brain spatial patterns of MEG source activity averaged within parcels. As stated in the manuscript, these 148 inter-parcel features reflect “lower spatially resolved whole-brain activity patterns” or global brain dynamics. We then independently test how well spatial patterns of MEG source activity for all voxels distributed within individual parcels can decode keypress actions. Again, the testing of these intra-parcel spatial patterns, intended to capture “higher spatially resolved regional brain activity patterns”, is completely independent from one another and independent from the weighting of individual inter-parcel features. These intra-parcel features could, for example, provide additional information about muscle activation patterns or the task environment. These approximately 1150 intra-parcel voxels (on average, within the total number varying between subjects) are then combined with the 148 inter-parcel features to construct the final hybrid-space decoder. In fact, this varied spatial filter approach shares some similarities to the construction of convolutional neural networks (CNNs) used to perform object recognition in image classification applications (Srinivas et al., 2016). One could also view this hybrid-space decoding approach as a spatial analogue to common timefrequency based analyses such as theta-gamma phase amplitude coupling (θ/γ PAC), which assess interactions between two or more narrow-band spectral features derived from the same time-series data (Lisman & Jensen, 2013).

      We directly tested this hypothesis – that spatially overlapping intra- and inter-parcel features portray different information – by constructing an alternative hybrid-space decoder (Hybrid<sub>Alt</sub>) that excluded average inter-parcel features which spatially overlapped with intra-parcel voxel features, and comparing the performance to the decoder used in the manuscript (Hybrid<sub>Orig</sub>). The prediction was that if the overlapping parcel contained similar information to the more spatially resolved voxel patterns, then removing the parcel features (n=8) from the decoding analysis should not impact performance. In fact, despite making up less than 1% of the overall input feature space, removing those parcels resulted in a significant drop in overall performance greater than 2% (78.15% ± 7.03% SD for Hybrid<sub>Orig</sub> vs. 75.49% ± 7.17% for Hybrid<sub>Alt</sub>; Wilcoxon signed rank test, z = 3.7410, p = 1.8326e-04; Author response image 2).

      Author response image 2.

      Comparison of decoding performances with two different hybrid approaches. Hybrid<sub>Alt</sub>: Intra-parcel voxel-space features of top ranked parcels and inter-parcel features of remaining parcels. Hybrid<sub>Orig</sub>: Voxel-space features of top ranked parcels and whole-brain parcel-space features (i.e. – the version used in the manuscript). Dots represent decoding accuracy for individual subjects. Dashed lines indicate the trend in performance change across participants. Note, that Hybrid<sub>Orig</sub> (the approach used in our manuscript) significantly outperforms the Hybrid<sub>Alt</sub> approach, indicating that the excluded parcel features provide unique information compared to the spatially overlapping intra-parcel voxel patterns (end of figure legend).

      Firstly, there will be a relatively high degree of spatial contiguity among voxels because of the nature of the signal measured, i.e. nearby individual voxels are unlikely to be independent. Secondly, the voxel data gives a somewhat misleading sense of precision; the inversion can be set up to give an estimate for each voxel, but there will not just be dependence among adjacent voxels, but also substantial variation in the sensitivity and confidence with which activity can be projected to different parts of the brain. Midline and deeper structures come to mind, where the inversion will be more problematic than for regions along the dorsal convexity of the brain, and a concern is that in those midline structures, the highest decoding accuracy is seen.

      We agree with the Reviewer that some inter-parcel features representing neighboring (or spatially contiguous) voxels are likely to be correlated, an important confound in connectivity analyses (Colclough et al., 2015; Colclough et al., 2016), not performed in our investigation.

      In our study, correlations between adjacent voxels effectively reduce the dimensionality of the input feature space. However, as long as there are multiple groups of correlated voxels within each parcel (i.e. – the rank is greater than 1), the intra-parcel spatial patterns could meaningfully contribute to the decoder performance, as shown by the following results:

      First, we obtained higher decoding accuracy with voxel-space features (74.51% ± 7.34% SD) compared to parcel space features (68.77% ± 7.6%; Figure 3B), indicating individual voxels carry more information in decoding the keypresses than the averaged voxel-space features or parcel space features. Second, individual voxels within a parcel showed varying feature importance scores in decoding keypresses (Author response image 3). This finding shows that correlated voxels form mini subclusters that are much smaller spatially than the parcel they reside within.

      Author response image 3.:

      Feature importance score of individual voxels in decoding keypresses: MRMR was used to rank the individual voxel space features in decoding keypresses and the min-max normalized MRMR score was mapped to a structural brain surface. Note that individual voxels within a parcel showed different contribution to decoding (end of figure legend).

      Some of these concerns could be addressed by recording head movement (with enough precision) to regress out these contributions. The authors state that head movement was monitored with 3 fiducials, and their time courses ought to provide a way to deal with this issue. The ICA procedure may not have sufficiently dealt with removing movement-related problems, but one could eg relate individual components that were identified to the keypresses as another means for checking. An alternative could be to focus on frequency ranges above the movement frequencies. The accuracy for those still seems impressive and may provide a slightly more biologically plausible assessment.

      We have already addressed the issue of movement related artefacts in the first response above. With respect to a focus on frequency ranges above movement frequencies, the Reviewer states the “accuracy for those still seems impressive and may provide a slightly more biologically plausible assessment”. First, it is important to note that cortical delta-band oscillations measured with local field potentials (LFPs) in macaques is known to contain important information related to end-effector kinematics (Bansal et al., 2011; Mollazadeh et al., 2011) muscle activation patterns (Flint et al., 2012) and temporal sequencing (Churchland et al., 2012) during skilled reaching and grasping actions. Thus, there is a substantial body of evidence that low-frequency neural oscillatory activity in this range contains important information about the skill learning behavior investigated in the present study. Second, our own data shows (which the Reviewer also points out) that significant information related to the skill learning behavior is also present in higher frequency bands (see Figure 2A and Figure 3—figure supplement 1). As we pointed out in our earlier response to questions about the hybrid space decoder architecture (see above), it is likely that different, yet complimentary, information is encoded across different temporal frequencies (just as it is encoded across different spatial frequencies) (Heusser et al., 2016). Again, this interpretation is supported by our data as the highest performing classifiers in all cases (when holding all parameters constant) were always constructed from broadband input MEG data (Figure 2A and Figure 3—figure supplement 1).

      One question concerns the interpretation of the results shown in Figure 4. They imply that during the course of learning, entirely different brain networks underpin the behaviour. Not only that, but they also include regions that would seem rather unexpected to be key nodes for learning and expressing relatively simple finger sequences, such as here. What then is the biological plausibility of these results? The authors seem to circumnavigate this issue by moving into a distance metric that captures the (neural network) changes over the course of learning, but the discussion seems detached from which regions are actually involved; or they offer a rather broad discussion of the anatomical regions identified here, eg in the context of LFOs, where they merely refer to "frontoparietal regions".

      The Reviewer notes the shift in brain networks driving keypress decoding performance between trials 1, 11 and 36 as shown in Figure 4A. The Reviewer questions whether these shifts in brain network states underpinning the skill are biologically plausible, as well as the likelihood that bilateral superior and middle frontal and parietal cortex are important nodes within these networks.

      First, previous fMRI work in humans assessed changes in functional connectivity patterns while participants performed a similar sequence learning task to our present study (Bassett et al., 2011). Using a dynamic network analysis approach, Bassett et al. showed that flexibility in the composition of individual network modules (i.e. – changes in functional brain region membership of orthogonal brain networks) is up-regulated in novel learning environments and explains differences in learning rates across individuals. Thus, consistent with our findings, it is likely that functional brain networks rapidly reconfigure during early learning of novel sequential motor skills.

      Second, frontoparietal network activity is known to support motor memory encoding during early learning (Albouy et al., 2013; Albouy et al., 2012). For example, reactivation events in the posterior parietal (Qin et al., 1997) and medial prefrontal (Euston et al., 2007; Molle & Born, 2009) cortex (MPFC) have been temporally linked to hippocampal replay, and are posited to support memory consolidation across several memory domains (Frankland & Bontempi, 2005), including motor sequence learning (Albouy et al., 2015; Buch et al., 2021; F. Jacobacci et al., 2020). Further, synchronized interactions between MPFC and hippocampus are more prominent during early as opposed to later learning stages (Albouy et al., 2013; Gais et al., 2007; Sterpenich et al., 2009), perhaps reflecting “redistribution of hippocampal memories to MPFC” (Albouy et al., 2013). MPFC contributes to very early memory formation by learning association between contexts, locations, events and adaptive responses during rapid learning (Euston et al., 2012). Consistently, coupling between hippocampus and MPFC has been shown during initial memory encoding and during subsequent rest (van Kesteren et al., 2010; van Kesteren et al., 2012). Importantly, MPFC activity during initial memory encoding predicts subsequent recall (Wagner et al., 1998). Thus, the spatial map required to encode a motor sequence memory may be “built under the supervision of the prefrontal cortex” (Albouy et al., 2012), also engaged in the development of an abstract representation of the sequence (Ashe et al., 2006). In more abstract terms, the prefrontal, premotor and parietal cortices support novice performance “by deploying attentional and control processes” (Doyon et al., 2009; Hikosaka et al., 2002; Penhune & Steele, 2012) required during early learning (Doyon et al., 2009; Hikosaka et al., 2002; Penhune & Steele, 2012). The dorsolateral prefrontal cortex DLPFC specifically is thought to engage in goal selection and sequence monitoring during early skill practice (Schendan et al., 2003), all consistent with the schema model of declarative memory in which prefrontal cortices play an important role in encoding (Morris, 2006; Tse et al., 2007). Thus, several prefrontal and frontoparietal regions contributing to long term learning (Berlot et al., 2020) are also engaged in early stages of encoding. Altogether, there is strong biological support for the involvement of bilateral prefrontal and frontoparietal regions to decoding during early skill learning. We now address this issue in the revised manuscript.

      If I understand correctly, the offline neural representation analysis is in essence the comparison of the last keypress vs the first keypress of the next sequence. In that sense, the activity during offline rest periods is actually not considered. This makes the nomenclature somewhat confusing. While it matches the behavioural analysis, having only key presses one can't do it in any other way, but here the authors actually do have recordings of brain activity during offline rest. So at the very least calling it offline neural representation is misleading to this reviewer because what is compared is activity during the last and during the next keypress, not activity during offline periods. But it also seems a missed opportunity - the authors argue that most of the relevant learning occurs during offline rest periods, yet there is no attempt to actually test whether activity during this period can be useful for the questions at hand here.

      We agree with the Reviewer that our previous “offline neural representation” nomenclature could be misinterpreted. In the revised manuscript we refer to this difference as the “offline neural representational change”. Please, note that our previous work did link offline neural activity (i.e. – 16-22 Hz beta power (Bonstrup et al., 2019) and neural replay density (Buch et al., 2021) during inter-practice rest periods) to observed micro-offline gains.

      Reviewer #2 (Public review):

      Summary

      Dash et al. asked whether and how the neural representation of individual finger movements is "contextualized" within a trained sequence during the very early period of sequential skill learning by using decoding of MEG signal. Specifically, they assessed whether/how the same finger presses (pressing index finger) embedded in the different ordinal positions of a practiced sequence (4-1-3-2-4; here, the numbers 1 through 4 correspond to the little through the index fingers of the non-dominant left hand) change their representation (MEG feature). They did this by computing either the decoding accuracy of the index finger at the ordinal positions 1 vs. 5 (index_OP1 vs index_OP5) or pattern distance between index_OP1 vs. index_OP5 at each training trial and found that both the decoding accuracy and the pattern distance progressively increase over the course of learning trials. More interestingly, they also computed the pattern distance for index_OP5 for the last execution of a practice trial vs. index_OP1 for the first execution in the next practice trial (i.e., across the rest period). This "off-line" distance was significantly larger than the "on-line" distance, which was computed within practice trials and predicted micro-offline skill gain. Based on these results, the authors conclude that the differentiation of representation for the identical movement embedded in different positions of a sequential skill ("contextualization") primarily occurs during early skill learning, especially during rest, consistent with the recent theory of the "micro-offline learning" proposed by the authors' group. I think this is an important and timely topic for the field of motor learning and beyond.

      Strengths

      The specific strengths of the current work are as follows. First, the use of temporally rich neural information (MEG signal) has a large advantage over previous studies testing sequential representations using fMRI. This allowed the authors to examine the earliest period (= the first few minutes of training) of skill learning with finer temporal resolution. Second, through the optimization of MEG feature extraction, the current study achieved extremely high decoding accuracy (approx. 94%) compared to previous works. As claimed by the authors, this is one of the strengths of the paper (but see my comments). Third, although some potential refinement might be needed, comparing "online" and "offline" pattern distance is a neat idea.

      Weaknesses

      Along with the strengths I raised above, the paper has some weaknesses. First, the pursuit of high decoding accuracy, especially the choice of time points and window length (i.e., 200 msec window starting from 0 msec from key press onset), casts a shadow on the interpretation of the main result. Currently, it is unclear whether the decoding results simply reflect behavioral change or true underlying neural change. As shown in the behavioral data, the key press speed reached 3~4 presses per second already at around the end of the early learning period (11th trial), which means inter-press intervals become as short as 250-330 msec. Thus, in almost more than 60% of training period data, the time window for MEG feature extraction (200 msec) spans around 60% of the inter-press intervals. Considering that the preparation/cueing of subsequent presses starts ahead of the actual press (e.g., Kornysheva et al., 2019) and/or potential online planning (e.g., Ariani and Diedrichsen, 2019), the decoder likely has captured these future press information as well as the signal related to the current key press, independent of the formation of genuine sequential representation (e.g., "contextualization" of individual press). This may also explain the gradual increase in decoding accuracy or pattern distance between index_OP1 vs. index_OP5 (Figure 4C and 5A), which co-occurred with performance improvement, as shorter inter-press intervals are more favorable for the dissociating the two index finger presses followed by different finger presses. The compromised decoding accuracies for the control sequences can be explained in similar logic. Therefore, more careful consideration and elaborated discussion seem necessary when trying to both achieve high-performance decoding and assess early skill learning, as it can impact all the subsequent analyses.

      The Reviewer raises the possibility that (given the windowing parameters used in the present study) an increase in “contextualization” with learning could simply reflect faster typing speeds as opposed to an actual change in the underlying neural representation.

      We now include a new control analysis that addresses this issue as well as additional re-examination of previously reported results with respect to this issue – all of which are inconsistent with this alternative explanation that “contextualization” reflects a change in mixing of keypress related MEG features as opposed to a change in the underlying representations themselves. As correct sequences are generated at higher and higher speeds over training, MEG activity patterns related to the planning, execution, evaluation and memory of individual keypresses overlap more in time. Thus, increased overlap between the “4” and “1” keypresses (at the start of the sequence) and “2” and “4” keypresses (at the end of the sequence) could artefactually increase contextualization distances even if the underlying neural representations for the individual keypresses remain unchanged. One must also keep in mind that since participants repeat the sequence multiple times within the same trial, a majority of the index finger keypresses are performed adjacent to one another (i.e. - the “4-4” transition marking the end of one sequence and the beginning of the next). Thus, increased overlap between consecutive index finger keypresses as typing speed increased should increase their similarity and mask contextualization related changes to the underlying neural representations.

      We addressed this question by conducting a new multivariate regression analysis to directly assess whether the neural representation distance score could be predicted by the 4-1, 2-4 and 4-4 keypress transition times observed for each complete correct sequence (both predictor and response variables were z-score normalized within-subject). The results of this analysis also affirmed that the possible alternative explanation that contextualization effects are simple reflections of increased mixing is not supported by the data (Adjusted R<sup>2</sup> = 0.00431; F = 5.62). We now include this new negative control analysis in the revised manuscript.

      We also re-examined our previously reported classification results with respect to this issue. We reasoned that if mixing effects reflecting the ordinal sequence structure is an important driver of the contextualization finding, these effects should be observable in the distribution of decoder misclassifications. For example, “4” keypresses would be more likely to be misclassified as “1” or “2” keypresses (or vice versa) than as “3” keypresses. The confusion matrices presented in Figures 3C and 4B and Figure 3—figure supplement 3A display a distribution of misclassifications that is inconsistent with an alternative mixing effect explanation of contextualization.

      Based upon the increased overlap between adjacent index finger keypresses (i.e. – “4-4” transition), we also reasoned that the decoder tasked with separating individual index finger keypresses into two distinct classes based upon sequence position, should show decreased performance as typing speed increases. However, Figure 4C in our manuscript shows that this is not the case. The 2-class hybrid classifier actually displays improved classification performance over early practice trials despite greater temporal overlap. Again, this is inconsistent with the idea that the contextualization effect simply reflects increased mixing of individual keypress features.

      In summary, both re-examination of previously reported data and new control analyses all converged on the idea that the proximity between keypresses does not explain contextualization.

      We do agree with the Reviewer that the naturalistic, generative, self-paced task employed in the present study results in overlapping brain processes related to planning, execution, evaluation and memory of the action sequence. We also agree that there are several tradeoffs to consider in the construction of the classifiers depending on the study aim. Given our aim of optimizing keypress decoder accuracy in the present study, the set of trade-offs resulted in representations reflecting more the latter three processes, and less so the planning component. Whether separate decoders can be constructed to tease apart the representations or networks supporting these overlapping processes is an important future direction of research in this area. For example, work presently underway in our lab constrains the selection of windowing parameters in a manner that allows individual classifiers to be temporally linked to specific planning, execution, evaluation or memory-related processes to discern which brain networks are involved and how they adaptively reorganize with learning. Results from the present study (Figure 4—figure supplement 2) showing hybrid-space decoder prediction accuracies exceeding 74% for temporal windows spanning as little as 25ms and located up to 100ms prior to the KeyDown event strongly support the feasibility of such an approach.

      Related to the above point, testing only one particular sequence (4-1-3-2-4), aside from the control ones, limits the generalizability of the finding. This also may have contributed to the extremely high decoding accuracy reported in the current study.

      The Reviewer raises a question about the generalizability of the decoder accuracy reported in our study. Fortunately, a comparison between decoder performances on Day 1 and Day 2 datasets does provide insight into this issue. As the Reviewer points out, the classifiers in this study were trained and tested on keypresses performed while practicing a specific sequence (4-1-3-2-4). The study was designed this way as to avoid the impact of interference effects on learning dynamics. The cross-validated performance of classifiers on MEG data collected within the same session was 90.47% overall accuracy (4-class; Figure 3C). We then tested classifier performance on data collected during a separate MEG session conducted approximately 24 hours later (Day 2; see Figure 3 — figure supplement 3). We observed a reduction in overall accuracy rate to 87.11% when tested on MEG data recorded while participants performed the same learned sequence, and 79.44% when they performed several previously unpracticed sequences. Both changes in accuracy are important with regards to the generalizability of our findings. First, 87.11% performance accuracy for the trained sequence data on Day 2 (a reduction of only 3.36%) indicates that the hybrid-space decoder performance is robust over multiple MEG sessions, and thus, robust to variations in SNR across the MEG sensor array caused by small differences in head position between scans. This indicates a substantial advantage over sensor-space decoding approaches. Furthermore, when tested on data from unpracticed sequences, overall performance dropped an additional 7.67%. This difference reflects the performance bias of the classifier for the trained sequence, possibly caused by high-order sequence structure being incorporated into the feature weights. In the future, it will be important to understand in more detail how random or repeated keypress sequence training data impacts overall decoder performance and generalization. We strongly agree with the Reviewer that the issue of generalizability is extremely important and have added a new paragraph to the Discussion in the revised manuscript highlighting the strengths and weaknesses of our study with respect to this issue.

      In terms of clinical BCI, one of the potential relevance of the study, as claimed by the authors, it is not clear that the specific time window chosen in the current study (up to 200 msec since key press onset) is really useful. In most cases, clinical BCI would target neural signals with no overt movement execution due to patients' inability to move (e.g., Hochberg et al., 2012). Given the time window, the surprisingly high performance of the current decoder may result from sensory feedback and/or planning of subsequent movement, which may not always be available in the clinical BCI context. Of course, the decoding accuracy is still much higher than chance even when using signal before the key press (as shown in Figure 4 Supplement 2), but it is not immediately clear to me that the authors relate their high decoding accuracy based on post-movement signal to clinical BCI settings.

      The Reviewer questions the relevance of the specific window parameters used in the present study for clinical BCI applications, particularly for paretic patients who are unable to produce finger movements or for whom afferent sensory feedback is no longer intact. We strongly agree with the Reviewer that any intended clinical application must carefully consider the specific input feature constraints dictated by the clinical cohort, and in turn impose appropriate and complimentary constraints on classifier parameters that may differ from the ones used in the present study. We now highlight this issue in the Discussion of the revised manuscript and relate our present findings to published clinical BCI work within this context.

      One of the important and fascinating claims of the current study is that the "contextualization" of individual finger movements in a trained sequence specifically occurs during short rest periods in very early skill learning, echoing the recent theory of micro-offline learning proposed by the authors' group. Here, I think two points need to be clarified. First, the concept of "contextualization" is kept somewhat blurry throughout the text. It is only at the later part of the Discussion (around line #330 on page 13) that some potential mechanism for the "contextualization" is provided as "what-and-where" binding. Still, it is unclear what "contextualization" actually is in the current data, as the MEG signal analyzed is extracted from 0-200 msec after the keypress. If one thinks something is contextualizing an action, that contextualization should come earlier than the action itself.

      The Reviewer requests that we: 1) more clearly define our use of the term “contextualization” and 2) provide the rationale for assessing it over a 200ms window aligned to the KeyDown event. This choice of window parameters means that the MEG activity used in our analysis was coincident with, rather than preceding, the actual keypresses. We define contextualization as the differentiation of representation for the identical movement embedded in different positions of a sequential skill. That is, representations of individual action elements progressively incorporate information about their relationship to the overall sequence structure as the skill is learned. We agree with the Reviewer that this can be appropriately interpreted as “what-and-where” binding. We now incorporate this definition in the Introduction of the revised manuscript as requested.

      The window parameters for optimizing accurate decoding individual finger movements were determined using a grid search of the parameter space (a sliding window of variable width between 25-350 ms with 25 ms increments variably aligned from 0 to +100ms with 10ms increments relative to the KeyDown event). This approach generated 140 different temporal windows for each keypress for each participant, with the final parameter selection determined through comparison of the resulting performance between each decoder. Importantly, the decision to optimize for decoding accuracy placed an emphasis on keypress representations characterized by the most consistent and robust features shared across subjects, which in turn maximize statistical power in detecting common learning-related changes. In this case, the optimal window encompassed a 200ms epoch aligned to the KeyDown event (t<sub>0</sub> = 0 ms). We then asked if the representations (i.e. – spatial patterns of combined parcel- and voxel-space activity) of the same digit at two different sequence positions changed with practice within this optimal decoding window. Of course, our findings do not rule out the possibility that contextualization can also be found before or even after this time window, as we did not directly address this issue in the present study. Future work in our lab, as pointed out above, are investigating contextualization within different time windows tailored specifically for assessing sequence skill action planning, execution, evaluation and memory processes.

      The second point is that the result provided by the authors is not yet convincing enough to support the claim that "contextualization" occurs during rest. In the original analysis, the authors presented the statistical significance regarding the correlation between the "offline" pattern differentiation and micro-offline skill gain (Figure 5. Supplement 1), as well as the larger "offline" distance than "online" distance (Figure 5B). However, this analysis looks like regressing two variables (monotonically) increasing as a function of the trial. Although some information in this analysis, such as what the independent/dependent variables were or how individual subjects were treated, was missing in the Methods, getting a statistically significant slope seems unsurprising in such a situation. Also, curiously, the same quantitative evidence was not provided for its "online" counterpart, and the authors only briefly mentioned in the text that there was no significant correlation between them. It may be true looking at the data in Figure 5A as the online representation distance looks less monotonically changing, but the classification accuracy presented in Figure 4C, which should reflect similar representational distance, shows a more monotonic increase up to the 11th trial. Further, the ways the "online" and "offline" representation distance was estimated seem to make them not directly comparable. While the "online" distance was computed using all the correct press data within each 10 sec of execution, the "offline" distance is basically computed by only two presses (i.e., the last index_OP5 vs. the first index_OP1 separated by 10 sec of rest). Theoretically, the distance between the neural activity patterns for temporally closer events tends to be closer than that between the patterns for temporally far-apart events. It would be fairer to use the distance between the first index_OP1 vs. the last index_OP5 within an execution period for "online" distance, as well.

      The Reviewer suggests that the current data is not enough to show that contextualization occurs during rest and raises two important concerns: 1) the relationship between online contextualization and micro-online gains is not shown, and 2) the online distance was calculated differently from its offline counterpart (i.e. - instead of calculating the distance between last Index<sub>OP5</sub> and first Index<sub>OP1</sub> from a single trial, the distance was calculated for each sequence within a trial and then averaged).

      We addressed the first concern by performing individual subject correlations between 1) contextualization changes during rest intervals and micro-offline gains; 2) contextualization changes during practice trials and micro-online gains, and 3) contextualization changes during practice trials and micro-offline gains (Figure 5 – figure supplement 4). We then statistically compared the resulting correlation coefficient distributions and found that within-subject correlations for contextualization changes during rest intervals and micro-offline gains were significantly higher than online contextualization and micro-online gains (t = 3.2827, p = 0.0015) and online contextualization and micro-offline gains (t = 3.7021, p = 5.3013e-04). These results are consistent with our interpretation that micro-offline gains are supported by contextualization changes during the inter-practice rest periods.

      With respect to the second concern, we agree with the Reviewer that one limitation of the analysis comparing online versus offline changes in contextualization as presented in the original manuscript, is that it does not eliminate the possibility that any differences could simply be explained by the passage of time (which is smaller for the online analysis compared to the offline analysis). The Reviewer suggests an approach that addresses this issue, which we have now carried out. When quantifying online changes in contextualization from the first Index<sub>OP1</sub> the last Index<sub>OP5</sub> keypress in the same trial we observed no learning-related trend (Figure 5 – figure supplement 5, right panel). Importantly, offline distances were significantly larger than online distances regardless of the measurement approach and neither predicted online learning (Figure 5 – figure supplement 6).

      A related concern regarding the control analysis, where individual values for max speed and the degree of online contextualization were compared (Figure 5 Supplement 3), is whether the individual difference is meaningful. If I understood correctly, the optimization of the decoding process (temporal window, feature inclusion/reduction, decoder, etc.) was performed for individual participants, and the same feature extraction was also employed for the analysis of representation distance (i.e., contextualization). If this is the case, the distances are individually differently calculated and they may need to be normalized relative to some stable reference (e.g., 1 vs. 4 or average distance within the control sequence presses) before comparison across the individuals.

      The Reviewer makes a good point here. We have now implemented the suggested normalization procedure in the analysis provided in the revised manuscript.

      Reviewer #3 (Public review):

      Summary:

      One goal of this paper is to introduce a new approach for highly accurate decoding of finger movements from human magnetoencephalography data via dimension reduction of a "multiscale, hybrid" feature space. Following this decoding approach, the authors aim to show that early skill learning involves "contextualization" of the neural coding of individual movements, relative to their position in a sequence of consecutive movements. Furthermore, they aim to show that this "contextualization" develops primarily during short rest periods interspersed with skill training and correlates with a performance metric which the authors interpret as an indicator of offline learning.

      Strengths:

      A clear strength of the paper is the innovative decoding approach, which achieves impressive decoding accuracies via dimension reduction of a "multi-scale, hybrid space". This hybrid-space approach follows the neurobiologically plausible idea of the concurrent distribution of neural coding across local circuits as well as large-scale networks. A further strength of the study is the large number of tested dimension reduction techniques and classifiers (though the manuscript reveals little about the comparison of the latter).

      We appreciate the Reviewer’s comments regarding the paper’s strengths.

      A simple control analysis based on shuffled class labels could lend further support to this complex decoding approach. As a control analysis that completely rules out any source of overfitting, the authors could test the decoder after shuffling class labels. Following such shuffling, decoding accuracies should drop to chance level for all decoding approaches, including the optimized decoder. This would also provide an estimate of actual chance-level performance (which is informative over and beyond the theoretical chance level). Furthermore, currently, the manuscript does not explain the huge drop in decoding accuracies for the voxel-space decoding (Figure 3B). Finally, the authors' approach to cortical parcellation raises questions regarding the information carried by varying dipole orientations within a parcel (which currently seems to be ignored?) and the implementation of the mean-flipping method (given that there are two dimensions - space and time - what do the authors refer to when they talk about the sign of the "average source", line 477?).

      The Reviewer recommends that we: 1) conduct an additional control analysis on classifier performance using shuffled class labels, 2) provide a more detailed explanation regarding the drop in decoding accuracies for the voxel-space decoding following LDA dimensionality reduction (see Fig 3B), and 3) provide additional details on how problems related to dipole solution orientations were addressed in the present study.

      In relation to the first point, we have now implemented a random shuffling approach as a control for the classification analyses. The results of this analysis indicated that the chance level accuracy was 22.12% (± SD 9.1%) for individual keypress decoding (4-class classification), and 18.41% (± SD 7.4%) for individual sequence item decoding (5-class classification), irrespective of the input feature set or the type of decoder used. Thus, the decoding accuracy observed with the final model was substantially higher than these chance levels.

      Second, please note that the dimensionality of the voxel-space feature set is very high (i.e. – 15684). LDA attempts to map the input features onto a much smaller dimensional space (number of classes – 1; e.g. – 3 dimensions, for 4-class keypress decoding). Given the very high dimension of the voxel-space input features in this case, the resulting mapping exhibits reduced accuracy. Despite this general consideration, please refer to Figure 3—figure supplement 3, where we observe improvement in voxel-space decoder performance when utilizing alternative dimensionality reduction techniques.

      The decoders constructed in the present study assess the average spatial patterns across time (as defined by the windowing procedure) in the input feature space. We now provide additional details in the Methods of the revised manuscript pertaining to the parcellation procedure and how the sign ambiguity problem was addressed in our analysis.

      Weaknesses:

      A clear weakness of the paper lies in the authors' conclusions regarding "contextualization". Several potential confounds, described below, question the neurobiological implications proposed by the authors and provide a simpler explanation of the results. Furthermore, the paper follows the assumption that short breaks result in offline skill learning, while recent evidence, described below, casts doubt on this assumption.

      We thank the Reviewer for giving us the opportunity to address these issues in detail (see below).

      The authors interpret the ordinal position information captured by their decoding approach as a reflection of neural coding dedicated to the local context of a movement (Figure 4). One way to dissociate ordinal position information from information about the moving effectors is to train a classifier on one sequence and test the classifier on other sequences that require the same movements, but in different positions (Kornysheva et al., 2019). In the present study, however, participants trained to repeat a single sequence (4-1-3-2-4). As a result, ordinal position information is potentially confounded by the fixed finger transitions around each of the two critical positions (first and fifth press). Across consecutive correct sequences, the first keypress in a given sequence was always preceded by a movement of the index finger (=last movement of the preceding sequence), and followed by a little finger movement. The last keypress, on the other hand, was always preceded by a ring finger movement, and followed by an index finger movement (=first movement of the next sequence). Figure 4 - Supplement 2 shows that finger identity can be decoded with high accuracy (>70%) across a large time window around the time of the key press, up to at least +/-100 ms (and likely beyond, given that decoding accuracy is still high at the boundaries of the window depicted in that figure). This time window approaches the keypress transition times in this study. Given that distinct finger transitions characterized the first and fifth keypress, the classifier could thus rely on persistent (or "lingering") information from the preceding finger movement, and/or "preparatory" information about the subsequent finger movement, in order to dissociate the first and fifth keypress. Currently, the manuscript provides no evidence that the context information captured by the decoding approach is more than a by-product of temporally extended, and therefore overlapping, but independent neural representations of consecutive keypresses that are executed in close temporal proximity - rather than a neural representation dedicated to context.

      Such temporal overlap of consecutive, independent finger representations may also account for the dynamics of "ordinal coding"/"contextualization", i.e., the increase in 2-class decoding accuracy, across Day 1 (Figure 4C). As learning progresses, both tapping speed and the consistency of keypress transition times increase (Figure 1), i.e., consecutive keypresses are closer in time, and more consistently so. As a result, information related to a given keypress is increasingly overlapping in time with information related to the preceding and subsequent keypresses. The authors seem to argue that their regression analysis in Figure 5 - Figure Supplement 3 speaks against any influence of tapping speed on "ordinal coding" (even though that argument is not made explicitly in the manuscript). However, Figure 5 - Figure Supplement 3 shows inter-individual differences in a between-subject analysis (across trials, as in panel A, or separately for each trial, as in panel B), and, therefore, says little about the within-subject dynamics of "ordinal coding" across the experiment. A regression of trial-by-trial "ordinal coding" on trial-by-trial tapping speed (either within-subject or at a group-level, after averaging across subjects) could address this issue. Given the highly similar dynamics of "ordinal coding" on the one hand (Figure 4C), and tapping speed on the other hand (Figure 1B), I would expect a strong relationship between the two in the suggested within-subject (or group-level) regression. Furthermore, learning should increase the number of (consecutively) correct sequences, and, thus, the consistency of finger transitions. Therefore, the increase in 2-class decoding accuracy may simply reflect an increasing overlap in time of increasingly consistent information from consecutive keypresses, which allows the classifier to dissociate the first and fifth keypress more reliably as learning progresses, simply based on the characteristic finger transitions associated with each. In other words, given that the physical context of a given keypress changes as learning progresses - keypresses move closer together in time and are more consistently correct - it seems problematic to conclude that the mental representation of that context changes. To draw that conclusion, the physical context should remain stable (or any changes to the physical context should be controlled for).

      The issues raised by Reviewer #3 here are similar to two issues raised by Reviewer #2 above. We agree they must both be carefully considered in any evaluation of our findings.

      As both Reviewers pointed out, the classifiers in this study were trained and tested on keypresses performed while practicing a specific sequence (4-1-3-2-4). The study was designed this way as to avoid the impact of interference effects on learning dynamics. The cross-validated performance of classifiers on MEG data collected within the same session was 90.47% overall accuracy (4class; Figure 3C). We then tested classifier performance on data collected during a separate MEG session conducted approximately 24 hours later (Day 2; see Figure 3—supplement 3). We observed a reduction in overall accuracy rate to 87.11% when tested on MEG data recorded while participants performed the same learned sequence, and 79.44% when they performed several previously unpracticed sequences. This classification performance difference of 7.67% when tested on the Day 2 data could reflect the performance bias of the classifier for the trained sequence, possibly caused by mixed information from temporally close keypresses being incorporated into the feature weights.

      Along these same lines, both Reviewers also raise the possibility that an increase in “ordinal coding/contextualization” with learning could simply reflect an increase in this mixing effect caused by faster typing speeds as opposed to an actual change in the underlying neural representation. The basic idea is that as correct sequences are generated at higher and higher speeds over training, MEG activity patterns related to the planning, execution, evaluation and memory of individual keypresses overlap more in time. Thus, increased overlap between the “4” and “1” keypresses (at the start of the sequence) and “2” and “4” keypresses (at the end of the sequence) could artefactually increase contextualization distances even if the underlying neural representations for the individual keypresses remain unchanged (assuming this mixing of representations is used by the classifier to differentially tag each index finger press). If this were the case, it follows that such mixing effects reflecting the ordinal sequence structure would also be observable in the distribution of decoder misclassifications. For example, “4” keypresses would be more likely to be misclassified as “1” or “2” keypresses (or vice versa) than as “3” keypresses. The confusion matrices presented in Figures 3C and 4B and Figure 3—figure supplement 3A in the previously submitted manuscript do not show this trend in the distribution of misclassifications across the four fingers.

      Following this logic, it’s also possible that if the ordinal coding is largely driven by this mixing effect, the increased overlap between consecutive index finger keypresses during the 4-4 transition marking the end of one sequence and the beginning of the next one could actually mask contextualization-related changes to the underlying neural representations and make them harder to detect. In this case, a decoder tasked with separating individual index finger keypresses into two distinct classes based upon sequence position might show decreased performance with learning as adjacent keypresses overlapped in time with each other to an increasing extent. However, Figure 4C in our previously submitted manuscript does not support this possibility, as the 2-class hybrid classifier displays improved classification performance over early practice trials despite greater temporal overlap.

      As noted in the above reply to Reviewer #2, we also conducted a new multivariate regression analysis to directly assess whether the neural representation distance score could be predicted by the 4-1, 2-4 and 4-4 keypress transition times observed for each complete correct sequence (both predictor and response variables were z-score normalized within-subject). The results of this analysis affirmed that the possible alternative explanation put forward by the Reviewer is not supported by our data (Adjusted R<sup>2</sup> = 0.00431; F = 5.62). We now include this new negative control analysis result in the revised manuscript.

      Finally, the Reviewer hints that one way to address this issue would be to compare MEG responses before and after learning for sequences typed at a fixed speed. However, given that the speed-accuracy trade-off should improve with learning, a comparison between unlearned and learned skill states would dictate that the skill be evaluated at a very low fixed speed. Essentially, such a design presents the problem that the post-training test is evaluating the representation in the unlearned behavioral state that is not representative of the acquired skill. Thus, this approach would miss most learning effects on a task in which speed is the main learning metrics.

      A similar difference in physical context may explain why neural representation distances ("differentiation") differ between rest and practice (Figure 5). The authors define "offline differentiation" by comparing the hybrid space features of the last index finger movement of a trial (ordinal position 5) and the first index finger movement of the next trial (ordinal position 1). However, the latter is not only the first movement in the sequence but also the very first movement in that trial (at least in trials that started with a correct sequence), i.e., not preceded by any recent movement. In contrast, the last index finger of the last correct sequence in the preceding trial includes the characteristic finger transition from the fourth to the fifth movement. Thus, there is more overlapping information arising from the consistent, neighbouring keypresses for the last index finger movement, compared to the first index finger movement of the next trial. A strong difference (larger neural representation distance) between these two movements is, therefore, not surprising, given the task design, and this difference is also expected to increase with learning, given the increase in tapping speed, and the consequent stronger overlap in representations for consecutive keypresses. Furthermore, initiating a new sequence involves pre-planning, while ongoing practice relies on online planning (Ariani et al., eNeuro 2021), i.e., two mental operations that are dissociable at the level of neural representation (Ariani et al., bioRxiv 2023).

      The Reviewer argues that the comparison of last finger movement of a trial and the first in the next trial are performed in different circumstances and contexts. This is an important point and one we tend to agree with. For this task, the first sequence in a practice trial is pre-planned before the first keypress is performed. This occurs in a somewhat different context from the sequence iterations that follow, which involve temporally overlapping planning, execution and evaluation processes. The Reviewer is concerned about a difference in the temporal mixing effect issue raised above between the first and last keypresses performed in a trial. Please, note that since neural representations of individual actions are competitively queued during the pre-planning period in a manner that reflects the ordinal structure of the learned sequence (Kornysheva et al., 2019), mixing effects are most likely present also for the first keypress in a trial.

      Separately, the Reviewer suggests that contextualization during early learning may reflect preplanning or online planning. This is an interesting proposal. Given the decoding time-window used in this investigation, we cannot dissect separate contributions of planning, memory and sensory feedback to contextualization. Taking advantage of the superior temporal resolution of MEG relative to fMRI tools, work under way in our lab is investigating decoding time-windows more appropriate to address each of these questions.

      Given these differences in the physical context and associated mental processes, it is not surprising that "offline differentiation", as defined here, is more pronounced than "online differentiation". For the latter, the authors compared movements that were better matched regarding the presence of consistent preceding and subsequent keypresses (online differentiation was defined as the mean difference between all first vs. last index finger movements during practice). It is unclear why the authors did not follow a similar definition for "online differentiation" as for "micro-online gains" (and, indeed, a definition that is more consistent with their definition of "offline differentiation"), i.e., the difference between the first index finger movement of the first correct sequence during practice, and the last index finger of the last correct sequence. While these two movements are, again, not matched for the presence of neighbouring keypresses (see the argument above), this mismatch would at least be the same across "offline differentiation" and "online differentiation", so they would be more comparable.

      This is the same point made earlier by Reviewer #2, and we agree with this assessment. As stated in the response to Reviewer #2 above, we have now carried out quantification of online contextualization using this approach and included it in the revised manuscript. We thank the Reviewer for this suggestion.

      A further complication in interpreting the results regarding "contextualization" stems from the visual feedback that participants received during the task. Each keypress generated an asterisk shown above the string on the screen, irrespective of whether the keypress was correct or incorrect. As a result, incorrect (e.g., additional, or missing) keypresses could shift the phase of the visual feedback string (of asterisks) relative to the ordinal position of the current movement in the sequence (e.g., the fifth movement in the sequence could coincide with the presentation of any asterisk in the string, from the first to the fifth). Given that more incorrect keypresses are expected at the start of the experiment, compared to later stages, the consistency in visual feedback position, relative to the ordinal position of the movement in the sequence, increased across the experiment. A better differentiation between the first and the fifth movement with learning could, therefore, simply reflect better decoding of the more consistent visual feedback, based either on the feedback-induced brain response, or feedback-induced eye movements (the study did not include eye tracking). It is not clear why the authors introduced this complicated visual feedback in their task, besides consistency with their previous studies.

      We strongly agree with the Reviewer that eye movements related to task engagement are important to rule out as a potential driver of the decoding accuracy or contextualizaton effect. We address this issue above in response to a question raised by Reviewer #1 about the impact of movement related artefacts on our findings.

      First, the assumption the Reviewer makes here about the distribution of errors in this task is incorrect. On average across subjects, 2.32% ± 1.48% (mean ± SD) of all keypresses performed were errors, which were evenly distributed across the four possible keypress responses. While errors increased progressively over practice trials, they did so in proportion to the increase in correct keypresses, so that the overall ratio of correct-to-incorrect keypresses remained stable over the training session. Thus, the Reviewer’s assumptions that there is a higher relative frequency of errors in early trials, and a resulting systematic trend phase shift differences between the visual display updates (i.e. – a change in asterisk position above the displayed sequence) and the keypress performed is not substantiated by the data. To the contrary, the asterisk position on the display and the keypress being executed remained highly correlated over the entire training session. We now include a statement about the frequency and distribution of errors in the revised manuscript.

      Given this high correlation, we firmly agree with the Reviewer that the issue of eye movement related artefacts is still an important one to address. Fortunately, we did collect eye movement data during the MEG recordings so were able to investigate this. As detailed in the response to Reviewer #1 above, we found that gaze positions and eye-movement velocity time-locked to visual display updates (i.e. – a change in asterisk position above the displayed sequence) did not reflect the asterisk location above chance levels (Overall cross-validated accuracy = 0.21817; see Author response image 1). Furthermore, an inspection of the eye position data revealed that most participants on most trials displayed random walk gaze patterns around a center fixation point, indicating that participants did not attend to the asterisk position on the display. This is consistent with intrinsic generation of the action sequence, and congruent with the fact that the display does not provide explicit feedback related to performance. As pointed out above, a similar real-world example would be manually inputting a long password into a secure online application. In this case, one intrinsically generates the sequence from memory and receives similar feedback about the password sequence position (also provided as asterisks), which is typically ignored by the user.

      The minimal participant engagement with the visual display in this explicit sequence learning motor task (which is highly generative in nature) contrasts markedly with behavior observed when reactive responses to stimulus cues are needed in the serial reaction time task (SRTT). This is a crucial difference that must be carefully considered when comparing findings across studies using the two sequence learning tasks.

      The authors report a significant correlation between "offline differentiation" and cumulative microoffline gains. However, it would be more informative to correlate trial-by-trial changes in each of the two variables. This would address the question of whether there is a trial-by-trial relation between the degree of "contextualization" and the amount of micro-offline gains - are performance changes (micro-offline gains) less pronounced across rest periods for which the change in "contextualization" is relatively low? Furthermore, is the relationship between micro-offline gains and "offline differentiation" significantly stronger than the relationship between micro-offline gains and "online differentiation"?

      In response to a similar issue raised above by Reviewer #2, we now include new analyses comparing correlation magnitudes between (1) “online differentiation” vs micro-online gains, (2) “online differentiation” vs micro-offline gains and (3) “offline differentiation” and micro-offline gains (see Figure 5 – figure supplement  4, 5 and 6). These new analyses and results have been added to the revised manuscript. Once again, we thank both Reviewers for this suggestion.

      The authors follow the assumption that micro-offline gains reflect offline learning.

      We disagree with this statement. The original (Bonstrup et al., 2019) paper clearly states that micro-offline gains do not necessarily reflect offline learning in some cases and must be carefully interpreted based upon the behavioral context within which they are observed. Further, the paper lays out the conditions under which one can have confidence that micro-offline gains reflect offline learning. In fact, the excellent meta-analysis of (Pan & Rickard, 2015), which re-interprets the benefits of sleep in overnight skill consolidation from a “reactive inhibition” perspective, was a crucial resource in the experimental design of our initial study (Bonstrup et al., 2019), as well as in all our subsequent work. Pan & Rickard state:

      “Empirically, reactive inhibition refers to performance worsening that can accumulate during a period of continuous training (Hull, 1943 . It tends to dissipate, at least in part, when brief breaks are inserted between blocks of training. If there are multiple performance-break cycles over a training session, as in the motor sequence literature, performance can exhibit a scalloped effect, worsening during each uninterrupted performance block but improving across blocks(Brawn et al., 2010; Rickard et al., 2008 . Rickard, Cai, Rieth, Jones, and Ard (2008 and Brawn, Fenn, Nusbaum, and Margoliash (2010 (Brawn et al., 2010; Rickard et al., 2008 demonstrated highly robust scalloped reactive inhibition effects using the commonly employed 30 s–30 s performance break cycle, as shown for Rickard et al.’s (2008 massed practice sleep group in Figure 2. The scalloped effect is evident for that group after the first few 30 s blocks of each session. The absence of the scalloped effect during the first few blocks of training in the massed group suggests that rapid learning during that period masks any reactive inhibition effect.”

      Crucially, Pan & Rickard make several concrete recommendations for reducing the impact of the reactive inhibition confound on offline learning studies. One of these recommendations was to reduce practice times to 10s (most prior sequence learning studies up until that point had employed 30s long practice trials). They state:

      “The traditional design involving 30 s-30 s performance break cycles should be abandoned given the evidence that it results in a reactive inhibition confound, and alternative designs with reduced performance duration per block used instead (Pan & Rickard, 2015 . One promising possibility is to switch to 10 s performance durations for each performance-break cycle Instead (Pan & Rickard, 2015 . That design appears sufficient to eliminate at least the majority of the reactive inhibition effect (Brawn et al., 2010; Rickard et al., 2008 .”

      We mindfully incorporated recommendations from (Pan & Rickard, 2015) into our own study designs including 1) utilizing 10s practice trials and 2) constraining our analysis of micro-offline gains to early learning trials (where performance monotonically increases and 95% of overall performance gains occur), which are prior to the emergence of the “scalloped” performance dynamics that are strongly linked to reactive inhibition effects.

      However, there is no direct evidence in the literature that micro-offline gains really result from offline learning, i.e., an improvement in skill level.

      We strongly disagree with the Reviewer’s assertion that “there is no direct evidence in the literature that micro-offline gains really result from offline learning, i.e., an improvement in skill level.” The initial (Bonstrup et al., 2019) report was followed up by a large online crowd-sourcing study (Bonstrup et al., 2020). This second (and much larger) study provided several additional important findings supporting our interpretation of micro-offline gains in cases where the important behavioral conditions clarified above were met (see Author response image 4 below for further details on these conditions).

      Author response image 4.

      This Figure shows that micro-offline gains o ser ed in learning and nonlearning contexts are attri uted to different underl ing causes. Micro-offline and online changes relative to overall trial-by-trial learning. This figure is based on data from (Bonstrup et al., 2019). During early learning, micro-offline gains (red bars) closely track trial-by-trial performance gains (green line with open circle markers), with minimal contribution from micro-online gains (blue bars). The stated conclusion in Bönstrup et al. (2019) is that micro-offline gains only during this Early Learning stage reflect rapid memory consolidation (see also (Bonstrup et al., 2020)). After early learning, about practice trial 11, skill plateaus. This plateau skill period is characterized by a striking emergence of coupled (and relatively stable) micro-online drops and micro-offline increases. Bönstrup et al. (2019) as well as others in the literature (Brooks et al., 2024; Gupta & Rickard, 2022; Florencia Jacobacci et al., 2020), argue that micro-offline gains during the plateau period likely reflect recovery from inhibitory performance factors such as reactive inhibition or fatigue, and thus must be excluded from analyses relating micro-offline gains to skill learning. The Non-repeating groups in Experiments 3 and 4 from Das et al. (2024) suffer from a lack of consideration of these known confounds (end of Fig legend).

      Evidence documented in that paper (Bonstrup et al., 2020) showed that micro-offline gains during early skill learning were: 1) replicable and generalized to subjects learning the task in their daily living environment (n=389); 2) equivalent when significantly shortening practice period duration, thus confirming that they are not a result of recovery from performance fatigue (n=118); 3) reduced (along with learning rates) by retroactive interference applied immediately after each practice period relative to interference applied after passage of time (n=373), indicating stabilization of the motor memory at a microscale of several seconds consistent with rapid consolidation; and 4) not modified by random termination of the practice periods, ruling out a contribution of predictive motor slowing (N = 71) (Bonstrup et al., 2020). Altogether, our findings were strongly consistent with the interpretation that micro-offline gains reflect memory consolidation supporting early skill learning. This is precisely the portion of the learning curve (Pan & Rickard, 2015) refer to when they state “…rapid learning during that period masks any reactive inhibition effect”.

      This interpretation is further supported by brain imaging evidence linking known memory-related networks and consolidation mechanisms to micro-offline gains. First, we reported that the density of fast hippocampo-neocortical skill memory replay events increases approximately three-fold during early learning inter-practice rest periods with the density explaining differences in the magnitude of micro-offline gains across subjects (Buch et al., 2021). Second, Jacobacci et al. (2020) independently reproduced our original behavioral findings and reported BOLD fMRI changes in the hippocampus and precuneus (regions also identified in our MEG study (Buch et al., 2021)) linked to micro-offline gains during early skill learning. These functional changes were coupled with rapid alterations in brain microstructure in the order of minutes, suggesting that the same network that operates during rest periods of early learning undergoes structural plasticity over several minutes following practice (Deleglise et al., 2023). Crucial to this point, Chen et al. (2024) and Sjøgård et al (2024) provided direct evidence from intracranial EEG in humans linking sharp-wave ripple density during rest periods (which are known markers for neural replay (Buzsaki, 2015)) in the human hippocampus (80-120 Hz) to micro-offline gains during early skill learning.

      Thus, there is now substantial converging evidence in humans across different indirect noninvasive and direct invasive recording techniques linking hippocampal activity, neural replay dynamics and offline performance gains in skill learning.

      On the contrary, recent evidence questions this interpretation (Gupta & Rickard, npj Sci Learn 2022; Gupta & Rickard, Sci Rep 2024; Das et al., bioRxiv 2024). Instead, there is evidence that micro-offline gains are transient performance benefits that emerge when participants train with breaks, compared to participants who train without breaks, however, these benefits vanish within seconds after training if both groups of participants perform under comparable conditions (Das et al., bioRxiv 2024).

      The recent work of (Gupta & Rickard, 2022, 2024) does not present any data that directly opposes our finding that early skill learning (Bonstrup et al., 2019) is expressed as micro-offline gains during rest breaks. These studies are an extension of the Rickard et al (2008) paper that employed a massed (30s practice followed by 30s breaks) vs spaced (10s practice followed by 10s breaks) experimental design to assess if recovery from reactive inhibition effects could account for performance gains measured after several minutes or hours. Gupta & Rickard (2022) added two additional groups (30s practice/10s break and 10s practice/10s break as used in the work from our group). The primary aim of the study was to assess whether it was more likely that changes in performance when retested 5 minutes after skill training (consisting of 12 practice trials for the massed groups and 36 practice trials for the spaced groups) had ended reflected memory consolidation effects or recovery from reactive inhibition effects. The Gupta & Rickard (2024) follow-up paper employed a similar design with the primary difference being that participants performed a fixed number of sequences on each trial as opposed to trials lasting a fixed duration. This was done to facilitate the fitting of a quantitative statistical model to the data.

      To reiterate, neither study included any analysis of micro-online or micro-offline gains and did not include any comparison focused on skill gains during early learning trials (only at retest 5 min later). Instead, Gupta & Rickard (2022), reported evidence for reactive inhibition effects for all groups over much longer training periods than early learning. In fact, we reported the same findings for trials following the early learning period in our original 2019 paper (Bonstrup et al., 2019) (Author response image 4). Please, note that we also reported that cumulative microoffline gains over early learning did not correlate with overnight offline consolidation measured 24 hours later (Bonstrup et al., 2019) (see the Results section and further elaboration in the Discussion). We interpreted these findings as indicative that the mechanisms underlying offline gains over the micro-scale of seconds during early skill learning versus over minutes or hours very likely differ.

      In the recent preprint from (Das et al., 2024), the authors make the strong claim that “micro-offline gains during early learning do not reflect offline learning” which is not supported by their own data. The authors hypothesize that if “micro-offline gains represent offline learning, participants should reach higher skill levels when training with breaks, compared to training without breaks”. The study utilizes a spaced vs. massed practice groups between-subjects design inspired by the reactive inhibition work from Rickard and others to test this hypothesis.

      Crucially, their design incorporates only a small fraction of the training used in other investigations to evaluate early skill learning (Bonstrup et al., 2020; Bonstrup et al., 2019; Brooks et al., 2024; Buch et al., 2021; Deleglise et al., 2023; F. Jacobacci et al., 2020; Mylonas et al., 2024). A direct comparison between the practice schedule designs for the spaced and massed groups in Das et al., and the training schedule all participants experienced in the original Bönstrup et al. (2019) paper highlights this issue as well as several others (Author response image 5):

      Author response image 5.

      This figure shows (A) Comparison of Das et al. Spaced & Massed group training session designs, and the training session design from the original (Bonstrup et al., 2019) paper. Similar to the approach taken by Das et al., all practice is visualized as 10-second practice trials with a variable number (either 0, 1 or 30) of 10-second-long inter-practice rest intervals to allow for direct comparisons between designs. The two key takeaways from this comparison are that (1) the intervention differences (i.e. – practice schedules) between the Massed and Spaced groups from the Das et al. report are extremely small (less than 12% of the overall session schedule) (gaps in the red shaded area) and (2) the overall amount of practice is much less than compared to the design from the original Bönstrup report (Bonstrup et al., 2019) (which has been utilized in several subsequent studies). (B) Group-level learning curve data from Bönstrup et al. (2019) (Bonstrup et al., 2019) is used to estimate the performance range accounted for by the equivalent periods covering Test 1, Training 1 and Test 2 from Das et al (2024). Note that the intervention in the Das et al. study is limited to a period covering less than 50% of the overall learning range (end of figure legend).

      Participants in the original (Bonstrup et al., 2019) experienced 157.14% more practice time and 46.97% less inter-practice rest time than the Spaced group in the Das et al. study (Author response image 5). Thus, the overall amount of practice and rest differ substantially between studies, with much more limited training occurring for participants in Das et al.

      In addition, the training interventions (i.e. – the practice schedule differences between the Spaced and Massed groups) were designed in a manner that minimized any chance of effectively testing their hypothesis. First, the interventions were applied over an extremely short period relative to the length of the total training session (5% and 12% of the total training session for Massed and Spaced groups, respectively; see gaps in the red shaded area in Author response image 5). Second, the intervention was applied during a period in which only half of the known total learning occurs. Specifically, we know from Bönstrup et al. (2019) that only 46.57% of the total performance gains occur in the practice interval covered by Das et al Training 1 intervention. Thus, early skill learning as evaluated by multiple groups (Bonstrup et al., 2020; Bonstrup et al., 2019; Brooks et al., 2024; Buch et al., 2021; Deleglise et al., 2023; F. Jacobacci et al., 2020; Mylonas et al., 2024), is in the Das et al experiment amputated to about half.

      Furthermore, a substantial amount of learning takes place during Das et al’s Test 1 and Test 2 periods (32.49% of total gains combined). The fact that substantial learning is known to occur over both the Test 1 (18.06%) and Test 2 (14.43%) intervals presents a fundamental problem described by Pan and Rickard (Pan & Rickard, 2015). They reported that averaging over intervals where substantial performance gains occur (i.e. – performance is not stable) inject crucial artefacts into analyses of skill learning:

      “A large amount of averaging has the advantage of yielding more precise estimates of each subject’s pretest and posttest scores and hence more statistical power to detect a performance gain. However, calculation of gain scores using that strategy runs the risk that learning that occurs during the pretest and (or posttest periods (i.e., online learning is incorporated into the gain score (Rickard et al., 2008; Robertson et al., 2004 .”

      The above statement indicates that the Test 1 and Test 2 performance scores from Das et al. (2024) are substantially contaminated by the learning rate within these intervals. This is particularly problematic if the intervention design results in different Test 2 learning rates between the two groups. This in fact, is apparent in their data (Figure 1C,E of the Das et al., 2024 preprint) as the Test 2 learning rate for the Spaced group is negative (indicating a unique interference effect observable only for this group). Specifically, the Massed group continues to show an increase in performance during Test 2 and 4 relative to the last 10 seconds of practice during Training 1 and 2, respectively, while the Spaced group displays a marked decrease. This post-training performance decrease for the Spaced group is in stark contrast to the monotonic performance increases observed for both groups at all other time-points. One possible cause could be related to the structure of the Test intervals, which include 20 seconds of uninterrupted practice. For the Spaced group, this effectively is a switch to a Massed practice environment (i.e., two 10-secondlong practice trials merged into one long trial), which interferes with greater Training 1 interval gains observed for the Space group. Interestingly, when statistical comparisons between the groups are made at the time-points when the intervention is present (Figure 1E) then the stated hypothesis, “If micro-offline gains represent offline learning, participants should reach higher skill levels when training with breaks, compared to training without breaks”, is confirmed.

      In summary, the experimental design and analyses used by Das et al does not contradict the view that early skill learning is expressed as micro-offline gains during rest breaks. The data presented by Gupta and Rickard (2022, 2024) and Das et al. (2024) is in many ways more confirmatory of the constraints employed by our group and others with respect to experimental design, analysis and interpretation of study findings, rather than contradictory. Still, it does highlight a limitation of the current micro-online/offline framework, which was originally only intended to be applied to early skill learning over spaced practice schedules when reactive inhibition effects are minimized (Bonstrup et al., 2019; Pan & Rickard, 2015). Extrapolation of this current framework to postplateau performance periods, longer timespans, or non-learning situations (e.g. – the Nonrepeating groups from Das et al. (2024)), when reactive inhibition plays a more substantive role, is not warranted. Ultimately, it will be important to develop new paradigms allowing one to independently estimate the different coincident or antagonistic features (e.g. - memory consolidation, planning, working memory and reactive inhibition) contributing to micro-online and micro-offline gains during and after early skill learning within a unifying framework.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) I found Figure 2B too small to be useful, as the actual elements of the cells are very hard to read.

      We have removed the grid colormap panel (top-right) from Figure 2B. All of this colormap data is actually a subset of data presented in Figure 2 – figure supplement 1, so can still be found there.

      Reviewer #2 (Recommendations for the authors):

      (1) Related to the first point in my concerns, I would suggest the authors compare decoding accuracy between correct presses followed by correct vs. incorrect presses. This would clarify if the decoder is actually taking the MEG signal for subsequent press into account. I would also suggest the authors use pre-movement MEG features and post-movement features with shorter windows and compare each result with the results for the original post-movement MEG feature with a longer window.

      The present study does not contain enough errors to perform the analysis proposed by the Reviewer. As noted above, we did re-examine our data and now report a new control regression analysis, all of which indicate that the proximity between keypresses does not explain contextualization effects.

      (2) I was several times confused by the author's use of "neural representation of an action" or "sequence action representations" in understanding whether these terms refer to representation on the level of whole-brain, region (as defined by the specific parcellation used), or voxels. In fact, what is submitted to the decoder is some complicated whole-brain MEG feature (i.e., the "neural representation"), which is a hybrid of voxel and parcel features that is further dimension-reduced and not immediately interpretable. Clarifying this point early in the text and possibly using some more sensible terms, such as adding "brain-wise" before the "sequence action representation", would be the most helpful for the readers.

      We now clarified this terminology in the revised manuscript.

      (3) Although comparing many different ways in feature selection/reduction, time window selection, and decoder types is undoubtedly a meticulous work, the current version of the manuscript seems still lacking some explanation about the details of these methodological choices, like which decoding method was actually used to report the accuracy, whether or not different decoding methods were chosen for individual participants' data, how training data was selected (is it all of the correct presses in Day 1 data?), whether the frequency power or signal amplitude was used, and so on. I would highly appreciate these additional details in the Methods section.

      The reported accuracies were based on linear discriminant analysis classifier. A comparison of different decoders (Figure 3 – figure supplement 4) shows LDA was the optimal choice.

      Whether or not different decoding methods were chosen for individual participants' data

      We selected the same decoder (LDA) performance to report the final accuracy.

      How training data was selected (is it all of the correct presses in Day 1 data?),

      Decoder training was conducted as a randomized split of the data (all correct keypresses of Day 1) into training (90%) and test (10%) samples for 8 iterations.

      Whether the frequency power or signal amplitude was used

      Signal amplitude was used for feature calculation.

      (4) In terms of the Methods, please consider adding some references about the 'F1 score', the 'feature importance score,' and the 'MRMR-based feature ranking,' as the main readers of the current paper would not be from the machine learning community. Also, why did the LDA dimensionality reduction reduce accuracy specifically for the voxel feature?

      We have now added the following statements to the Methods section that provide more detailed descriptions and references for these metrics:

      “The F1 score, defined as the harmonic mean of the precision (percentage of true predictions that are actually true positive) and recall (percentage of true positives that were correctly predicted as true) scores, was used as a comprehensive metric for all one-versus-all keypress state decoders to assess class-wise performance that accounts for both false-positive and false-negative prediction tendencies [REF]. A weighted mean F1 score was then computed across all classes to assess the overall prediction performance of the multi-class model.”

      and

      “Feature Importance Scores

      The relative contribution of source-space voxels and parcels to decoding performance (i.e. – feature importance score) was calculated using minimum redundant maximum relevance (MRMR) and highlighted in topography plots. MRMR, an approach that combines both relevance and redundancy metrics, ranked individual features based upon their significance to the target variable (i.e. – keypress state identity) prediction accuracy and their non-redundancy with other features.”

      As stated in the Reviewer responses above, the dimensionality of the voxel-space feature set is very high (i.e. – 15684). LDA attempts to map the input features onto a much smaller dimensional space (number of classes-1; e.g. – 3 dimensions for 4-class keypress decoding). It is likely that the reduction in accuracy observed only for the voxel-space feature was due to the loss of relevant information during the mapping process that resulted in reduced accuracy. This reduction in accuracy for voxel-space decoding was specific to LDA. Figure 3—figure supplement 3 shows that voxel-space decoder performance actually improved when utilizing alternative dimensionality reduction techniques.

      (5) Paragraph 9, lines #139-142: "Notably, decoding associated with index finger keypresses (executed at two different ordinal positions in the sequence) exhibited the highest number of misclassifications of all digits (N = 141 or 47.5% of all decoding errors; Figure 3C), raising the hypothesis that the same action could be differentially represented when executed at different learning state or sequence context locations."

      This does not seem to be a fair comparison, as the index finger appears twice as many as the other fingers do in the sequence. To claim this, proper statistical analysis needs to be done taking this difference into account.

      We thank the Reviewer for bringing this issue to our attention. We have now corrected this comparison to evaluate relative false negative and false positive rates between individual keypress state decoders, and have revised this statement in the manuscript as follows:

      “Notably, decoding of index finger keypresses (executed at two different ordinal positions in the sequence) exhibited the highest false negative (0.116 per keypress) and false positive (0.043 per keypress) misclassification rates compared with all other digits (false negative rate range = [0.067 0.114]; false positive rate range = [0.020 0.037]; Figure 3C), raising the hypothesis that the same action could be differentially represented when executed within different contexts (i.e. - different learning states or sequence locations).”

      (6) Finally, the authors could consider acknowledging in the Discussion that the contribution of micro-offline learning to genuine skill learning is still under debate (e.g., Gupta and Rickard, 2023; 2024; Das et al., bioRxiv, 2024).

      We have added a paragraph in the Discussion that addresses this point.

      Reviewer #3 (Recommendations for the authors):

      In addition to the additional analyses suggested in the public review, I have the following suggestions/questions:

      (1) Given that the authors introduce a new decoding approach, it would be very helpful for readers to see a distribution of window sizes and window onsets eventually used across individuals, at least for the optimized decoder.

      We have now included a new supplemental figure (Figure 4 – figure Supplement 2) that provides this information.

      (2) Please explain in detail how you arrived at the (interpolated?) group-level plot shown in Figure 1B, starting from the discrete single-trial keypress transition times. Also, please specify what the shading shows.

      Instantaneous correct sequence speed (skill measure) was quantified as the inverse of time (in seconds) required to complete a single iteration of a correctly generated full 5-item sequence. Individual keypress responses were labeled as members of correct sequences if they occurred within a 5-item response pattern matching any possible circular shifts of the 5-item sequence displayed on the monitor (41324). This approach allowed us to quantify a measure of skill within each practice trial at the resolution of individual keypresses. The dark line indicates the group mean performance dynamics for each trial. The shaded region indicates the 95% confidence limit of the mean (see Methods).

      (3) Similarly, please explain how you arrived at the group-level plot shown in Figure 1C. What are the different colored lines (rows) within each trial? How exactly did the authors reach the conclusion that KTT variability stabilizes by trial 6?

      Figure 1C provides additional information to the correct sequence speed measure above, as it also tracks individual transition speed composition over learning. Figure 1C, thus, represents both changes in overall correct sequence speed dynamics (indicated by the overall narrowing of the horizontal speed lines moving from top to bottom) and the underlying composition of the individual transition patterns within and across trials. The coloring of the lines is a shading convention used to discriminate between different keypress transitions. These curves were sampled with 1ms resolution, as in Figure 1B. Addressing the underlying keypress transition patterns requires within-subject normalization before averaging across subjects. The distribution of KTTs was normalized to the median correct sequence time for each participant and centered on the mid-point for each full sequence iteration during early learning.

      (4) Maybe I missed it, but it was not clear to me which of the tested classifiers was eventually used. Or was that individualized as well? More generally, a comparison of the different classifiers would be helpful, similar to the comparison of dimension reduction techniques.

      We have now included a new supplemental figure that provides this information.

      (5) Please add df and effect sizes to all statistics.

      Done.

      (6) Please explain in more detail your power calculation.

      The study was powered to determine the minimum sample size needed to detect a significant change in skill performance following training using a one-sample t-test (two-sided; alpha = 0.05; 95% statistical power; Cohen’s D effect size = 0.8115 calculated from previously acquired data in our lab). The calculated minimum sample size was 22. The included study sample size (n = 27) exceeded this minimum.

      This information is now included in the revised manuscript.

      (7) The cut-off for the high-pass filter is unusually high and seems risky in terms of potential signal distortions (de Cheveigne, Neuron 2019). Why did the authors choose such a high cut-off?

      The 1Hz high-pass cut-off frequency for the 1-150Hz band-pass filter applied to the continuous raw MEG data during preprocessing has been used in multiple previous MEG publications (Barratt et al., 2018; Brookes et al., 2012; Higgins et al., 2021; Seedat et al., 2020; Vidaurre et al., 2018).

      (8) "Furthermore, the magnitude of offline contextualization predicted skill gains while online contextualization did not", lines 336/337 - where is that analysis?

      Additional details pertaining to this analysis are now provided in the Results section (Figure 5 – figure supplement 4).

      (9) How were feature importance scores computed?

      We have now added a new subheading in the Methods section with a more detailed description of how feature importance scores were computed.

      (10)  Please add x and y ticks plus tick labels to Figure 5 - Figure Supplement 3, panel A

      Done

      (11) Line 369, what does "comparable" mean in this context?

      The sentence in the “Study Participants” part of the Methods section referred to here has now been revised for clarity.

      (12) In lines 496/497, please specify what t=0 means (KeyDown event, I guess?).

      Yes, the KeyDown event occurs at t = 0. This has now been clarified in the revised manuscript.

      (13) Please specify consistent boundaries between alpha- and beta-bands (they are currently not consistent in the Results vs. Methods (14/15 Hz or 15/16 Hz)).

      We thank the Reviewer for alerting us to this discrepancy caused by a typographic error in the Methods. We have now corrected this so that the alpha (8-14 Hz) and beta-band (15-24 Hz) frequency limits are described consistently throughout the revised manuscript.

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    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Based on previous publications suggesting a potential role for miR-26b in the pathogenesis of metabolic dysfunction-associated steatohepatitis (MASH), the researchers aim to clarify its function in hepatic health and explore the therapeutical potential of lipid nanoparticles (LNPs) to treat this condition. First, they employed both whole-body and myeloid cell-specific miR-26b KO mice and observed elevated hepatic steatosis features in these mice compared to WT controls when subjected to WTD. Moreover, livers from whole-body miR-26b KO mice also displayed increased levels of inflammation and fibrosis markers. Kinase activity profiling analyses revealed distinct alterations, particularly in kinases associated with inflammatory pathways, in these samples. Treatment with LNPs containing miR-26b mimics restored lipid metabolism and kinase activity in these animals. Finally, similar anti-inflammatory effects were observed in the livers of individuals with cirrhosis, whereas elevated miR-26b levels were found in the plasma of these patients in comparison with healthy control. Overall, the authors conclude that miR-26b plays a protective role in MASH and that its delivery via LNPs efficiently mitigates MASH development.

      The study has some strengths, most notably, its employ of a combination of animal models, analyses of potential underlying mechanisms, as well as innovative treatment delivery methods with significant promise. However, it also presents numerous weaknesses that leave the research work somewhat incomplete. The precise role of miR-26b in a human context remains elusive, hindering direct translation to clinical practice. Additionally, the evaluation of the kinase activity, although innovative, does not provide a clear molecular mechanisms-based explanation behind the protective role of this miRNA.

      Therefore, to fortify the solidity of their conclusions, these concerns require careful attention and resolution. Once these issues are comprehensively addressed, the study stands to make a significant impact on the field.

      We would like the reviewer for his/her careful evaluation of our manuscript and appreciate his/her appraisal for the strengths of our study. Regarding the weaknesses, we have addressed these as good as possible during the revision of our manuscript.

      We can already state that miR-26b has clear anti-inflammatory effects on human liver slices, which is in line with our results demonstrating that miR-26b plays a protective role in MASH development in mice. The notion that patients with liver cirrhosis have increasing plasma levels of miR-26b, seems contradictory at first glance. However, we believe that this increased miR-26b expression is a compensatory mechanism to counteract the MASH/cirrhotic effects. However, the exact source of this miR-26b remains to be elucidated in future studies.

      The performed kinase activity analysis revealed that miR-26b affects kinases that particularly play an important role in inflammation and angiogenesis. Strikingly and supporting these data, these effects could be inverted again by LNP treatment. Combined, these results already provide strong mechanistic insights on molecular and intracellular signalling level. Although the exact target of miR-26b remains elusive and its identification is probably beyond the scope of the current manuscript due to its complexity, we believe that the kinase activity results already provide a solid mechanistic basis.

      Reviewer #1 (Recommendations For The Authors):

      A list of recommendations for the authors is presented below:

      (1) The title should emphasize that the majority of experiments were conducted in mice to accurately reflect the scope of the study.

      As suggested we have updated our title to include the statement that we primarily used a murine model:

      “MicroRNA-26b protects against MASH development in mice and can be efficiently targeted with lipid nanoparticles.”

      (2) It would be useful to know more about miR-26b function, including its target genes, tissue-specific expression, and tissue vs. circulating levels. Is it expected that the two strains of the miRNA (i.e., -3p and -5p) act this similarly? Also, miR-26b expression in the liver of individuals with cirrhosis should be determined.

      The function of miR-26b is still rather elusive, making functional studies using this miR very interesting. In a previous study, describing our used mouse model (Van der Vorst et al. BMC Genom Data, 2021) we have eluded several functions of miR-26b that are already investigated. This was particularly already described in carcinogenesis and the neurological field.

      Target gene wise, there are already several targets described in miRbase. However, for our experiments we feel that determination of the specific target genes is beyond the scope of the current manuscript and rather a focus of follow-up projects.

      Regarding the expression of miR-26b, the liver and blood have rather high and similar expressions of both miR-26b-3p and miR-26b-5p as shown in Author response image 1.

      Author response image 1.

      Expression of miR-26b-3p and -5p. Expression of miR-26b-3p (left) and miR-26b-5p (right), generated by using the miRNATissueAtlas 2025 (Rishik et al. Nucleic Acids Research, 2024). Unfortunately, due to restrictions in tissue availability and the lack of stored RNA samples, we are unable to measure miR-26b expression in the human livers. However, based on the potency of the miR-26b mimic loaded LNPs in the mice (Revised Supplemental Figure 2A-B), we are confident that these LNPs also resulted in a overexpression of miR-26b in the human livers.

      (3) Please explain the rationale behind primarily using whole-body miR-26b KO mice rather than the myeloid cell-specific KO model for the studies.

      The main goal of our study is the elucidation of the general role of miR-26b in MASH formation. Therefore, we decided to primarily focus on the whole-body KO model. While we used the myeloid cell-specific KO model to highlight that myeloid cells play an important role in the observed phenotypes, we believe the whole-body KO model is more appropriate as main focus, particularly also in light of the used LNP targeting that also provides a whole-body approach. Furthermore, this focus on the whole-body model also reflects a more therapeutically relevant approach.

      (4) The authors claim that treatment with LNPs containing miR-26b "replenish the miR-26b level in the whole-body deficient mouse" but the results of this observation are not presented.

      This is indeed a valid point that we have now addressed. We have measured the mir26b-3p and mir26b-5p expression levels in livers from mice after 4-week WTD with simultaneous injection with either empty LNPs as vehicle control (eLNP) or LNPs containing miR-26b mimics (mLNP) every 3 days. As shown in Revised Supplemental Figure 2A-B, mLNP treatment clearly results in an overexpression of the mir26b in the livers of these mice. We have rephrased the text accordingly by stating that mLNP results in an “overexpression” rather than “replenishment”.

      (5) The number of 3 human donors for the precision-cut liver slices is clearly insufficient and clinical parameters need to be shown. Additionally, inconsistencies in individual values in Figures 8B-E need clarification.

      Unfortunately, due to restrictions in tissue availability, we are unable to increase our n-number for these experiments. Clinical parameters are not available, but the liver slices were from healthy tissue.

      We have performed these experiments in duplicates for each individual donor. We have now specified this also in the figure legend to explain the individual values in the graphs:

      “…(3 individual donors, cultured in duplicates).”

      (6) Figure 2D: Please include representative images.

      As suggested we have included representative images in our revised manuscript.

      (7) Address discrepancies in the findings across different experimental settings. For example, the expression levels of the lipid metabolism-related genes are not significantly modulated in whole-body miR-26b KO mice (except for Sra), but they are in the myeloid cell-specific model (but not Sra), and none of them are restored after LNPs injections.

      Although Cd36 is not significantly increased in the whole-body miR-26b KO mice, there is a clear tendency towards increased expression, which is now also validated on protein level (Revised Figure 1K-L). In the myeloid cell-specific model we see a similar tendency, although the gene expression difference of Sra is not significantly changed. This could be due to the difference in the model, since only myeloid cells are affected, suggesting that the effects on Sra are to a large extend driven by non-myeloid cells. This would also fit to the tendency to decreased Sra expression in the mimic-LNP treated mice. Due to the larger variation, this difference did not reach significance, which is rather a statistical issue due to relatively small n-numbers. At this moment, we cannot exclude that these receptors are differentially regulated by different cell-types. For this, future studies are needed focussing on cell-specific targeting of miR-26b in somatic cells, like hepatocytes.

      (8) Figure 4A the images are not representative of the quantification.

      We have selected another representative image that is exactly reflecting the average Sirius red positive area, to reflect the quantification appropriately.

      (9) Figures 5 and 7: Are there not significantly decreased/increased kinases? A deeper analysis of these kinase alterations is necessary to understand how miR-26b exerts its role. A comparison analysis of these two datasets might clarify this regard.

      We indeed very often see in these kinome analysis that the general tendency of kinase activity is unidirectional. We believe that this is caused by the highly interconnected nature of kinases. Activation of one signalling cascade will also results in the activation of many other cascades. However, it is interesting to see which pathways are affected in our study and we find it particularly interesting to see that the tendencies is exactly opposite between both comparisons as KO vs. WT shows increase kinase activities, while KO-LNP vs. KO shows a decrease again. Further showing that the method is reflecting a true biological effect that is mediated by miR26b.

      (10) Determinations of the effect of LNPs containing miR-26b in the KO mice are limited to only a few observations (that are not only significant). More extensive findings are needed to conclusively demonstrate the effectiveness of this treatment method. Similar to the experiments with human liver samples (Figures 8A-E).

      We have now elaborated our observations in the mouse model using LNPs by also analysing the effects on inflammation and fibrosis. However, it seems that the treatment time was not long enough to see pronounced changes on these later stages of disease development. Interestingly, the expression of Tgfb was significantly reduced, suggesting at least that the LNPs on genetic levels have an effect already on fibrotic processes. Thereby, it can be suggested that longer mLNP treatment may result in more effects on protein level as well, which remains to be determined in future studies.

      Unfortunately, due to restrictions in tissue availability, we are unable to increase our n-number or read-outs for these experiments at this moment.

      (11) In Figures 8F-H, the observed increase in circulating miR-26b levels in the plasma of cirrhotic individuals seems contradictory to its proposed protective role. This discrepancy requires clarification.

      In the revised discussion (second to last paragraph), we have now elaborated more on the findings in the plasma of cirrhotic individuals in comparison to our murine in-vivo results, to highlight and discuss this discrepancy.

      (12) Figures 8F-H legend mentions using 8-11 patients per group, but the methods section lacks corresponding information about these individuals.

      These patients, together with inclusion/exclusion criteria and definition of cirrhosis are described in the method section 2.14.

      (13) Figure 8G has 7 data points in the cirrhosis group, instead of 8. Any data exclusion should be justified in the methods section.

      As defined in method section 2.15, we have identified outliers using the ROUT = 1 method, which is the reason why Figure 8G only has 7 data points instead of 8.

      Reviewer #2 (Public Review):

      Summary:

      This manuscript by Peters, Rakateli, et al. aims to characterize the contribution of miR-26b in a mouse model of metabolic dysfunction-associated steatohepatitis (MASH) generated by a Western-type diet on the background of Apoe knock-out. In addition, the authors provide a rescue of the miR-26b using lipid nanoparticles (LNPs), with potential therapeutic implications. In addition, the authors provide useful insights into the role of macrophages and some validation of the effect of miR-26b LNPs on human liver samples.

      Strengths:

      The authors provide a well-designed mouse model, that aims to characterize the role of miR-26b in a mouse model of metabolic dysfunction-associated steatohepatitis (MASH) generated by a Western-type diet on the background of Apoe knock-out. The rescue of the phenotypes associated with the model used using miR-26b using lipid nanoparticles (LNPs) provides an interesting avenue to novel potential therapeutic avenues.

      Weaknesses:

      Although the authors provide a new and interesting avenue to understand the role of miR-26b in MASH, the study needs some additional validations and mechanistic insights in order to strengthen the author's conclusions.

      (1) Analysis of the expression of miRNAs based on miRNA-seq of human samples (see https://ccb-compute.cs.uni-saarland.de/isomirdb/mirnas) suggests that miR-26b-5p is highly abundant both on liver and blood. It seems hard to reconcile that despite miRNA abundance being similar in both tissues, the physiological effects claimed by the authors in Figure 2 come exclusively from the myeloid (macrophages).

      We agree with the reviewer that the effects observed in the whole-body KO model are most likely a combination of cellular effects, particularly since miR-26b is also highly expressed in the liver. However, with the LysM-model we merely want to demonstrate that the myeloid cells at least play an important, though not exclusive, role in the phenotype. In the discussion, we also further elaborate on the fact that the observed changes in the liver can me mediated by hepatic changes.

      To stress this, we have adjusted the conclusion of Figure 2:

      “Interestingly, mice that have a myeloid-specific lack of miR-26b also show increased hepatic cholesterol levels and lipid accumulation demonstrated by Oil-red-O staining, coinciding with an increased hepatic Cd36 expression (Figure 2), demonstrating that myeloid miR-26b plays a major, but not exclusive, role in the observed steatosis.”

      (2) Similarly, the miRNA-seq expression from isomirdb suggests also that expression of miR-26a-5p is indeed 4-fold higher than miR-26b-5p both in the liver and blood. Since both miRNAs share the same seed sequence, and most of the supplemental regions (only 2 nt difference), their endogenous targets must be highly overlapped. It would be interesting to know whether deletion of miR-26b is somehow compensated by increased expression of miR-26a-5p loci. That would suggest that the model is rather a depletion of miR-26.

      UUCAAGUAAUUCAGGAUAGGU mmu-miR-26b-5p mature miRNA

      UUCAAGUAAUCCAGGAUAGGCU mmu-miR-26a-5p mature miRNA

      This is a very valid point raised by the reviewer, which we actually already explored in a previous study, describing our used mouse model (Van der Vorst et al. BMC Genom Data, 2021). In this manuscript, we could show that miR-26a is not affected by the deficiency of miR-26b (Figure 1G in: Van der Vorst et al. BMC Genom Data, 2021).

      (3) Similarly, the miRNA-seq expression from isomirdb suggests also that expression of miR-26b-5p is indeed 50-fold higher than miR-26b-3p in the liver and blood. This difference in abundance of the two strands is usually regarded as one of them being the guide strand (in this case the 5p) and the other being the passenger (in this case the 3p). In some cases, passenger strands can be a byproduct of miRNA biogenesis, thus the rescue experiments using LNPs with both strands in equimolar amounts would not reflect the physiological abundance miR-26b-3p. The non-physiological overabundance of miR-26b-3p would constitute a source of undesired off-targets.

      We agree with the reviewer on this aspect and this is something we had to consider while generating the mimic LNPs. However, we believe that we do not observe and undesired off-target effects, as the effects of the mimic LNPs at least on functional outcomes are relatively mild and only restricted to the expected effects on lipids. Furthermore, the effects on the kinase profile due to the mimic LNP treatment are in line with our expectations. Combined these results suggest at least that potential off-target effects are minor.

      (4) It would also be valuable to check the miRNA levels on the liver upon LNP treatment, or at least the signatures of miR-26b-3p and miR-26b-5p activity using RNA-seq on the RNA samples already collected.

      This is indeed a valid point that we have now addressed. We have measured the mir26b-3p and mir26b-5p expression levels in livers from mice after 4-week WTD with simultaneous injection with either empty LNPs as vehicle control (eLNP) or LNPs containing miR-26b mimics (mLNP) every 3 days. As shown in Supplemental Figure 2A-B, mLNP treatment clearly results in an overexpression of the mir26b in the livers of these mice. We have rephrased the text accordingly by stating that mLNP results in an “overexpression” rather than “replenishment”.

      (5) Some of the phenotypes described, such as the increase in cholesterol, overlap with the previous publication by van der Vorst et al. BMC Genom Data (2021), despite in this case the authors are doing their model in Apoe knock-out and Western-type diet. I would encourage the authors to investigate more or discuss why the initial phenotypes don't become more obvious despite the stressors added in the current manuscript.

      In our previous publication (BMC Genom Data; 2021), we actually did not see any changes in circulating lipid levels. However, in that study we did not evaluate the livers of the mice, so we do not have any information about the hepatic lipid levels.

      As mentioned by the reviewer, we believe that we see much more pronounced phenotypes in the current model because we use the combined stressor of Apoe-/- and Western-type diet, which cannot be compared to the wildtype and chow-fed mice used in the BMC Genom Data manuscript.

      (6) The authors have focused part of their analysis on a few gene makers that show relatively modest changes. Deeper characterization using RNA-seq might reveal other genes that are more profoundly impacted by miR-26 depletion. It would strengthen the conclusions proposed if the authors validated that changes in mRNA abundance (Sra, Cd36) do impact the protein abundance. These relatively small changes or trends in mRNA expression, might not translate into changes in protein abundance.

      As suggested by the reviewer we have now also confirmed that the protein expression of CD36 and SRA is significantly increased upon miR-26b depletion, visualized as Figure 1K-L in the revised manuscript. Unfortunately, we do not have enough material left to perform similar analysis for the LysM-model or the LNP-model, although based on the whole-body effects we are confident that at least for CD36/SRA in this case the gene expression matches effects observed on protein level.

      (7) In Figures 5 and 7, the authors run a phosphorylation array (STK) to analyze the changes in the activity of the kinome. It seems that a relatively large number of signaling pathways are being altered, I think that should be strengthened by further validations by Western blot on the collected tissue samples. For quite a few of the kinases, there might be antibodies that recognise phosphorylation. The two figures lack a mechanistic connection to the rest of the manuscript.<br /> On this point we respectfully have to disagree with the reviewer. We have used a kinase activity profiling approach (PamGene) to analyse the real-time activity of kinases in our lysates. This approach is different than the classical Western blot approach in which only the presence or absence of a specific phosphorylation is detected. Thereby, Western blot analysis does not analyse phosphorylation in real-time, but rather determines whether there has been phosphorylation in the past. Our approach actually determines the real-time, current activity of the kinases, which we believe is a different and perhaps even more reliable read-out measurement. Therefore, validation by Western blot would not strengthen these observations.

      We have particularly tried to connect these observations to the rest of the manuscript by highlighting the observed signalling cascades that are affected, highlighting a role in inflammation and angiogenesis, thereby providing some mechanistic insights.

      Reviewer #2 (Recommendations For The Authors):

      I would encourage the authors to follow-up on some of the more miRNA focused comments made above, which would strengthen the mechanistic part of the work presented.

      I suggest the authors tone down some of some of the claims made (eg. "clearly increased expression", "exacerbated hepatic fibrosis"), given that some of it might need further validation.

      Wherever needed we have tuned down the tone of some claims, although we believe that most claims are already written carefully enough and in line with the observed results.

      Some of the panels that are supposed to have the same amount of animals have variable N, despite they come from the same exact number of RNA samples or tissue lysates (eg. 1G and 1H, vs 1I and 1J).

      This is indeed correct and caused by the fact that some analysis resulted in statistical outliers as identified using the ROUT = 1 method, as also specified in section 2.15 of the method section.

      It would be nice to have representative images of oil-red-o in all the figures where it is quantified (or at least in the supplementary figures).

      As suggested by the reviewer, we have now included representative images for the LysM-model (Revised Figure 2D) and the LNP-model (Revised Figure 6D) as well.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public Review):  

      Summary:

      In this manuscript, Shao et al. investigate the contribution of different cortical areas to working memory maintenance and control processes, an important topic involving different ideas about how the human brain represents and uses information when it is no longer available to sensory systems. In two fMRI experiments, they demonstrate that the human frontal cortex (area sPCS) represents stimulus (orientation) information both during typical maintenance, but even more so when a categorical response demand is present. That is, when participants have to apply an added level of decision control to the WM stimulus, sPCS areas encode stimulus information more than conditions without this added demand. These effects are then expanded upon using multi-area neural network models, recapitulating the empirical gradient of memory vs control effects from visual to parietal and frontal cortices. In general, the experiments and analyses provide solid support for the authors' conclusions, and control experiments and analyses are provided to help interpret and isolate the frontal cortex effect of interest. However, I suggest some alternative explanations and important additional analyses that would help ensure an even stronger level of support for these results and interpretations.

      Strengths:

      -  The authors use an interesting and clever task design across two fMRI experiments that is able to parse out contributions of WM maintenance alone along with categorical, rule-based decisions. Importantly, the second experiment only uses one fixed rule, providing both an internal replication of Experiment 1's effects and extending them to a different situation when rule-switching effects are not involved across mini-blocks.

      - The reported analyses using both inverted encoding models (IEM) and decoders (SVM) demonstrate the stimulus reconstruction effects across different methods, which may be sensitive to different aspects of the relationship between patterns of brain activity and the experimental stimuli.

      - Linking the multivariate activity patterns to memory behavior is critical in thinking about the potential differential roles of cortical areas in sub-serving successful working memory. Figure 3 nicely shows a similar interaction to that of Figure 2 in the role of sPCS in the categorization vs. maintenance tasks.

      - The cross-decoding analysis in Figure 4 is a clever and interesting way to parse out how stimulus and rule/category information may be intertwined, which would have been one of the foremost potential questions or analyses requested by careful readers. However, I think more additional text in the Methods and Results to lay out the exact logic of this abstract category metric will help readers bet0ter interpret the potential importance of this analysis and result.

      We thank the reviewer for the positive assessment of our manuscript. Please see lines 366-372, 885-894 in the revised manuscript for a detailed description of the abstract category index, and see below for a detailed point-by-point response.

      Weaknesses:

      - Selection and presentation of regions of interest: I appreciate the authors' care in separating the sPCS region as "frontal cortex", which is not necessarily part of the prefrontal cortex, on which many ideas of working memory maintenance activity are based. However, to help myself and readers interpret these findings, at a minimum the boundaries of each ROI should be provided as part of the main text or extended data figures. Relatedly, the authors use a probabilistic visual atlas to define ROIs in the visual, parietal, and frontal cortices. But other regions of both lateral frontal and parietal cortices show retinotopic responses (Mackey and Curtis, eLife, 2017: https://elifesciences.org/articles/22974) and are perhaps worth considering. Do the inferior PCS regions or inferior frontal sulcus show a similar pattern of effects across tasks? And what about the middle frontal gyrus areas of the prefrontal cortex, which are most analogous to the findings in NHP studies that the authors mention in their discussion, but do not show retinotopic responses? Reporting the effects (or lack thereof) in other areas of the frontal cortex will be critical for readers to interpret the role of the frontal cortex in guiding WM behavior and supporting the strongly worded conclusions of broad frontal cortex functioning in the paper. For example, to what extent can sPCS results be explained by visual retinotopic responses? (Mackey and Curtis, eLife, 2017: https://elifesciences.org/articles/22974).

      We thank the reviewer for the suggestions. We have added a Supplemental Figure 1 to better illustrate the anatomical locations of ROIs.  

      Following the reviewer’s suggestion, we defined three additional subregions in the frontal cortex based on the HCP atlas [1], including the inferior precentral sulcus (iPCS, generated by merging 6v, 6r, and PEF), inferior frontal sulcus (IFS, generated by merging IFJp, IFJa, IFSp, IFSa, and p47r), and middle frontal gyrus (MFG, generated by merging 9-46d, 46, a9-46v, and p9-46v). We then performed the same analyses as in the main text using both mixed-model and within-condition IEMs. Overall, we found that none of the ROIs demonstrated significant orientation representation in Experiment 1, for either IEM analysis (Author response image 1A and 1C). In Experiment 2, however, the IFS and MFG (but not iPCS) demonstrated a similar pattern to sPCS for orientation representation, though these results did not persist in the within-condition IEM with lower SNR (Author response image 1B and 1D). Moreover, when we performed the abstract category decoding analysis in the three ROIs, only the MFG in Experiment 2 showed significant abstract category decoding results, with no significant difference between experiments (Author response image 1E). To summarize, the orientation and category results observed in sPCS in the original manuscript were largely absent in other frontal regions. There was some indication that the MFG might share some results for orientation representation and category decoding, although this pattern was weaker and was only observed in some analyses in Experiment 2. Therefore, although we did not perform retinotopic mapping and cannot obtain a direct measure of retinotopic responses in the frontal cortex, these results suggest that our findings are unlikely to be explained by visual retinotopic responses: the iPCS, which is another retinotopic region, did not show the observed pattern in any of the analyses. Notably, the iPCS results are consistent with our previous work demonstrating that orientation information cannot be decoded from iPCS during working memory delay [2]. We have included these results on lines 395-403, 563-572 in the revised manuscript to provide a more comprehensive understanding of the current findings. 

      Author response image 1.

      Orientation reconstruction and abstract category decoding results in iPCS, IFS, and MFG.

      - When looking at the time course of effects in Figure 2, for example, the sPCS maintenance vs categorization effects occur very late into the WM delay period. More information is needed to help separate this potential effect from that of the response period and potential premotor/motor-related influences. For example, are the timecourses shifted to account for hemodynamic lag, and if so, by how much? Do the sPCS effects blend into the response period? This is critical, too, for a task that does not use a jittered delay period, and potential response timing and planning can be conducted by participants near the end of the WM delay. For example, the authors say that " significant stimulus representation in EVC even when memoranda had been transformed into a motor format (24)". But, I *think* this paper shows the exact opposite interpretation - EVC stimulus information is only detectable when a motor response *cannot* be planned (https://elifesciences.org/articles/75688). Regardless, parsing out the timing and relationship to response planning is important, and an ROI for M1 or premotor cortex could also help as a control comparison point, as in reference (24).

      We thank the reviewer for raising this point. We agree that examining the contribution of response-related activity in our study is crucial, as we detail below:

      First, the time course results in the manuscript are presented without time shifting. The difference in orientation representation in Figure 2 emerged at around 7 s after task cue onset and 1 s before probe onset. Considering a 4-6 s hemodynamic response lag, the difference should occur around 1-3 s after task cue onset and 5-7 s prior to probe onset. This suggests that a substantial portion of the effect likely occurred during the delay rather than response period.

      Second, our experimental design makes it unlikely that response planning would have influenced our results, as participants were unable to plan their motor responses in advance due to randomized response mapping at the probe stage on a trial-by-trial basis. Moreover, even if response planning had impacted the results in sPCS, it would have affected both conditions similarly, which again, would not explain the observed differences between conditions.

      Third, following the reviewer’s suggestion, we defined an additional ROI (the primary motor cortex, M1) using the HCP atlas and repeated the IEM analysis. No significant orientation representation was observed in either condition in M1, even during the response period (Figure S3), further suggesting that our results are unlikely to be explained by motor responses or motor planning.

      Based on the evidence above, we believe motor responses or planning are unlikely to account for our current findings. We have included these results on lines 264-267 to further clarify this issue.

      Lastly, upon re-reading the Henderson et al. paper [3], we confirmed that stimulus information was still decodable in EVC when a motor response could be planned (Figure 2 of Henderson et al.). In fact, the authors also discussed this result in paragraph 5 of their discussion. This finding, together with our results in EVC, indicates that EVC maintains stimulus information in working memory even when the information is no longer task-relevant, the functional relevance of which warrants further investigation in future research.

      - Interpreting effect sizes of IEM and decoding analysis in different ROIs. Here, the authors are interested in the interaction effects across maintenance and categorization tasks (bar plots in Figure 2), but the effect sizes in even the categorization task (y-axes) are always larger in EVC and IPS than in the sPCS region... To what extent do the authors think this representational fidelity result can or cannot be compared across regions? For example, a reader may wonder how much the sPCS representation matters for the task, perhaps, if memory access is always there in EVC and IPS? Or perhaps late sPCS representations are borrowing/accessing these earlier representations? Giving the reader some more intuition for the effect sizes of representational fidelity will be important. Even in Figure 3 for the behavior, all effects are also seen in IPS as well. More detail or context at minimum is needed about the representational fidelity metric, which is cited in ref (35) but not given in detail. These considerations are important given the claims of the frontal cortex serving such an important for flexible control, here.

      We thank the reviewer for raising this point. We agree that the effect sizes are always larger in EVC and IPS. This is because the specific decoding method we adopted, IEM, is based on the concept of population-level feature-selective responses, and decoding results would be most robust in regions with strong feature-tuning responses, such as EVC and parts of IPS. Therefore, to minimize the impact of effect size on our results, we avoided direct comparisons of representational strength across ROIs, focusing instead on differences in representational strength between conditions within the same ROI. With this approach, we found that EVC and IPS showed high representational fidelity throughout the trial, but only in sPCS did we observe significant higher fidelity in categorization condition, where orientation was actually not a behavioral goal but was manipulated in working memory to achieve the goal. Moreover, although representational fidelity in the EVC was the highest, its behavioral predictability decreased during the delay period, unlike sPCS. These results suggest that the magnitude of fidelity alone is not the determining factor for the observed categorization vs. maintenance effect or for behavioral performance. We have included further discussion on this issue on lines 208-211 of the revised manuscript.

      The reviewer also raised a good point that IPS showed similar behavioral correlation results as sPCS. In the original manuscript, we discussed the functional similarities and distinctions between IPS and sPCS in the discussion. We have expanded on this point on lines 610-627 in the revised manuscript:

      “While many previous WM studies have focused on the functional distinction between sensory and frontoparietal cortex, it has remained less clear how frontal and parietal cortex might differ in terms of WM functions. Some studies have reported stimulus representations with similar functionality in frontal and parietal cortex [4, 5], while others have observed differential patterns [6-8]. We interpret the differential patterns as reflecting a difference in the potential origin of the corresponding cognitive functions. For example, in our study, sPCS demonstrated the most prominent effect for enhanced stimulus representation during categorization as well as the tradeoff between stimulus difference and category representation, suggesting that sPCS might serve as the source region for such effects. On the other hand, IPS did show visually similar patterns to sPCS in some analyses. For instance, stimulus representation in IPS was visually but not statistically higher in the categorization task. Additionally, stimulus representation in IPS also predicted behavioral performance in the categorization task. These results together support the view that our findings in sPCS do not occur in isolation, but rather reflect a dynamic reconfiguration of functional gradients along the cortical hierarchy from early visual to parietal and then to frontal cortex.”

      Lastly, following the reviewer’s suggestion, we have included more details on the representational fidelity metric on lines 201-206, 856-863 in the revised manuscript for clarity.

      Recommendations:

      Figure 3 layout - this result is very interesting and compelling, but I think could be presented to have the effect demonstrated more simply for readers. The scatter plots in the second and third rows take up a lot of space, and perhaps having a barplot as in Figure 2 showing the effects of brain-behavior correlations collapsed across the WM delay period timing would make the effect stand out more.

      We thank the reviewer for the suggestion. We have added a subplot (C) to Figure 3 to demonstrate the brain-behavior correlation collapsed across the late task epoch.

      When discussing the link between sPCS representations and behavior, I think this paper should likely be cited ([https://www.jneurosci.org/content/24/16/3944](https://www.jneurosci.org/content/24/ 16/3944)), which shows univariate relationships between sPCS delay activity and memory-guided saccade performance.

      We thank the reviewer for the suggestion and have included this citation on lines 278-279 in the revised manuscript.

      Interpretation of "control" versus categorization - the authors interpret that "It would be of interest to further investigate whether this active control in the frontal cortex could be generalized to tasks that require other types of WM control such as mental rotation." I think more discussion on the relationship between categorization and "control" is needed, especially given the claim of "flexible control" throughout. Is stimulus categorization a form of cognitive control, and if so, how?  

      We thank the reviewer for raising this point. Cognitive control is generally defined as the process by which behavior is flexibly adapted based on task context and goals, and most theories agree that this process occurs within working memory [9, 10]. With this definition, we consider stimulus categorization to be a form of cognitive control, because participants needed to adapt the stimulus based on the categorization rule in working memory for subsequent category judgements. With two categorization rules, the flexibility in cognitive control increased, because participants need to switch between the two rules multiple times throughout the experiment, instead of being fixed on one rule. We now clarify these two types of controls on lines 112-116 in the introduction.

      However, we agree that the latter form of control could be more related to rule switching that might not be specific to categorization per se. For instance, if participants perform rule switching in another type of WM task that requires WM control such as mental rotation, it remains to be tested whether similar results would be observed and/or whether same brain regions would be recruited. We have included further information on this issue on lines 572-575 in the revised manuscript.

      Reviewer #2 (Public Review):

      Summary:

      The authors provide evidence that helps resolve long-standing questions about the differential involvement of the frontal and posterior cortex in working memory. They show that whereas the early visual cortex shows stronger decoding of memory content in a memorization task vs a more complex categorization task, the frontal cortex shows stronger decoding during categorization tasks than memorization tasks. They find that task-optimized RNNs trained to reproduce the memorized orientations show some similarities in neural decoding to people. Together, this paper presents interesting evidence for differential responsibilities of brain areas in working memory.

      Strengths:

      This paper was strong overall. It had a well-designed task, best-practice decoding methods, and careful control analyses. The neural network modelling adds additional insight into the potential computational roles of different regions.

      We thank the reviewer for the positive assessment of our manuscript.

      Weaknesses:

      While the RNN model matches some of the properties of the task and decoding, its ability to reproduce the detailed findings of the paper was limited. Overall, the RRN model was not as well-motivated as the fMRI analyses.

      We are grateful for the reviewer’s suggestions on improving our RNN results. Please see below for a detailed point-by-point response.

      Recommendations:

      Overall, I thought that this paper was excellent. I have some conceptual concerns about the RNN model, and minor recommendations for visualization.

      (1) I think that the RNN modelling was certainly interesting and well-executed. However, it was not clear how much it contributed to the results. On the one hand, it wasn't clear why reproducing the stimulus was a critical objective of the task (ie could be more strongly motivated on biological grounds). On the other hand, the agreement between the model and the fMRI results is not that strong. The model does not reproduce stronger decoding in 'EVC' for maintenance vs categorization. Also, the pattern of abstract decoding is very different from the fMRI (eg the RNN has stronger categorical encoding in 'EVC' than 'PFC' and larger differences between fixed and flexible rules in earlier areas than is evident in the fMRI). Together, the RNN modelling comes across as a little ad hoc, without really nailing the performance.

      We thank the reviewer for prompting us to further elaborate on the rationale for our RNN analysis. In our fMRI results, we observed a tradeoff between maintaining stimulus information in more flexible tasks (Experiment 1) and maintaining abstract category information in less flexible tasks (Experiment 2). This led to the hypothesis that participants might have employed different coding strategies in the two experiments. Specifically, in flexible environments, stimulus information might be preserved in its original identity in the higher-order cortex, potentially reducing processing demands in each task and thereby facilitating efficiency and flexibility; whereas in less flexible tasks, participants might generate more abstract category representations based on task rules to facilitate learning. To directly test this idea, we examined whether explicitly placing a demand for the RNN to preserve stimulus representation would recapitulate our fMRI findings in frontal cortex by having stimulus information as an output, in comparison to a model that did not specify such a demand. Meanwhile, we totally agree with the reviewer that there are alternative ways to implement this objective in the model. For instance, changing the network encoding weights (lazy vs. rich regime) to make feedforward neural networks either produce high-dimensional stimulus or low-dimensional category representations [11]. However, we feel that exploring these alternatives may fall outside the scope of the current study.

      Regarding the alignment between the fMRI and RNN results: for the stimulus decoding results in EVC, we found that with an alternative decoding method (IEM), a similar maintenance > categorization pattern was observed in EVC-equivalent module, suggesting that our RNN was capable of reproducing EVC results, albeit in a weaker manner (please see our response to the reviewer’s next point). For the category decoding results, we would like to clarify that the category decoding results in EVC was not necessarily better than those in sPCS. Although category decoding accuracy was numerically higher in EVC, it was more variable compared to IPS and sPCS. To illustrate this point, we calculated the Bayes factor for the category decoding results of RNN2 in Figure 6C, and found that the amount of evidence for category decoding as well as for the decoding difference between RNNs in IPS and sPCS modules was high, whereas the evidence in the EVC was insufficient (Response Table 1).

      Author response table 1.

      Bayes factors for category decoding and decoding differences in Figure 6C lower panel.

      Nevertheless, we agree with the reviewer that all three modules demonstrated the category decoding difference between experiments, which differs from our fMRI results. This discrepancy may be partially due to differences in signal sensitivity. RNN signals typically have a higher SNR compared to fMRI signals, as fMRI aggregates signals from multiple neurons and single-neuron tuning effects can be reduced. We have acknowledged this point on lines 633-636 in the revised manuscript. Nonetheless, the current RNNs effectively captured our key fMRI findings, including increased stimulus representation in frontal cortex as well as the tradeoff in category representation with varying levels of flexible control. We believe the RNN results remain valuable in this regard.

      Honestly, I think the paper would have a very similar impact without the modelling results, but I appreciate that you put a lot of work into the modeling, and this is an interesting direction for future research. I have a few suggestions, but nothing that I feel too strongly about.

      - It might be informative to use IEM to better understand the RNN representations (and how similar they are to fMRI). For example, this could show whether any of the modules just encode categorical information. 

      - You could try providing the task and/or retro cue directly to the PFC units. This is a little unrealistic, but may encourage a stronger role for PFC.

      - You might adjust the ratio of feedforward/feedback connections, if you can find good anatomical guidance on what these should be.

      Obviously, I don't have much - it's a tricky problem!

      We thank the reviewer for the suggestions. To better align the fMRI and RNN results, we first performed the same IEM analyses used in the fMRI analyses on the RNN data. We found that with IEM, the orientation representation in the EVC module demonstrated a pattern similar to that in the fMRI data, showing a negative trend for the difference between categorization and maintenance, although the trend did not reach statistical significance (Author response image 2A). Meanwhile, the difference between categorization and maintenance remained a positive trend in the sPCS module.

      Second, following the reviewer’s suggestion, we adjusted the ratio of feedforward/feedback connections between modules to 1:2, such that between Modules 1 and 2 and between Modules 2 and 3, there were always more feedback than feedforward connections, consistent with recent theoretical proposals [12]. We found that, this change preserved the positive trend for orientation differences in the sPCS module, but in the meantime also made the orientation difference in the EVC and IPS modules more positive (Author response image 2B).

      To summarize, we found that the positive difference between categorization and maintenance in the sPCS module was robust across difference RNNs and analytical approaches, further supporting that RNNs with stimulus outputs can replicate our key fMRI findings in the frontal cortex. By contrast, the negative difference between categorization and maintenance in EVC was much weaker. It was weakly present using some analytical methods (i.e., the IEM) but not others (i.e., SVMs), and increasing the feedback ratio of the entire network further weakened this difference. We believe that this could be due to that the positive difference was mainly caused by top-down, feedback modulations from higher cortex during categorization, such that increasing the feedback connection strengthens this pattern across modules. We speculate that enhancing the negative difference in the EVC module might require additional modules or inputs to strengthen fine-grained stimulus representation in EVC, a mechanism that might be of interest to future research. We have added a paragraph to the discussion on the limitations of the RNN results on lines 629-644.

      Author response image 2.

      Stimulus difference across RNN modules.  (A). Results using IEM (p-values from Module 1 to 3: 0.10, 0.48, 0.01). (B). Results using modified RNN2 with changed connection ratio (p-values from Module 1 to 3: 0.12, 0.22, 0.08). All p-values remain uncorrected.

      (2) Can you rule out that during the categorization task, the orientation encoding in PFC isn't just category coding? You had good controls for category coding, but it would be nice to see something for orientation coding. e.g., fit your orientation encoding model after residualizing category encoding, or show that category encoding has worse CV prediction than orientation encoding.

      We thank the reviewer for raising this point. To decouple orientation and category representations, we performed representational similarity analysis (RSA) in combination with linear mixed-effects modeling (LMEM) on the fMRI data. Specifically, we constructed three hypothesized representational dissimilarity matrices (RDMs), one for graded stimulus (increasing distance between orientations as they move farther apart, corresponding to graded feature tuning responses), one for abstract category (0 for all orientations within the same category and 1 for different categories), and another for discrete stimulus (indicating equidistant orientation representations). We then fit the three model RDMs together using LMEM with subject as the random effect (Author response image 3A). This approach is intended to minimize the influence of collinearity between RDMs on the results [13].

      Overall, the LMEM results (Author response image 3B-D) replicated the decoding results in the main text, with significant stimulus but not category representation in sPCS in Experiment 1, and marginally significant category representation in the same brain region in Experiment 2. These results further support the validity of our main findings and emphasize the contribution of stimulus representation independent of category representation.

      Author response image 3.

      Delineating stimulus and category effects using LMEM.  (A) Schematic illustration of this method. (B) Results for late epoch in Experiment 1, showing the fit of each model RDM. (C) Results for early epoch in Experiment 2. (D) Results for late epoch in Experiment 2.

      (3) Is it possible that this region of PFC is involved in categorization in particular and not 'control-demanding working memory'? 

      We thank the reviewer for raising this possibility. Cognitive control is generally defined as the process by which behavior is flexibly adapted based on task context and goals, and most theories agree that this process occurs within working memory [9, 10]. With this definition, we consider stimulus categorization to be a form of cognitive control, because participants need to adapt the stimulus based on the categorization rule in working memory for subsequent category judgements.  However, in the current study we only used one type of control-demanding working memory task (categorization) to test our hypothesis, and therefore it remains unclear whether the current results in sPCS can generalize to other types of WM control tasks.

      We have included a discussion on this issue on lines 572-575 in the revised manuscript.

      (4) Some of the figures could be refined to make them more clear:

      a.  Figure 4 b/c should have informative titles and y-axis labels.

      b.  Figure 5, the flexible vs fixed rule isn't used a ton up to this point - it would help to (also include? Replace?) with something like exp1/exp2 in the legend. It would also help to show the true & orthogonal rule encoding in these different regions (in C, or in a separate panel), especially to the extent that this is a proxy for stimulus encoding.

      c.  Figure 6: B and C are very hard to parse right now. (i) The y-axis on B could use a better label. (ii) It would be useful to include an inset of the relevant data panel from fMRI that you are reproducing. (iii) Why aren't there fixed rules for RNN1?

      We thank the reviewer for the suggestions and have updated the figures accordingly as following:

      Overall I think this is excellent - my feedback is mostly on interpretation and presentation. I think the work itself is really well done, congrats!

      References

      (1) Glasser, M.F., et al., A multi-modal parcellation of human cerebral cortex. Nature, 2016. 536(7615): p. 171-178.

      (2) Yu, Q. and Shim, W.M., Occipital, parietal, and frontal cortices selectively maintain taskrelevant features of multi-feature objects in visual working memory. Neuroimage, 2017. 157: p. 97-107.

      (3) Henderson, M.M., Rademaker, R.L., and Serences, J.T., Flexible utilization of spatial- and motor-based codes for the storage of visuo-spatial information. Elife, 2022. 11.

      (4) Christophel, T.B., et al., Cortical specialization for attended versus unattended working memory. Nat Neurosci, 2018. 21(4): p. 494-496.

      (5) Yu, Q. and Shim, W.M., Temporal-Order-Based Attentional Priority Modulates Mnemonic Representations in Parietal and Frontal Cortices. Cereb Cortex, 2019. 29(7): p. 3182-3192.

      (6) Li, S., et al., Neural Representations in Visual and Parietal Cortex Differentiate between Imagined, Perceived, and Illusory Experiences. J Neurosci, 2023. 43(38): p. 6508-6524.

      (7) Hu, Y. and Yu, Q., Spatiotemporal dynamics of self-generated imagery reveal a reverse cortical hierarchy from cue-induced imagery. Cell Rep, 2023. 42(10): p. 113242.

      (8) Lee, S.H., Kravitz, D.J., and Baker, C.I., Goal-dependent dissociation of visual and prefrontal cortices during working memory. Nat Neurosci, 2013. 16(8): p. 997-9.

      (9) Miller, E.K. and Cohen, J.D., An integrative theory of prefrontal cortex function. Annu Rev Neurosci, 2001. 24: p. 167-202.

      (10) Badre, D., et al., The dimensionality of neural representations for control. Curr Opin Behav Sci, 2021. 38: p. 20-28.

      (11) Flesch, T., et al., Orthogonal representations for robust context-dependent task performance in brains and neural networks. Neuron, 2022. 110(7): p. 1258-1270 e11.

      (12) Wang, X.J., Theory of the Multiregional Neocortex: Large-Scale Neural Dynamics and Distributed Cognition. Annu Rev Neurosci, 2022. 45: p. 533-560.

      (13) Bellmund, J.L.S., et al., Mnemonic construction and representation of temporal structure in the hippocampal formation. Nat Commun, 2022. 13(1): p. 3395.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript co-authored by Pál Barzó et al is very clear and very well written, demonstrating the electrophysiological and morphological properties of human cortical layer 2/3 pyramidal cells across a wide age range, from age 1 month to 85 years using whole-cell patch clamp. To my knowledge, this is the first study that looks at the cross-age differences in biophysical and morphological properties of human cortical pyramidal cells. The community will also appreciate the significant effort involved in recording data from 485 cells, given the challenges associated with collecting data from human tissue. Understanding the electrophysiological properties of individual cells, which are essential for brain function, is crucial for comprehending human cortical circuits. I think this research enhances our knowledge of how biophysical properties change over time in the human cortex. I also think that by building models of human single cells at different ages using these data, we can develop more accurate representations of brain function. This, in turn, provides valuable insights into human cortical circuits and function and helps in predicting changes in biophysical properties in both health and disease.

      Strengths:

      The strength of this work lies in demonstrating how the electrophysiological and morphological features of human cortical layer 2/3 pyramidal cells change with age, offering crucial insights into brain function throughout life.

      Weaknesses:

      One potential weakness of the paper is that the methodology could be clearer, especially in how different cells were used for various electrophysiological measurements and the conditions under which the recordings were made. Clarifying these points would improve the study's rigor and make the results easier to interpret.

      Reviewer #2 (Public review):

      Summary:

      In this study, Barzo and colleagues aim to establish an appraisal for the development of basal electrophysiology of human layer 2/3 pyramidal cells across life and compare their morphological features at the same ages.

      Strengths:

      The authors have generated recordings from an impressive array of patient samples, allowing them to directly compare the same electrophysiological features as a function of age and other biological features. These data are extremely robust and well organised.

      Weaknesses:

      The use of spine density and shape characteristics is performed from an extremely limited sample (2 individuals). How reflective these data are of the population is not possible to interpret. Furthermore, these data assume that spines fall into discrete types - which is an increasingly controversial assumption.

      Many data are shown according to somewhat arbitrary age ranges. It would have been more informative to plot by absolute age, and then perform more rigourous statistics to test age-dependent effects.

      Overall, the authors achieve their aims by assessing the physiological and morphological properties of human L2/3 pyramidal neurons across life. Their findings have extremely important ramifications for our understanding of human life and implications for how different neuronal properties may influence neurological conditions.

      Reviewer #3 (Public review):

      Summary:

      To understand the specificity of age-dependent changes in the human neocortex, this paper investigated the electrophysiological and morphological characteristics of pyramidal cells in a wide age range from infants to the elderly.

      The results show that some electrophysiological characteristics change with age, particularly in early childhood. In contrast, the larger morphological structures, such as the spatial extent and branching frequency of dendrites, remained largely stable from infancy to old age. On the other hand, the shape of dendritic spines is considered immature in infancy, i.e., the proportion of mushroom-shaped spines increases with age.

      Strengths:

      Whole-cell recordings and intracellular staining of pyramidal cells in defined areas of the human neocortex allowed the authors to compare quantitative parameters of electrophysiological and morphological properties between finely divided age groups.

      They succeeded in finding symmetrical changes specific to both infants and the elderly, and asymmetrical changes specific to either infants or the elderly. The similarity of pyramidal cell characteristics between areas is unexpected.

      Weaknesses:

      Human L2/3 pyramidal cells are thought to be heterogeneous, as L2/3 has expanded to a high degree during the evolution from rodents to humans. However, the diversity (subtyping) is not revealed in this paper.

      Recommendations for the authors: 

      Reviewer #1 (Recommendations for the authors):

      The manuscript co-authored by Pál Barzó et al is very clear and very well written, demonstrating the electrophysiological and morphological properties of the human cortical layer 2/3 pyramidal cells across a wide age range, from age 1 month to 85 years using whole-cell patch clamp. To my knowledge, this is the first study that looks at the cross-age differences in morphological and electrophysiological properties of human cortical pyramidal cells. The community will also appreciate the significant effort involved in recording data from 485 cells, given the challenges associated with collecting data from human tissue. understanding the electrophysiological properties of individual cells, which are essential for brain function, is crucial for comprehending human cortical circuits. I think this research enhances our knowledge of how biophysical properties change over time in the human cortex. I also think that by building models of human single cells at different ages using these data, we can develop more accurate representations of brain function. This, in turn, provides valuable insights into human cortical circuits and function and helps in predicting changes in biophysical properties in both health and disease.

      We are grateful for the positive evaluation of our work. We also thank the reviewers for their comments and believe that our manuscript has improved significantly with their help. In addition to the reviewer’s suggestions for improvement, further cell reconstructions were performed to make the anatomical data more robust (n = 1,2,3,3,4,3,2 additional reconstruction in age groups infant, early childhood, late childhood, adolescence, young adulthood, middle adulthood and late adulthood, respectively; Σn = 18). Four additional cells were added to the spine analysis and the statistics associated with each additional dataset were updated.

      I have some comments, particularly regarding the methodology and data presentation, to improve the clarity of the paper

      (1) I assume the tissue is from the resected area adjacent to the tumor. Could you please clarify this in the Methods section?

      Thank you for this comment, it has been clarified in the Methods section with the following sentence: “We used human cortical tissue adjacent to the pathological lesion  that had to be surgically removed from patients (n = 63 female  n = 45 male) as part of the treatment for tumors, hydrocephalus, apoplexy, cysts, and arteriovenous malformation.”

      (2) Regarding the presentation of data in the Methods section, could you please clarify whether the authors used different cells for measuring the various electrophysiological properties? The number of recorded cells for calculating subthreshold properties (e.g., late adulthood: n = 113) differs from the number the cells used for calculating suprathreshold properties (e.g., late adulthood: n = 83). If this is the case, it may make it difficult to compare the electrophysiological properties. Could you please clarify this?

      The different element numbers are indeed due to the fact that different quality criteria were defined for the analysis of fast and slow signals. For the analysis of fast signals (e.g. AP half-width, AP upstroke velocity, AP amplitude), higher quality requirements were established therefore cells with high series resistance (> 30 MΩ) were excluded. We have updated and clarified the recording conditions in the text, figures, and methodology section accordingly.

      (3) Additionally, they mentioned that their recordings were done at zero holding current and at more than -50 pA. Could you clarify whether the data from these two sets of experiments were combined? If so, please provide an explanation in the methods section.

      Basically, we wanted to determine the parameters of the potential changes of the membrane at rest. However, for technical reasons related to the biological amplifier, in some of the experiments a certain continuous holding current may be present during the measurement (3.5% of all experiments). The holding currents were in the range of -50 pA to +60 pA. Within this range, previously checked on mouse neurons we have not found linear correlation between the electrophysiological properties and the holding current. This is reported in the Methods section.

      (4) This section needs revision. It is unclear why different series resistances (Rs) or different cells were used to compute various electrophysiological properties." To calculate passive membrane properties (resting membrane potential, input resistance, time constant, and sag) either cells with series resistance (Rs): 22.85 {plus minus} 9.04 MΩ (ranging between -4.55 MΩ and 56.76 MΩ) and 0 pA holding current (n = 154), or cells with holding current > -50 pA (-7.46 {plus minus} 28.56 pA, min: -49.89 pA, max: 59.68pA) and Rs < 30 MΩ (18.96 {plus minus} 6.48 MΩ) (n = 23) were used. For the analysis of high frequency action potential features (AP half-width, AP up-stroke velocity, AP amplitude and rheobase) cells with Rs < 30 MΩ (n = 331 cells with Rs 19.2 {plus minus} 6.6 MΩ) and holding current > -50pA (n = 308 with 0 pA holding current and Rs: 19.22 {plus minus} 6.59 MΩ, n = 23 withholding current: -7.46 {plus minus} 28.56 pA and Rs: 18.96 {plus minus} 6.48 MΩ) were used."

      To make the chapter clearer, we simplified the cell groups used to analyse the different electrophysical properties and revised the Method section as follows: “For the analysis of the electrophysiological recordings n = 457 recordings with a series resistance (Rs) of 24.93 ± 11.18 MΩ (max: 63.77 MΩ) were used. For the analysis of fast parameters related to the action potential (AP half-width, AP upstroke velocity, AP amplitude and rheobase), higher quality requirements were set and cells with Rs > 30 MΩ were excluded. This reduced the data set to n = 331 cells with Rs 19.42 ± 6.2 MΩ.”

      (5) The authors recorded the sag ratio using a -100 pA injected current. Is there a technical reason why they did not inject more than -100 PA?

      There is no particular technical reason, we use similar to others this current amplitude for voltage response recordings over the years to record electrophysiological traces.

      (6) In the abstract, the authors mentioned that data were recorded from ages 1 month to 85 years. However, in the results, they stated that data were recorded from ages 0 to 85 years. Could you please clarify this discrepancy?

      We corrected this discrepancy.

      (7) Additionally, the results mention that data were collected from 485 human cortical layer 2/3 (L2/3) pyramidal cells, but subthreshold membrane features such as resting membrane potential, input resistance, time constant (tau), and sag ratio were calculated in 475 cortical pyramidal cells from 99 patients. Could you please clarify these discrepancies? In the discussion "We recorded from n = 457 human cortical excitatory pyramidal cells from the supragranular layer from birth to 85 years"

      Thank you for pointing this out, we have corrected the error. Although our full data set contained 485 pyramidal cells, 28 recordings were excluded from the electrophysiological analysis and were used for morphological evaluation only, therefore 457 recordings were used for passive parameter measurements.

      (8) Regarding the distance from the pia to the border layer L1/L2, did the authors notice any differences across ages?

      To investigate whether the thickness of cortical layer 1 changes throughout life, we measured the L1 thickness and found no significant differences between age groups (P = 0.09, Kruskal-Wallis test) (Author response image 1).

      Author response image 1.

      Thickness of cortical layer 1 at different life stages. (A) Boxplot shows the thickness of layer 1. (B) Scatter plot shows the distribution of L1 thickness measured on the reconstructed cells. Age is shown in years on a logarithmic scale, dots are color-coded according to the corresponding age groups.

      (9) I am not sure why they referred to the data as layer 2/3 when most of the data, based on Figure 1E, were recorded from a distance of 0-200 µm from the L1/L2 border. Could it be that there is no significant depth-dependent variation in electrophysiological properties, as reported by Berg (2021), Kalmbach (2018), and Chameh (2021)?

      Although the vast majority of our data comes from a distance of less than 200 μm from the L1/L2 border, we cannot neglect the fact that our dataset also contains a small number of cells deeper than this, which are layer 3 cells. Apart from some differences shown in Supplementary Figures 7-9, we found no general difference between cells located at a distance of less than 200 μm and more than 200 μm from the L1 border.

      (10) In Figure 1, there is variability in resting membrane potential (RMP), tau, and input resistance (IR) within the infant age group. However, this trend is not observed in the sag ratio. Could you please discuss this finding?

      The large variance in the data is due to dramatic changes in these three parameters during the first year of life. Supplementary Figure 3 shows the comparisons of parameter distributions of patients between 0-6 months and 6-12 months. The sag amplitude in these cells is generally low therefore no such large changes could have occurred in them.

      (11) Did the authors use a K-Nearest Neighbors (KNN) test to assess the accuracy of the infant cluster in Figure 3F?

      Based on eight electrophysiological features of the cells (resting Vm, input resistance, tau, sag ratio, rheobase, AP half-width, AP up-stroke, and AP amplitude), the infant pyramidal cells on a UMAP form a distinct group (Author response image 2A) represented by cluster 4 on Author response image 2B. When calculating the sum of the Euclidean distances of cells within the cluster from the centroid, the isolated infant group (cluster 4) shows the smallest distance value from the centroid (cluster 1: 40.2, cluster 2: 36.21, cluster 3: 39.96, cluster 4: 5.72, cluster 5: 39.2, cluster 6: 55.74, cluster 7: 54.27), demonstrating that infant cells create a discrete cluster distinct from other age groups (Author response image 2B).

      Author response image 2.

      (A) Uniform Manifold Approximation and Projection (UMAP) of 8 selected electrophysiological properties (resting Vm, input resistance, tau, sag ratio, rheobase, AP half-width, AP up-stroke, and AP amplitude) with data points for 331 cortical L2/3 pyramidal cells, colored with the corresponding age groups. (B) UMAP colored by k-means clustering with 7 clusters, red crosses represent the centroids of the clusters.

      (12) Missing citation: 'Previous research has shown that the biophysical properties of human pyramidal cells show depth-related correlations throughout L2/3 (Berg et al., 2021).' Please include citations for Kalmbach (2018) and Chameh (2021).

      We thank for the additional references, these studies are now cited.

      (13) Have they noticed any morphological properties differences among the different cortical lobes (Parietal, Temporal, Frontal, and Occipital). It would be beneficial to present this data, especially since they have a sufficient sample size from each cortical lobe.

      The majority of our data set on the morphological properties of pyramidal cells comes from the parietal (n = 17 cells) and temporal lobe (n = 15). We found no significant differences in the morphological properties of cells from these two brain regions and no differences between age groups in the same cortical lobes.

      (14) Have the authors found differences in spine characteristics among different cortical areas, as reported previously by 10.1023/a:1024134312173).

      We found morphological differences in dendritic spines in the different brain regions, yet, our data are limited to draw definitive conclusions.

      Reviewer #2 (Recommendations for the authors):

      Major

      (1) I believe that these data presented in all main text figures would be more intuitive to be plotted on a log(age) scale, such as shown in supplementary Figure 13. The bounds of the ages used for different groups, as summarised in Figure 1 feel somewhat arbitrary.

      Recent neuroscientific studies on postnatal ageing mainly use the age-group comparison format (Kang 2011, Bethlehem 2022), which has been defined based on milestones in the cognitive, motor, social-emotional, and language/communications domains of observable behaviour (Zubler et al. 2022, for detailed definitions see Kang 2011). Since many parameters do not vary linearly but take a U-shape (or inverted U-shape), statistical quantification of these is not straightforward, so we would retain the age-group format for the main graphs. However, at the reviewer's suggestion, electrophysiological and morphological parameters are presented on a log(age) scale as supplementary figures (Supplementary Figures 2,4 and 6), also further statistical analysis was also carried out without grouping the data (see response 5).

      (2) The authors present a lot of data values in the text, which is also shown in the figures. This makes reading of the manuscript somewhat difficult in places. For brevity, it may be best to present this data as supplementary tables.

      Thank you for this suggestion. We have inserted these data as tables.

      (3) I am unclear why the authors excluded cells that fired doublets or triplets in Figure 4? Were these included in the passive and AP-specific analysis - but excluded from F-I plots? Please clarify the rationale and the relative abundance of these physiological types based on age - one might predict that more initial-burst firing types are associated with older neurons?

      Thank you for drawing attention to this anomaly. We have updated the figures and text by adding the cells with initial burst firing. These cells are also included in the analysis of passive and action potential properties. In our overall dataset, 6.78% of cells show burst firing; infant: 0%, early childhood: 3.57% (1 cell), late childhood: 0%, adolescence: 11.11% (6 cells), young adulthood: 10.11% (9), middle adulthood: 10.71% (6 cells), late adulthood: 7.96 (9 cells) of all cells including the age groups.

      (4) The statistical analyses performed in Figure 6 are not justified. From the authors' description of these data, they derive spine density measurements from 1 infant and 1 aged adult, then perform pseudoreplicated analysis in these individuals. These data would require greater replication from infant and aged groups - with the possible inclusion of a younger adult group also. It would be ideal to have n=3/age group to allow robust statistical analysis.

      Thank you for this point. Accordingly, we have expanded our data set to include n = 3 infant pyramidal cells (83 days old, from one patient) and n = 3 pyramidal cells from three late adulthood patients (64.3 ± 2.08 years old).

      (5) Given the high number of individuals and replicates throughout this manuscript, a more circumspect approach to statistics would be appreciated, e.g. a generalised linear mixed effects model - with age as a fixed effect and sex, patient, etc as random effects. This may reveal the greatest statistical power of these important and rich data.

      Of the generative models we used the Generalized Additive Mixed Model (GAMM) to describe the relationship between age and the various passive and active electrophysiological features. We defined age with cubic spline smoothing term as the fixed effect and gender, brain area, surgical procedure, and hemisphere as random effects. With GAMM we found that the age-dependent correlation of the examined parameters (resting membrane potential, input resistance, tau, sag ratio, rheobase current, AP half-width, AP up-stroke velocity, AP amplitude, first AP latency, adaptation) was significant, except for F-I slope, described by the model incorporating the four random effects.  We also observed correlation with gender, brain area, hemisphere, and surgical procedure in various intrinsic properties. The Author response table 1 below shows the statistical values of GAMM and the statistical tests used in the manuscript to compare.

      Author response table 1.

      Statistical significance of patient attributes *In the pairwise comparison, the age of cells in the two groups was significantly different: female (subthreshold: 37.36 ± 26.25 years old, suprathreshold: 38.3 ± 25.6 y.o.) - male (subthreshold: 24.86 ± 23.7 y.o., suprathreshold: 25.7 ± 23.93 y.o.), subthreshold: P = 1.96*10-6, suprathreshold: P = 3.25*10-5 Mann-Whitney test. **In the pairwise comparison, the age of cells in the two groups was significantly different: surgical procedure: tumor removal (subthreshold: 33.72 ± 24.33 y.o., suprathreshold: 36.43 ± 27.07 y.o.) - VP shunt (subthreshold: 27.38 ± 29.69 y.o., suprathreshold: 27.07 ± 29.37 y.o.) subthreshold: P = 3.68*10-3, suprathreshold: P = 1.64-10-3, Mann-Whitney test)

      (6) Regarding the morphological diversity of dendritic spines. There is some debate in the field as to whether the distinction of specific dendritic spine types - as conveyed in this manuscript - are true subtypes or reflect a continuum of diverse morphology (see Tønneson et al., 2014 Nature Neuroscience). It is appreciated that the approach taken by the authors is the dogma within the field - however, dogma should continue to be challenged. Given that the authors have used DAB labelling combined with light microscopy, the possibility of accurately measuring spine morphology required for determining this continuum is extremely limited (e.g. Li et al., (2023) ACS Chemical Neuroscience). I would suggest that alongside the inclusion of further replicates for their spine analysis, the authors tone down their discussion of spine subtypes given the absence of any synaptic data presented in this current study to support the maturation (or otherwise) of dendritic spine synapses.

      Many thanks to the reviewer for this comment. We agree with the drawbacks of our method for testing spine categorization. To increase the reliability of our results, we increased the number of pyramidal cells in the infant and late adult groups. We also revised the figure and as suggested by Reviewer#3 added photos of spines to each category in addition to schematic drawings to give an impression of the phenotype. In the discussion, we only address the differences between two readily separable mushroom and filopodial forms and highlight results that only confirm findings already known in the literature. Although the concerns are valid, we apply the sentence from the above Li et al. (2023) reference “...the most sophisticated equipment may not always be necessary for answering some research questions”. We believe that it is worth sharing our data and the somewhat subjective grouping, which we hope to report in more detail in the future.

      Minor

      (1) The order of the supplemental materials is out of order with their introduction in the text. These should be revised to reflect the order mentioned in the text.

      Thank you for your comment, we have corrected the order of the supplementary figures.

      (2) In Supplementary Figure 13, it would be informative to include some form of linear regression to confirm whether an age-dependent effect on neuronal morphology exists.

      We have added linear regression to the figure.

      (3) Figure 3D = should this be AP - not Ap?

      Thank you for drawing attention to this, we have corrected the incorrect typing on the figure.

      (4) For UMAP analysis in Figure 3, please provide a table of the features that were used for the 32 & 8-parameter UMAPs respectively.

      We have added a table to the Materials and methods section of all the electrophysiological features included in the UMAP.

      (5) For morphology, please include pia and L1/2 border for reconstructions shown for clarity.

      We indicated both the pia mater and the L1/2 border on the figure showing all the reconstructions (Supplementary Figure 10).

      Reviewer #3 (Recommendations for the authors):

      Major:

      (1) Data were obtained from different cortical areas of human patients of different ages. The electrophysiological characteristics were largely independent of other attributes such as disease, gender, and cortical areas (Supplementary Figure 2). To support the conclusion that age is one of the key attributes responsible for change, a similar morphological analysis would be necessary for gender.

      We updated the text and the supplementary section with Supplementary Figures 18-21. to determine if age-related differences in biophysical characteristics are affected by the patient's gender.

      (2) 'mushroom-shaped, thin, filopodial, branched, and stubby spines'

      Show photographs of individual typical spine types to make the classification easier to understand.

      To make the classification more understandable, we have updated the corresponding figure (Figure 6) with representative photos of the dendritic spine types.

      (3) Some electrophysiological parameters of the infant group showed higher deviations compared to other age groups. A UMAP (Supplementary Figure 2) shows that some infant neurons form a small cluster, while other infant neurons are scattered with neurons of other ages. Are there any differences between infant neurons in the small cluster and other infant neurons with respect to attributes other than age?

      For most of the electrophysiological parameters, the infant age group showed age-dependent variability, as illustrated in Supplementary Figures 3, 2,4 and 6 . The small group of infant cells is not clustered by gender, brain region, or medical condition, as shown in Supplementary Figure 5.

      (4) A recent paper (Benavides-Piccione et al. 2024, doi:10.1093/cercor/bhae180) reported that some morphological parameters of human layer 3 neurons differ between occipital and temporal regions. Area-dependent morphological differences have been also reported in non-human primates. Discussion of potential contradictions may therefore be requested.

      Most of the cells we reconstructed originated from the parietal and temporal regions (parietal: n = 20, temporal: n = 23, frontal: n = 15, occipital: n = 5). We found no differences in morphological features between these two regions, and we also found no significant differences when we compared the cells from the same brain regions by age group.

      (5) L2/3 cells of rodents are morphologically differentiated according to cortical depth. If individual L2/3 cells of humans are less differentiated than those of rodents, this point should be discussed.

      Depth-related morphological heterogeneity has already been reported previously (Berg 2021), however, our dataset on the morphological characteristics of pyramidal cells is from the upper L2/3 region, with their soma located at a distance of 117.85 ± 65.3 μm (between: 11.05 and 243.3 μm) from the L1/L2 border. Therefore, we cannot conclude from our data whether humans are less differentiated than rodents.

      Minor:

      (1) Cell body morphology may affect electrophysiological properties. However, morphological quantification of cell bodies has not been reported. It may be added.

      In our DAB-labeled samples, we could not perfectly measure the total volume of the cell body in the reconstructions, therefore our measurements regarding the soma morphology are not shown in the manuscript. When comparing the cell body area of the middle sections of the soma of the reconstructed cells between the age groups, we found no significant differences (P = 0.082, Kruskal–Wallis test).

      (2) 'The adaptation of the AP frequency response'

      Describe how this parameter was obtained.

      The adaptation of the AP frequency response or adaptation was calculated as the average adaptation of the interspike interval between consecutive APs.

      (3) 'we excluded cells showing initial duplet or triplet action potential bursts'

      Why were the burst cells excluded from the analysis?

      We have modified the figures and text to include cells with initial burst firing.

      (4) Electrophysiological characteristics to be analyzed:

      Spike thresholds and afterhyperpolarizations

      We found age-related differences in the amplitude of the afterhyperpolarization (P = 2.56*10<sup>-30</sup>, Kruskal-Wallis test) and in the threshold of the action potential (P = 5.24*10<sup>-12</sup>, Kruskal-Wallis test) (Author response image 3).

      Author response image 3.

      Age-dependence of afterhyperpolarization and AP threshold. (A-B) Boxplots show the differences in afterhyperpolarization (AHP) amplitude (A) and AP threshold (B) between age groups. Asterisks indicate statistical significance (* P < 0.05, ** P < 0.01, *** P < 0.001, Kruskal-Wallis test with post-hoc Dunn test). (C-D) Scatter plots show AHP amplitude (C) and AP threshold (D) across the lifespan. Age is shown on a logarithmic scale, dots are colored according to the corresponding age group.

      (5) 'We identified and labeled each spine on n = 2 fully 3D-reconstructed cells'

      To which cortical area do these cells belong?

      At what depths are they distributed?

      Is it possible to report the number of spines, in addition to the density per unit length?

      We increased the number of cells in which we analyzed dendritic spine density. The data shown in Figure 6. are from pyramidal cells from an infant patient (n = 3 from a single patient) and late adulthood patients (n = 3 from 3 patients) (Supplementary Figure 13). The infant cells are from the same patient, the sample is from the right parietal lobe, and the patient is 83 days old. The older cells are from three different patients (#1: 65 years old, right temporal lobe; #2: 66 years old, right parietal lobe; #3: 62 years old, right frontal lobe). Infant cells are located 144.43 ± 45.26 µm (#1: 109.3, #2: 128.49, #3: 195.5 µm), late adult cells 161.22 ± 66.22 µm (#1: 183.5, #2: 213.42, #3: 86.73 µm) from the L1/2 border. We provide the number of spines in an additional supplementary table (Supplementary table 2.).

    1. Author response:

      The following is the authors’ response to the original reviews

      We thank the reviewers for their careful review of our manuscript and the constructive comments. We have addressed the majority of comments with either new experiments, analyses, and/or text revisions. A summary of the major changes is listed below, followed by our point-by-point responses to the reviewer comments.

      Major changes:

      (1) We sought to gain insight into the potential mechanistic cause of the increased intrinsic excitability of Cntnap2<sup>-/-</sup> dSPNs. Given that Kv1.1 and 1.2 potassium channels are known to interact with Caspr2 (the protein encoded by Cntnap2), we hypothesized that altered number, location, and/or function of these channels may underlie the excitability change in these cells. To investigate this, we performed new analyses of the initial dataset to assess action potential (AP) properties known to be impacted by potassium channel function. Indeed, we found that AP frequency was increased, and rheobase current, AP latency and AP threshold were decreased in Cntnap2<sup>-/-</sup> dSPNs, suggestive of altered Kv1.2 function. These data are in the new Supplemental Fig. 4. We also performed new electrophysiology experiments in which we pharmacologically blocked Kv1.1 and 1.2 to assess whether the effects of blocking these channels would be occluded in Cntnap2<sup>-/-</sup> dSPNs. We found that 1) WT dSPNs responded to blockade of Kv1.1/1.2 channels by increasing their excitability but Cntnap2<sup>-/-</sup> dSPNs did not and 2) Kv1.1/1.2 channels were more important contributors to the excitability of dSPNs compared to iSPNs. These new data are presented in the revised Fig. 4 and Supplemental. Figs. 5 and 6.

      (2) We performed additional experiments to assess excitatory synaptic properties, specifically AMPA/NMDA receptor ratio. This has been added to Fig. 1.

      (3) We performed more rigorous statistical analyses of the initial physiology datasets to align with the statistics performed for the revision experiments. This applies to Fig. 1, Fig. 2, Fig. 3, Fig. 5, and Supp. Fig. 2.

      (4) In the discussion section, we now highlight potential limitations of the study and further discuss the variable impact that Cntnap2 loss has on different cell types and brain regions.  

      Reviewer #1 (Public Review):

      Summary:

      Cording et al. investigated how deletion of CNTNAP2, a gene associated with autism spectrum disorder, alters corticostriatal engagement and behavior. Specifically, the authors present slice electrophysiology data showing that striatal projection neurons (SPNs) are more readily driven to fire action potentials in response to stimulation of corticostriatal afferents, and this is due to increases in SPN intrinsic excitability rather than changes in excitatory or inhibitory synaptic inputs. The authors show that CNTNAP2 mice display repetitive behaviors, enhanced motor learning, and cognitive inflexibility. Overall the authors' conclusions are supported by their data, but a few claims could use some more evidence to be convincing.

      Strengths:

      The use of multiple behavioral techniques, both traditional and cutting-edge machine learning-based analyses, provides a powerful means of assessing repetitive behaviors and behavioral transitions/rigidity.

      Characterization of both excitatory and inhibitory synaptic responses in slice electrophysiology experiments offers a broad survey of the synaptic alterations that may lead to increased corticostriatal engagement of SPNs.

      Weaknesses:

      (1) The authors conclude that increased cortical engagement of SPNs is due to changes in SPN intrinsic excitability rather than synaptic strength (either excitatory or inhibitory). One weakness is that only AMPA receptor-mediated responses were measured. Though the holding potential used for experiments in Figure 1FI wasn't clear, recordings were presumably performed at a hyperpolarized potential that limits NMDA receptormediated responses. Because the input-output experiments used to conclude that corticostriatal engagement of SPNs is elevated (Figure 1B-E) were conducted in the current clamp, it is possible that enhanced NMDA receptor engagement contributed to increased SPN responses to cortical stimulation. Confirming that NMDA receptor-mediated EPSC components are not altered would strengthen the main conclusion.

      The reviewer is correct, the initial optically-evoked EPSC assessments were performed at a hyperpolarized potential (-70mV), thus measuring primarily AMPAR-mediated currents. We agree that assessing potential changes in the NMDAR-mediated EPSC component is important and we have completed new experiments to assess this. We find no differences in NMDAR-mediated EPSCs assessed at +40mV or the AMPA:NMDA ratio.

      These results have been added to Fig. 1. An expanded analysis of these results is shown in Author response image 1. We note that the previous AMPAR-mediated EPSC results have been replicated in this additional experiment, again showing no change in Cntnap2<sup>-/-</sup> SPNs. 

      Author response image 1.

      AMPA and NMDA receptor-mediated EPSCs are unchanged in Cntnap2<sup>-/-</sup> SPNs. (A) Quantification (mean ± SEM) of AMPA:NMDA ratio per cell for Cntnap2<sup>+/+</sup> and Cntnap2<sup>-/-</sup> dSPNs, p=0.9537, MannWhitney test. (B) dSPN AMPA current per cell, p=0.6172, Mann-Whitney test. (C) dSPN NMDA current per cell, p=0.6009, Mann-Whitney test. (D) dSPN AMPA:NMDA ratio averaged by animal, p=0.8413, Mann-Whitney test. (E) dSPN AMPA current averaged by animal, p>0.9999, Mann-Whitney test. (F) dSPN NMDA current averaged by animal, p=0.6905, Mann-Whitney test. (G) Quantification (mean ± SEM) of AMPA:NMDA ratio per cell for Cntnap2<sup>+/+</sup> and Cntnap2<sup>-/-</sup> iSPNs, p=0.4104, Mann-Whitney test. (H) iSPN AMPA current per cell, p=0.9010, Mann-Whitney test. (I) iSPN NMDA current per cell, p=0.9512, two-tailed unpaired t test. (J) iSPN AMPA:NMDA averaged by animal, p=0.3095, Mann-Whitney test. (K) iSPN AMPA current averaged by animal, p=>0.9999, Mann-Whitney test. (L) iSPN NMDA current averaged by animal, p=0.8413, MannWhitney test. All values were recorded using 20% blue light intensity. For dSPNs: Cntnap2<sup>+/+</sup> n=22 cells from 5 mice, Cntnap2<sup>-/-</sup> n=22 cells from 5 mice. For iSPNs: Cntnap2<sup>+/+</sup> n=21 cells from 5 mice, Cntnap2<sup>-/-</sup>n=21 cells from 5 mice.

      (2) Data clearly show that SPN intrinsic excitability is increased in knockout mice. Given that CNTNAP2 has been linked to potassium channel regulation, it would be helpful to show and quantify additional related electrophysiology data such as negative IV curve responses and action potential hyperpolarization.

      We appreciate this suggestion. As indicated by the reviewer, Caspr2, has previously been shown to control the clustering of Kv1-family potassium channels in axons isolated from optic nerve and corpus callosum (PMIDs: 10624965, 12963709, 29300891). In particular, Caspr2 is known to associate directly with Kv1.2 (PMID: 29300891). To assess a potential contribution of Kv1.2 to the excitability phenotype, we performed additional analyses of our original dataset to quantify AP properties known to be impacted by changes in Kv1.2 function (i.e. latency to fire and AP threshold, new Supp. Fig. 4). We identified several changes in Cntnap2<sup>-/-</sup> dSPNs resembling those that occur in wild-type cells when Kv1.2 is blocked (i.e. reduced threshold and reduced latency to fire, Supp. Fig. 4). 

      We then performed a pharmacological experiment, blocking Kv1.2 using α-dendrotoxin (α-DTX) while recording intrinsic excitability to assess whether the effects of this drug on dSPN excitability were occluded in Cntnap2<sup>-/-</sup> cells. Indeed, we found that while blocking Kv1.2 in wild-type dSPNs significantly reduced threshold and increased intrinsic excitability, these effects were not seen in Cntnap2<sup>-/-</sup> dSPNs (new Fig. 4). We believe that this suggests an altered contribution of Kv1.2 to the intrinsic excitability of mutant dSPNs, owing to a change in the clustering, number, or function of these channels. Therefore, loss-of-function of Kv1.2 is a likely explanation for the enhanced intrinsic excitability of Cntnap2<sup>-/-</sup> dSPNs. Interestingly, we found that α-DTX had only subtle effects on iSPNs (Cntnap2 WT or mutant), suggesting a lesser contribution of this channel in controlling the excitability of indirect pathway cells. This finding can account for the relatively stronger effect of Cntnap2 loss on dSPN physiology. The results of these new experiments and analyses are presented in the new Fig. 4, Supp. Fig. 5 and Supp. Fig. 6. 

      (3) As it stands, the reported changes in dorsolateral striatum SPN excitability are only correlative with reported changes in repetitive behaviors, motor learning, and cognitive flexibility.

      We agree that we have not identified a causative relationship between the change in dorsolateral dSPN excitability and the behaviors that we measured in Cntnap2<sup>-/-</sup> mice. That said, in a previous study, we showed that selective deletion of the autism spectrum disorder (ASD) risk gene Tsc1 from dorsal striatal dSPNs resulted in increased corticostriatal drive and this was sufficient to increase rotarod motor learning (PMID: 34380034). Therefore, while we have not demonstrated causality in this study, we hypothesize that changes in dSPN excitability are likely to contribute to the behavioral phenotypes observed in Cntnap2<sup>-/-</sup> mice. 

      Reviewer #2 (Public Review):

      Summary:

      This is an important study characterizing striatal dysfunction and behavioral deficits in Cntnap2<sup>-/-</sup> mice. There is growing evidence suggesting that striatal dysfunction underlies core symptoms of ASD but the specific cellular and circuit level abnormalities disrupted by different risk genes remain unclear. This study addresses how the deletion of Cntnap2 affects the intrinsic properties and synaptic connectivity of striatal spiny projection neurons (SPN) of the direct (dSPN) and indirect (iSPN) pathways. Using Thy1-ChR2 mice and optogenetics the authors found increased firing of both types of SPNs in response to cortical afferent stimulation. However, there was no significant difference in the amplitude of optically-evoked excitatory postsynaptic currents (EPSCs) or spine density between Cntnap2<sup>-/-</sup> and WT SPNs, suggesting that the increased corticostriatal coupling might be due to changes in intrinsic excitability. Indeed, the authors found Cntnap2<sup>-/-</sup> SPNs, particularly dSPNs, exhibited higher intrinsic excitability, reduced rheobase current, and increased membrane resistance compared to WT SPNs. The enhanced spiking probability in Cntnap2<sup>-/-</sup> SPNs is not due to reduced inhibition. Despite previous reports of decreased parvalbumin-expressing (PV) interneurons in various brain regions of Cntnap2<sup>-/-</sup> mice, the number and function (IPSC amplitude and intrinsic excitability) of these interneurons in the striatum were comparable to WT controls.

      This study also includes a comprehensive behavioral analysis of striatal-related behaviors. Cntnap2<sup>-/-</sup> mice demonstrated increased repetitive behaviors (RRBs), including more grooming bouts, increased marble burying, and increased nose poking in the holeboard assay. MoSeq analysis of behavior further showed signs of altered grooming behaviors and sequencing of behavioral syllables. Cntnap2<sup>-/-</sup> mice also displayed cognitive inflexibility in a four-choice odor-based reversal learning assay. While they performed similarly to WT controls during acquisition and recall phases, they required significantly more trials to learn a new odor-reward association during reversal, consistent with potential deficits in corticostriatal function.

      Strengths:

      This study provides significant contributions to the field. The finding of altered SPN excitability, the detailed characterization of striatal inhibition, and the comprehensive behavioral analysis are novel and valuable to understanding the pathophysiology of Cntnap2<sup>-/-</sup> mice.

      Weaknesses:

      (1) The approach based on Thy-ChR2 mice has the advantage of overcoming issues caused by injection efficiency and targeting variability. However, the spread of oEPSC amplitudes across mice shown in panels of Figure 1 G/I is very high with almost one order of magnitude difference between some mice. Given this is one of the most important points of the study it will be important to further analyze and discuss what this variability might be due to. Typically, in acute slice recordings, the within-animal variability is larger than the variability across animals. From the sample sizes reported it seems the authors sampled a large number of animals, but with a relatively low number of neurons per animal (per condition). Could this be one of the reasons for this variability?

      We agree with the reviewer that the variability in these experiments is quite large. We have replicated these experiments in the process of performing AMPA:NMDA ratio recordings (see above response to Reviewer 1’s comment). We again find no differences in AMPAR-mediated EPSC amplitude between WT and mutant SPNs (Author response image 2). Notably, these experiments also demonstrate a large amount of variability. In the original dataset, a small number of cells were collected from each animal (~1-3 cells/mouse). However, the variability remains in the new dataset, in which more cells were collected from each animal (~4-6 cells/mouse). We find both withinanimal and between-animal variability, as can be seen in Author response image 2 (recordings made from the same animal are color-coordinated). Potential sources of variability in this experiment include: 1) variable expression of ChR2 per mouse, 2) variable innervation of ChR2-expressing terminals onto any given recorded cell, and/or 3) differences in prior plasticity state between cells (i.e. some neurons may have recently undergone corticostriatal LTP or LTD). 

      Author response image 2.

      Optically-evoked AMPAR EPSCs exhibit within- and between-animal variability. (A) Quantification of EPSC amplitude evoked in dSPNs at different light intensities from the original dataset, plotted by cell (line represents the mean, dots/squares represent average EPSC amplitude for each recorded cell). Cntnap2<sup>+/+</sup> n=17 cells from 8 mice, Cntnap2<sup>-/-</sup> n=13 cells from 5 mice. Repeated measures two-way ANOVA p values are shown; g x s F (2, 56) = 0.3879, geno F (1, 28) = 0.8098, stim F (1.047, 29.32) = 76.56. (B) Quantification of EPSC amplitude evoked in dSPNs, averaged by mouse (line represents the mean, dots/squares represent average EPSC amplitude for each mouse). Cntnap2<sup>+/+</sup> n=8 mice, Cntnap2<sup>-/-</sup> n=5 mice. Repeated measures two-way ANOVA p values are shown; g x s F (2, 22) = 0.2154, geno F (1, 11) = 0.2585, stim F (1.053, 11.58) = 49.68. (C) Quantification of EPSC amplitude in dSPNs from the revision dataset, plotted by cell (line represents the mean, dots/squares represent average EPSC amplitude for each recorded cell). Cntnap2<sup>+/+</sup> n=22 cells from 5 mice, Cntnap2<sup>-/-</sup> n=22 cells from 5 mice. Repeated measures two-way ANOVA p values are shown; g x s F (2, 84) = 0.01885, geno F (1, 42) = 0.002732, stim F (1.863, 78.26) = 20.93. (D) Quantification of EPSC amplitude in dSPNs from the revision dataset, averaged by mouse (line represents the mean, dots/squares represent average EPSC amplitude for each mouse). Cntnap2<sup>+/+</sup> n=5 mice, Cntnap2<sup>-/-</sup> n=5 mice. Repeated measures two-way ANOVA p values are shown; g x s F (2, 16) = 0.06288, geno F (1, 8) = 0.006548, stim F (1.585, 12.68) = 16.97. (E) Quantification of EPSC amplitude evoked in iSPNs from the original dataset, plotted by cell (line represents the mean, dots/squares represent average EPSC amplitude for each recorded cell). Cntnap2<sup>+/+</sup> n=13 cells from 6 mice, Cntnap2<sup>-/-</sup> n=11 cells from 5 mice. Repeated measures two-way ANOVA p values are shown; g x s F (2, 44) = 0.9414, geno F (1, 22) = 1.333, stim F (1.099, 24.18) = 52.26. (F) Quantification of EPSC amplitude evoked in iSPNs from original dataset, averaged by mouse (line represents the mean, dots/squares represent average EPSC amplitude for each mouse). Cntnap2<sup>+/+</sup> n=6 mice, Cntnap2<sup>-/-</sup> n=5 mice. Repeated measures two-way ANOVA p values are shown; g x s F (2, 18) = 0.4428, geno F (1, 9) = 0.5635, stim F (1.095, 9.851) = 23.82. (G) Quantification of EPSC amplitude evoked in iSPNs from the revision dataset, plotted by cell (line represents the mean, dots/squares represent average EPSC amplitude for each recorded cell). Cntnap2<sup>+/+</sup> n=21 cells from 5 mice, Cntnap2<sup>-/-</sup> n=21 cells from 5 mice. Repeated measures two-way ANOVA p values are shown; g x s F (2, 80) = 0.04134, geno F (1, 40) = 0.007025, stim F (1.208, 48.31) = 102.9. (H) Quantification of EPSC amplitude evoked in iSPNs from the revision dataset, averaged by mouse (line represents the mean, dots/squares represent average EPSC amplitude for each mouse). Cntnap2<sup>+/+</sup> n=5 mice, Cntnap2<sup>-/-</sup> n=5 mice. Repeated measures two-way ANOVA p values are shown; g x s F (2, 16) = 0.001865, geno F (1, 8) = 0.1004, stim F (1.179, 9.433) = 61.31.

      (2) This is particularly important because the analysis of corticostriatal evoked APs in panels C and E is performed on pooled data without considering the variability in evoked current amplitudes across animals shown in G and I. Were the neurons in panels C/E recorded from the same mice as shown in G/I? If so, it would be informative to regress AP firing data (say at 20% LED) to the average oEPSC amplitude recorded on those mice at the same light intensity. However, if the low number of neurons recorded per mouse is due to technical limitations, then increasing the sample size of these experiments would strengthen the study.

      We appreciate this point; however, the evoked AP experiment and the evoked EPSC experiment were performed on different mice, so it is not possible to correlate the data across experiments. While the evoked AP experiments were performed using potassium-based internal, we used a cesium-based internal to measure AMPAR-mediated EPSCs to more accurately detect synaptic currents. We note that the evoked AP experiments share a similar amount of variability as the evoked EPSC experiments, again possibly owing to variable expression of channelrhodopsin per mouse, variable innervation of ChR2-positive terminals onto individual cells, and/or differences in prior plasticity status between cells.  

      (3) On a similar note, there is no discussion of why iSPNs also show increased corticostriatal evoked firing in Figure 1E, despite the difference in intrinsic excitability shown in Figure 3. This suggests other potential mechanisms that might underlie altered corticostriatal responses. Given the role of Caspr2 in clustering K channels in axons, altered presynaptic function or excitability could also contribute to this phenotype, but potential changes in PPR have not been explored in this study.

      We have now performed more rigorous statistics on the data in Fig. 1 (repeated measures two-way ANOVA) such that the difference in corticostriatal evoked firing in Cntnap2<sup>-/-</sup> iSPNs no longer reaches statistical significance. This is consistent with the modest but statistically non-significant effect of Cntnap2 loss on iSPN intrinsic excitability. We agree with the reviewer that presynaptic alterations could potentially contribute to the changes in cortically-driven action potentials, especially as this experiment was performed without any synaptic blockers present, and Cntnap2 is deleted from all cells. That said, if changes in presynaptic release probability accounted for the increased corticostriatal drive, we would expect to see differences in cortically-evoked EPSCs onto SPNs. 

      While we can’t rule out the possibility of pre-synaptic changes, a straightforward explanation for our findings is that loss or alteration of Kv1.2 channel function is responsible for the increased excitability of Cntnap2<sup>-/-</sup> dSPNs, resulting in enhanced spiking in response to cortical input. Given the fact that Kv1.2 channels appear less important for regulating iSPN excitability (see new Fig. 4 and Supp. Fig. 6), this can explain the greater impact of Cntnap2 loss on dSPN physiology.

      (4) Male and female SPNs have different intrinsic properties but the number and/or balance of M/F mice used for each experiment is not reported.

      We agree that this is an important consideration. Author response table 1 provides the sex breakdown for the intrinsic excitability experiments. While we did not explicitly power the experiments to test for sex differences, Author response image 3 shows the data separated by sex and genotype for the intrinsic excitability experiments. Within genotype, we find no significant differences between males and females, except for Cntnap2<sup>-/-</sup> iSPNs which showed a significant interaction between sex and current step (Author response image 3F). Interestingly, while present in both sexes, the excitability shift of Cntnap2<sup>-/-</sup> dSPNs may be slightly more pronounced in females compared to males (Author response image 3C and D). However, this result would require further validation with a greater sample size.

      Author response table 1.

      Numbers of male and female mice used for the intrinsic excitability experiments.

      Author response image 3.

      Enhanced excitability of Cntnap2<sup>-/-</sup> dSPNs is present in both males and females. (A) Quantification (mean ± SEM) of the number of APs evoked in dSPNs in Cntnap2<sup>+/+</sup> males and females at different current step amplitudes. Cntnap2<sup>+/+</sup> males n=12 cells from 4 mice, Cntnap2<sup>+/+</sup> females n=8 cells from 4 mice. Repeated measures two-way ANOVA p values are shown; s x c F (28, 560) = 0.8992, sex F (1, 20) = 0.3754, current F (1.279, 25.57) = 56.85. (B) Quantification (mean ± SEM) of the number of APs evoked in dSPNs in Cntnap2<sup>-/-</sup> males and females at different current step amplitudes. Cntnap2<sup>-/-</sup> males n=12 cells from 4 mice, Cntnap2<sup>-/-</sup> females n=11 cells from 4 mice. Repeated measures two-way ANOVA p values are shown; s x c F (28, 588) = 0.6752, sex F (1, 21) = 0.04534, current F (2.198, 46.15) = 78.89. (C) Quantification (mean ± SEM) of the number of APs evoked in dSPNs in Cntnap2<sup>+/+</sup> males and Cntnap2<sup>-/-</sup> males at different current step amplitudes. Cntnap2<sup>+/+</sup> males n=12 cells from 4 mice, Cntnap2<sup>-/-</sup> males n=12 cells from 4 mice. Repeated measures two-way ANOVA p values are shown; g x c F (28, 672) = 2.233, geno F (1, 24) = 3.746, current F (1.708, 40.98) = 79.82. (D) Quantification (mean ± SEM) of the number of APs evoked in dSPNs in Cntnap2<sup>+/+</sup> females and Cntnap2<sup>-/-</sup> females at different current step amplitudes. Cntnap2<sup>+/+</sup> females n=8 cells from 4 mice, Cntnap2<sup>-/-</sup> females n=11 cells from 4 mice. Repeated measures two-way ANOVA p values are shown; g x c F (28, 476) = 1.547, geno F (1, 17) = 5.912, current F (1.892, 32.17) = 58.76. (E) Quantification (mean ± SEM) of the number of APs evoked in iSPNs in Cntnap2<sup>+/+</sup> males and females at different current step amplitudes. Cntnap2<sup>+/+</sup> males n=10 cells from 4 mice, Cntnap2<sup>+/+</sup> females n=12 cells from 4 mice. Repeated measures two-way ANOVA p values are shown; s x c F (28, 560) = 1.236, sex F (1, 20) = 1.074, current F (2.217, 44.34) = 179.6. (F) Quantification (mean ± SEM) of the number of APs evoked in iSPNs in Cntnap2<sup>-/-</sup> males and females at different current step amplitudes. Cntnap2<sup>-/-</sup> males n=12 cells from 4 mice, Cntnap2<sup>-/-</sup> females n=9 cells from 4 mice. Repeated measures two-way ANOVA p values are shown; s x c F (28, 532) = 2.513, sex F (1, 19) = 2.639, current F (1.858, 35.31) = 152.5. (G) Quantification (mean ± SEM) of the number of APs evoked in iSPNs in Cntnap2<sup>+/+</sup> males and Cntnap2<sup>-/-</sup> males at different current step amplitudes. Cntnap2<sup>+/+</sup> males n=10 cells from 4 mice, Cntnap2<sup>-/-</sup> males n=12 cells from 4 mice. Repeated measures twoway ANOVA p values are shown; g x c F (28, 560) = 0.4723, geno F (1, 20) = 0.5675, current F (2.423, 48.47) = 301.7. (H) Quantification (mean ± SEM) of the number of APs evoked in iSPNs in Cntnap2<sup>+/+</sup> females and Cntnap2<sup>-/-</sup> females at different current step amplitudes. Cntnap2<sup>+/+</sup> females n=12 cells from 4 mice, Cntnap2<sup>-/-</sup> females n=9 cells from 4 mice. Repeated measures two-way ANOVA p values are shown; g x c F (28, 532) = 1.655, geno F (1, 19) = 0.2322, current F (2.081, 39.55) = 99.45.

      (5) There is no mention of how membrane resistance was calculated, and no I/V plots are shown.

      Passive properties were calculated from the average of five -5 mV, 100 ms long test pulse steps applied at the beginning of every experiment. Membrane resistance was calculated from the double exponential curve fit. This has now been added to the methods section.

      (6) It would be interesting to see which behavior transitions most contribute to the decrease in entropy. Are these caused by repeated or perseverative grooming bouts? Or is this inflexibility also observed across other behaviors? The transition map in Figure S5 shows the overall number of syllables and transitions but not their sequence during behavior. Can this be analyzed by calculating the ratio of individual 𝑢𝑖 × 𝑝𝑖,𝑗 × log2 𝑝𝑖,𝑗 factors across genotypes?

      We thank the reviewer for raising an insightful question. Here we use a finite state Markov chain model to describe the syllable transitions in animal behavior. To quantify the randomness in the system, we calculated the entropy of the Markov chain (see methods section). The reviewer suggested calculating the partial entropy of the transition matrix, which would allow us to estimate the contribution of a subset of states to the entropy of the whole system, given by the equation:

      The partial equation can indeed quantify the stochasticity, or “flexibility” in our context, of the sub-system containing only a subset of the behavior syllables. However, there are two main limitations to this approach:

      (1) The partial entropy fails to account for the transitions connecting the subset with the rest of the states in the system

      (2) The stationary distribution may not reflect the actual probabilities in the isolated sub-system S.

      Consequently, the partial entropy cannot be directly interpreted as the fraction of contributions from specific syllable pairs or sub-system to the entropy of the whole system. To be more specific, while a significant difference between the same sub-system in WT and KO groups could indicate that the sub-system contributes significantly to the difference of overall entropy, a non-significant result does not mean that the sub-system does not contribute to overall entropy difference, as interactions between the sub-system and other notconsidered states are not accounted for.

      Author response image 4.

      Grooming syllables contribute to some but not all differences in syllable transitions in Cntnap2<sup>-/-</sup> mice. We calculated the entropy of each syllable pair using 𝑢𝑖 × 𝑝𝑖,𝑗 × log2 𝑝𝑖,𝑗 for every syllable pair and every animal. We then statistically tested the difference between genotypes for each syllable pair using Mann-Whitney tests. This plot displays those adjusted p-values for each syllable pair between WT and KO groups. The significant p-values suggest that the transitions to syllables 24 and 25 are different between genotypes (note that these correspond to grooming syllables, see Fig. 5N). However, since the overall entropy is a summation of every pair, it is difficult to conclude that syllables 24 and 25 are the sole contributors to the different entropy we observed.

      Reviewer #3 (Public Review):

      Summary:

      The authors analyzed Cntnap2 KO mice to determine whether loss of the ASD risk gene CNTNAP2 alters the dorsal striatum's function.

      Strengths:

      The results demonstrate that loss of Cntnap2 results in increased excitability of striatal projection neurons (SPNs) and altered striatal-dependent behaviors, such as repetitive, inflexible behaviors. Unlike other brain areas and cell types, synaptic inputs onto SPNs were normal in Cntnap2 KO mice. The experiments are welldesigned, and the results support the authors' conclusions.

      Weaknesses:

      The mechanism underlying SPN hyperexcitability was not explored, and it is unclear whether this cellular phenotype alone can account for the behavioral alterations in Cntnap2 KO mice. No clear explanation emerges for the variable phenotype in different brain areas and cell types.

      We agree that identifying the mechanism by which Cntnap2 loss affects intrinsic excitability is interesting and important. We have added experiments to address this and conclude that the improper clustering, number, or function of Kv1.2 channels in Cntnap2<sup>-/-</sup> dSPNs is likely responsible for their increased excitability. These channels are known to be clustered/organized in part by Caspr2 (PMIDs: 10624965, 12963709, 29300891), and Kv1.2 channels are known to play an important role in regulating excitability in SPNs (PMIDs: 13679409, 32075716). In the case of dSPNs, blocking these channels with α-DTX significantly increased the excitability of WT cells (as has been previously reported); however, this effect was occluded in mutant cells, perhaps owing to a decreased contribution of Kv1.2 channels to excitability in Cntnap2<sup>-/-</sup> dSPNs. In addition, we found that blockade of these channels with α-DTX only modestly affected the excitability of iSPNs. Therefore, this can explain why loss of Cntnap2 more strongly affects the excitability of dSPNs. Please see new Fig. 4, Supp. Fig. 5 and Supp. Fig. 6 for these new data. 

      We agree with the reviewer that we have not identified a causative relationship between the change in dSPN excitability and the behavioral alterations in Cntnap2<sup>-/-</sup> mice. This is a limitation of the study. 

      It is interesting to speculate on the root of the varying impacts to excitability that occur across different brain regions and cell types in Cntnap2<sup>-/-</sup> mice. Increased excitability, as we see in dSPNs, has been identified in cerebellar Purkinje cells and L2/3 pyramidal neurons in somatosensory cortex in the context of Cntnap2 loss (PMIDs: 34593517, 30679017, 36793543). However, other cell types in Cntnap2<sup>-/-</sup> mice have exhibited no change in excitability (mPFC, L2/3 pyramidal neurons, PMID: 31141683) or hypoexcitability (subset of L5/6 pyramidal neurons, PMID: 29112191). While all of these cell types express Kv1.2 channels, they fundamentally vary in their intrinsic properties, owing to the role that other ion channels play in membrane excitability. As a result, loss of Cntnap2 is expected to have a variable effect on excitability depending on the cell type and the complement of other ion channels that are present. In addition, an initial change in excitability may drive secondary, potentially compensatory, changes in other channels that lead to a different excitability state. These changes are also expected to be cell type-specific. We do note that both of the cell types that show increased excitability in the context of Cntnap2 loss have been shown to exhibit an α-DTX-sensitive Kv1 channel current, such that application of α-DTX results in increased firing of these cells (cerebellar Purkinje cells; PMIDs: 17087603, 16210348 and L2/3 pyramidal neurons in somatosensory cortex; PMID: 17215507). These findings are consistent with our results in Cntnap2<sup>-/-</sup> dSPNs. 

      Reviewer #1 (Recommendations For The Authors):

      More thorough analysis of some of the manually quantified behaviors would be helpful. For example, only the grooming bout number was presented- what about the duration of bouts and total time grooming? Similarly, for the open field the number of center entries was reported but what about the total time in the center?

      We have quantified the time spent grooming and total time spent in the center during the open field test from our original data (Author response image 5). These data were not originally included in the manuscript because they were recorded for only a subset of the total animals. For each of these measures we find trend level changes, which are consistent with the primary measures reported in the main manuscript. 

      Author response image 5.

      Time in center and time spent grooming trend towards an increase in Cntnap2<sup>-/-</sup> mice.  (A) Quantification (mean ± SEM) of total time spent in the center of the open field during a 60 minute test, p=0.0656, Mann-Whitney test. (B) Time spent grooming during the first 20 minutes of the open field test, p=0.0611, Mann-Whitney test. For both measurements, Cntnap2<sup>+/+</sup> n=18 mice, Cntnap2<sup>-/-</sup> n=19 mice.

      Reviewer #3 (Recommendations For The Authors):

      What accounts for the hyperexcitability observed in Cntnap2-deficient SPNs? The authors noted that excitability is reportedly increased, reduced, or unchanged in different brain areas. What accounts for this disparity? Is it about the subcellular localization of Kv1 channels? The authors may want to test this possibility experimentally. At least, they may want to test whether Kv1 channels are mislocalized in SPNs.

      We agree that this is an important point, and we have performed additional experiments to address this. We find that the Kv1.2 blocker a-DTX significantly increases the excitability of WT dSPNs but not Cntnap2<sup>-/-</sup> dSPNs. This suggests that the mechanism underlying dSPN hyperexcitability in Cntnap2 mutants is the improper clustering, number, or function of Kv1.2 channels. These channels are known to be clustered and organized in part by Caspr2 (PMIDs: 10624965, 12963709, 29300891) and have been shown to play an important role in regulating the excitability of SPNs (PMIDs: 13679409, 32075716). Interestingly, we find that a-DTX has less of an effect on the excitability of iSPNs, which may account for the greater impact of Cntnap2 loss on dSPNs. Please see new Fig. 4, Supp. Fig. 5 and Supp. Fig. 6 for these added data and analyses. 

      Please see above response to Reviewer #3 for our speculation on the variable impact of Cntnap2 loss on different cell types and brain regions. 

      We agree with the reviewer that assessing potential differences in subcellular localization of Kv1 channels in our model would bolster the conclusion that these channels are mislocalized in the Cntnap2<sup>-/-</sup> striatum. We piloted these experiments using immunohistochemistry to stain for Kv1.1 and 1.2 but found that without very high-resolution imaging, it would be challenging to accurately quantify Kv1 puncta in a cell type-specific manner. We instead chose to investigate the functional contribution of Kv1 channels to the dSPN hyperexcitability phenotype through the a-DTX experiments outlined above. α-DTX strongly inhibits Kv1.2 channels, but also Kv1.1 channels to some extent (PMIDs: 12042352, 13679409). We find that the effects of a-DTX on SPN excitability are occluded in Cntnap2<sup>-/-</sup> dSPNs; therefore, we conclude that Kv1.2 (and possibly Kv1.1) channels have reduced function in these cells. Further work will be needed to determine if this is a result of channel mislocalization or another type of alteration. 

      The authors did not detect synaptic changes in Cntnap-deficient SPNs. This important observation should be briefly discussed in the context of previous work in other brain regions and cell types. For example, some studies reported structural and functional changes at excitatory synapses. The variable impact on synapses suggests distinct compensatory mechanisms in different brain areas.

      Given the prior literature showing effects of Cntnap2 loss on synapses in other brain regions, we were surprised that striatal synapses were not impacted in our model. We agree with the reviewer that the variable changes in synaptic properties across brain regions in Cntnap2 mutant mice is likely a result of distinct compensatory changes in these regions. Differences may also arise depending on whether the synaptic changes originate from the post-synaptic cell or from pre-synaptic changes. An interesting direction for future studies would be to explore the developmental trajectory of excitability and synaptic changes to determine which may be initial perturbations versus those that are secondary and potentially compensatory.

      Line 138: "synaptic excitability". How is this term defined? Consider "synaptic changes" instead.

      “Synaptic excitability” was used to mean a change in the number and/or function of glutamate receptors. We have now changed this term to “excitatory synaptic changes.”

      Consider a short paragraph to highlight some limitations of this study. For example, it is unclear whether SPN hyperexcitability results from a compensatory change in Cntnap2 KO mice and whether the behavioral phenotype is solely due to this cellular phenotype. The study focuses on cortical projections onto SPNs, but these cells receive inputs from other brain areas that were not explored. Lastly, no clear explanation emerges for the variable phenotype in different brain areas and cell types.

      We thank the reviewer for this suggestion and have added several paragraphs to the discussion highlighting some limitations of this study.

      We hypothesize that the dSPN hyperexcitability in Cntnap2<sup>-/-</sup> mice is a primary change, due to the direct relationship between Caspr2 and Kv1.2 channels. The results of our -DTX experiments suggest that the function and/or contribution of these channels to excitability is altered in Cntnap2<sup>-/-</sup> dSPNs. However, it is possible that there are additional changes in dSPNs that occur as a result of Cntnap2 loss and contribute to the hyperexcitability of these cells. Rather surprisingly, we don’t find evidence for altered excitatory (specifically from cortical inputs) or inhibitory synaptic function, suggesting lack of engagement of homeostatic mechanisms at the synaptic level.

      We have not yet determined whether there is a causative relationship between the change in dSPN excitability and the behavioral alterations in Cntnap2<sup>-/-</sup> mice. This is a limitation of the current study. In our discussion section, we highlight that the dSPN changes we observe in dorsolateral striatum (DLS) are known to be sufficient to enhance rotarod learning in other mouse models and thus supports a connection between this cellular change and behavior. For the other behaviors we measured, we acknowledge that both DLS and other striatal or extra-striatal brain regions have been implicated in these behaviors, and therefore less of a direct connection can be made. 

      In terms of the inputs, we focused on cortical inputs given their known role in mediating motor and habit learning (PMID: 15242609, 16237445, 19198605). Notably, corticostriatal synapses have been shown to be altered across a variety of mouse models with mutations in ASD risk genes and therefore may be a point of convergence for disparate genetic insults (PMID: 31758607). We agree that the striatum receives inputs from a variety of brain regions, notably the thalamus, which we did not explore in this study. This would be an interesting area for future studies.

      Finally, it is difficult to speculate on the root of the varying impacts to excitability that occur across different brain regions and cell types in Cntnap2<sup>-/-</sup> mice. Please see above response to Reviewer #3 for some speculation on this point in regard to the potential involvement of Kv1.2 in the excitability changes in various Cntnap2<sup>-/-</sup> cell types. To expand upon this, it is known that ASD-associated mutations can have varying impacts on cell function even across similar cell types within a given brain region – we have seen this between dSPNs and iSPNs (this study, PMIDs: 34380034, 39358043), as have other groups studying ASD risk gene mutations in striatum (PMID: 24995986). This differential impact of the same mutation on intrinsic and/or synaptic physiology across cell types has been identified in other brain regions as well (PMID: 22884327, 26601124). Differences in transcriptional programs, protein expression, neuronal morphology, synaptic inputs and plasticity state make up a non-exhaustive set of variables that will impact the physiological function of a neuron, both in terms of the direct but also indirect consequences of an ASD risk gene mutation. To better address this important question, future studies would benefit from a systematic approach to assessing physiological changes in a given ASD mouse model, both across development and across brain regions.

    1. Author response:

      The following is the authors’ response to the current reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study by Wang et al. identifies a new type of deacetylase, CobQ, in Aeromonas hydrophila. Notably, the identification of this deacetylase reveals a lack of homology with eukaryotic counterparts, thus underscoring its unique evolutionary trajectory within the bacterial domain.

      Strengths:

      The manuscript convincingly illustrates CobQ's deacetylase activity through robust in vitro experiments, establishing its distinctiveness from known prokaryotic deacetylases. Additionally, the authors elucidate CobQ's potential cooperation with other deacetylases in vivo to regulate bacterial cellular processes. Furthermore, the study highlights CobQ's significance in the regulation of acetylation within prokaryotic cells.

      Weaknesses:

      The problem I raised has been well resolved. I have no further questions.

      Thanks for your valuable comments very much.

      Reviewer #2 (Public review):

      In recent years, lots of researchers tried to explore the existence of new acetyltransferase and deacetylase by using specific antibody enrichment technologies and high resolution mass spectrometry. Here is an example for this effort. Yuqian Wang et al. studied a novel Zn2+- and NAD+-independent KDAC protein, AhCobQ, in Aeromonas hydrophila. They studied the biological function of AhCobQ by using biochemistry method and MS identification technology to confirm it. These results extended our understanding of the regulatory mechanism of bacterial lysine acetylation modifications. However, I find this conclusion is a little speculative, and unfortunately it also doesn't totally support the conclusion as the authors provided.

      Major concerns:

      - It is a little arbitrary to come to the title "Aeromonas hydrophila CobQ is a new type of NAD+- and Zn2+-independent protein lysine deacetylase in prokaryotes." It should be modified to delete the "in the prokaryotes" except that the authors get new more evidence in the other prokaryotes for the existence of the AhCobQ.

      Thank you for your suggestion. However, I believe there has been some confusion regarding the title. In the revised manuscript we have already updated the title to: "Aeromonas hydrophila CobQ is a new type of NAD+- and Zn2+-independent protein lysine deacetylase."

      This title does not include the phrase "in prokaryotes," as you mentioned. We kindly suggest verifying the version of the manuscript that was reviewed to ensure you are reviewing the most recent changes.

      - I was confused about the arrangement of the supplementary results. Because there are no citations for Figures S9-S19.

      Thank you for your feedback. It appears there may have been a misunderstanding, possibly due to reviewing an outdated version of the manuscript. In the revised manuscript we revised the supplementary figures and now have only 12 figures, all of which are correctly cited in the manuscript on pages 12 to 15. Below is a detailed list of the updated figure citations:

      Figures S1: page 8, line 148;

      Figures S2: page 9, line 168;

      Figures S3 and S4: page 10, line 178;

      Figures S5: page 10, line 186;

      Figures S6: page 10, line 189;

      Figures S7: page 12, line 221;

      Figures S8-S10: page 13, line 245;

      Figures S11: page 11, line 282;

      Figures S12: page 15, line 286

      - Same to the above, there are no data about Tables S1-S6.

      Thank you for your attention to the supplementary materials. As with the figures, we have already uploaded the data for Tables S1-S6 in the revised manuscript on November 19, 2024, and properly cited Tables S1 – S6 in the manuscript. Below is the citation information:

      Tables S1: page 10, line 194;

      Tables S2: page 13, line 245;

      Tables S3: page 21, line 438;

      Tables S4: page 22, line 439;

      Tables S5: page 22, line 445;

      Tables S6: page 27, line 564.

      Please note that Tables S3 – S4 include the chemical reagents, primers, and other experimental materials, which are not intended to be cited in the results section.)

      - All the load control is not integrated. Please provide all of the load controls with whole PAGE gel or whole membrane western blot results. Without these whole results, it is not convincing to come the conclusion as the authors mentioned in the context.

      Thank you for your comment. Please note that the full membrane western blot results were included in the revised manuscript. We hope this satisfies your request. If you need further clarification or additional data, please do not hesitate to let us know.

      - Thoroughly review the materials & methods section. It is unclear to me what exactly the authors describe in the method. All the experimental designs and protocols should be described in detail, including growth conditions, assay conditions, and purification conditions, etc.

      Thank you for your valuable suggestion. In response to your comment and previous feedback, we have alredy revised the Materials & Methods section thoroughly in the revised manuscript. The experimental details, including growth conditions, assay protocols, and purification procedures, are described in full on pages 22 to 30 of the revised manuscript.

      - Include relevant information about the experiments performed in the figure legends, such as experimental conditions, replicates, etc. Often it is not clear what was done based on the figure legend description.

      Thank you very much for your detailed feedback and suggestions. We have made sure to describe what each data point represents in the figure legends, as per the previous feedback. However, we would like to clarify that while we have provided detailed descriptions in the legends, the inclusion of every specific experimental condition in the figure legends could result in redundancy, as these details are already thoroughly outlined in the Materials & Methods section.

      We hope this explanation addresses your concern.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      I have no further revision comments.

      Thank you very much.

      Reviewer #2 (Recommendations for the authors):

      I carefully read the point-to-point response from the author. Although they listed lots of the reasons for the ugly results, it still can not persuade me to accept their conclusions. While, as I know, it is impossible to reject their work in eLife as it was sent out for peer-review. I also can't accuse them of being wrong, but I have my opinion on this point. That is not the results, but the attitude.

      Thank you for your feedback. However, I must express some concerns regarding the nature of your comments. Based on the issues you've raised, it seems that you may have reviewed an outdated version of the manuscript. In the updated revision we addressed all the points you've raised, including the figure and table citations, experimental methods, and data integration.

      We understand that differing opinions are part of the peer-review process, but we respectfully believe that your conclusion regarding our attitude is based on a misunderstanding, possibly caused by reviewing an incorrect version of the manuscript. We have always strived to approach this manuscript with utmost professionalism and have diligently responded to each of your concerns.

      We sincerely suggest reviewing the latest version of our manuscript, and we welcome any further constructive feedback. We hope this clarifies any misunderstandings and look forward to your continued support.

      Thank you for your time and thoughtful consideration.


      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study by Wang et al. identifies a new type of deacetylase, CobQ, in Aeromonas hydrophila. Notably, the identification of this deacetylase reveals a lack of homology with eukaryotic counterparts, thus underscoring its unique evolutionary trajectory within the bacterial domain.

      Strengths:

      The manuscript convincingly illustrates CobQ's deacetylase activity through robust in vitro experiments, establishing its distinctiveness from known prokaryotic deacetylases. Additionally, the authors elucidate CobQ's potential cooperation with other deacetylases in vivo to regulate bacterial cellular processes. Furthermore, the study highlights CobQ's significance in the regulation of acetylation within prokaryotic cells.

      Weaknesses:

      The problem I raised has been well resolved. I have no further questions.

      Reviewer #2 (Public review):

      In recent years, lots of researchers tried to explore the existence of new acetyltransferase and deacetylase by using specific antibody enrichment technologies and high resolution mass spectrometry. Here is an example for this effort. Yuqian Wang et al. studied a novel Zn2+- and NAD+-independent KDAC protein, AhCobQ, in Aeromonas hydrophila. They studied the biological function of AhCobQ by using biochemistry method and MS identification technology to confirm it. These results extended our understanding of the regulatory mechanism of bacterial lysine acetylation modifications. However, I find this conclusion is a little speculative, and unfortunately, it also doesn't totally support the conclusion as the authors provided.

      Reviewer #3 (Public review):

      Summary:

      This study reports on a novel NAD+ and Zn2+-independent protein lysine deacetylase (KDAC) in Aeromonas hydrophila, termed as AhCobQ (AHA_1389). This protein is annotated as a CobQ/CobB/MinD/ParA family protein and does not show similarity with known NAD+-dependent or Zn2+-dependent KDACs. The authors showed that AhCobQ has NAD+ and Zn2+-independent deacetylase activity with acetylated BSA by western blot and MS analyses. They also provided evidence that the 195-245 aa region of AhCobQ is responsible for the deacetylase activity, which is conserved in some marine prokaryotes and has no similarity with eukaryotic proteins. They identified target proteins of AhCobQ deacetylase by proteomic analysis and verified the deacetylase activity using site-specific Kac proteins. Finally, they showed that AhCobQ activates isocitrate dehydrogenase by deacetylation at K388.

      Strengths:

      The finding of a new type of KDAC has a valuable impact on the field of protein acetylation. The characters (NAD+ and Zn2+-independent deacetylase activity in an unknown domain) shown in this study are very unexpected.

      Weaknesses:

      (1) The characters (NAD+ and Zn2+-independent deacetylase activity in an unknown domain) shown in this study are very unexpected. To convince readers, MSMS data must be necessary to accurately detect (de)acetylation at the target site in the deacetylase activity assay. The authors showed the MSMS data in assays with acetylated BSA, but other assays only rely on western blot.

      (2) They prepared site-specific Kac proteins and used them in deacetylase activity assays. Incorporation of acetyllysine at the target site should be confirmed by MSMS and shown as supplementary data.

      (3) The authors imply that the 195-245 aa region of AhCobQ may represent a new domain responsible for deacetylase activity. The feature of the region would be of interest but is not sufficiently described in Figure 5. The amino acid sequence alignments with representative proteins with conserved residues would be informative. It would be also informative if the modeled structure predicted by AlphaFold is shown and the structural similarity with known deacetylases is discussed.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The problem I raised has been well resolved. I have no further questions.

      Reviewer #2 (Recommendations for the authors):

      Questions to response of"-The load control is not all integrated. All of the load controls with whole PAGE gel or whole membrane western blot results should be provided. Without these whole results, it is not convincing to come to the conclusion that the authors have."

      Just as the Authors answered. The Coomassie Blue R-350 staining outcomes from the PVDF membranes. That is a good control for the experiment. However, I still have several questions about it:

      (1) The first is the quality of these Western blot. Why all the bands of these Western blot is so ugly? To tell the truth, it is very difficult to come to a conclusion from these poor western blots.

      We appreciate your feedback regarding the quality of the Western blots presented in Figure 7. We believe the “ugly bands” you referred to reflect our results validating the functions of CobQ through the use of recombinant site-specific Kac protein substrates.

      In our study, we meticulously engineered these recombinant site-specific Kac proteins using a two-plasmid system, based on foundational research published in Nature Chemical Biology (2017, 13(12): 1253-1260), which introduced the genetic encoding of Nε-acetyllysine into recombinant proteins. However, we faced a common challenge: protein truncation due to premature translation termination at the reassigned codon. This issue not only hampers protein yields, as discussed in ChemBioChem (2017, 18(20): 1973-1983), but also contributes to the suboptimal appearance of the Western blot results.

      Despite conducting at least two independent repetitions for the Western blot analysis of the site-specific Kac proteins, which yielded consistent results, we recognize that the overall quality remains less than ideal. This variability is inherently related to the characteristics of the target proteins. Nevertheless, the primary aim of our manuscript is to validate the novel deacetylase activity of CobQ. We have provided multiple lines of evidence, including mass spectrometry (MS/MS) and Western blot analyses, to substantiate this claim. In response to your comments, we have decided to remove the ambiguous Western blot results from Figure 7, retaining only four figures that demonstrate significant differences across at least two independent replicates (Author response images 1-5). Additionally, we have included four biological replicates of the Western blot results for ICD Kac388 + CobQ in the supplementary materials (Author response image 5) to further validate the deacetylase function of CobQ.

      Author response image 1.

      Western blot validation of the Kac26 AcrA-2 protein substrates regulated by the three KDACs in two biological replicates.

      Author response image 2.

      Western blot validation of the Kac48 Sun protein substrates regulated by the three KDACs in two biological replicates.

      Author response image 3.

      Western blot validation of the Kac103 Sun protein substrates regulated by the three KDACs in two biological replicates.

      Author response image 4.

      Western blot validation of the Kac195 Eno protein substrates regulated by the three KDACs in three biological replicates.

      Author response image 5.

      Western blot validation of the Kac388 ICD protein substrates regulated by AhCobQ in this study. Each sample was independently repeated at least three time.

      (2) The second is why some of the results are not from the same PVDF by comparing the Coommassie staining with the WB results just as authors responded. For example, the HrpA-K816 (ac), Eno-K195 (ac), ArcA-2-K26 (ac), ArcA-2-K26 (ac), IscS-K93(ac), A0KJ75-K81(ac), GyrB-K331(ac), GyrB-K449(ac), FtsA-K320(ac), FtsA-K409(ac), RecA-K279(ac), and the RecA-K306(ac). All of them are clearly not from the same staining results of PVDF membrane but from a new PVDF membrane.

      We assure you that the R-350 stained PVDF membranes originate from the same Western blot membranes. However, we acknowledge that visual discrepancies may arise due to differences in imaging techniques. The Western blot results were scanned using a ChemiDoc MP (Bio-Rad, Hercules, CA, USA), while the Coomassie R-350 stained PVDF membranes were captured using a standard camera. These differences can create a misleading appearance, making it seem as though they come from different membranes.

      It is also important to note that the intensity of the protein marker cannot be directly compared between the two imaging methods. As illustrated in Author response image 6, the protein marker at 70 kDa is clearly detectable in the Coomassie R-350 image, whereas it may not be as apparent in the Western blot result due to inherent differences in detection sensitivity.

      Author response image 6.

      The comparison of Western blotting and R-350 strained results of same protein marker in the same PVDF membrane. The protein marker located at 70 kDa can be detected easily in Coomassie R-350, while is difficult to display in WB result.

      Additionally, we have removed some of the so-called "ugly" Western blot results in the updated manuscript and provided the original full film of the relevant images as an attachment. This documentation demonstrates that all the data you referenced originate from the same film, as shown in Figures 1-5.

      (3) The third is why there is no replication for all these WB results. We should draw a conclusion with serious attitude, but not from the only one repeat, even say nothing about the poor results.

      Thank you for your valuable suggestion. In the second version of the manuscript, we have included the original full film of the relevant images. While we previously explained the reasons behind the "ugly" Western blot results, we have decided to remove some, or even all, of these results from Figure 7 in the updated version. The related images will be updated in the supplementary materials (Figures 1-5 in responding letter and Figure 7 in the revised manuscript).

      Furthermore, we have provided a more detailed discussion regarding the poor results in the updated manuscript to ensure clarity and transparency. We appreciate your understanding and hope these changes meet your expectations.

      Questions to response of " L174-187, L795 (Please show the whole membrane (or PAGE gel) of the loading control of CobB, and CobQ, except for the Kac-BSA)".

      (1) As we all educated that there is no control, and no biology. Where is the band of CobQ? Why do not stain the same PVDF membrane with R-350 staining but with a new membrane?

      Thank you for your insightful feedback. As noted in our previous response, the absence of visible bands for AhCobQ and AhCobB on the Coomassie R-350 stained PVDF membrane is primarily due to the low loading amounts and protein loss during the Western blotting process.

      To reinforce our findings, we repeated the analysis of the protein samples via SDS-PAGE, using the same loading quantity as in the previous Western blot shown in Figure 2 of the manuscript. As illustrated in Author response image 7, the bands for CobB and CobQ are discernible, albeit with significantly lower intensities compared to the Kac-BSA bands. Upon examining the full Coomassie R-350 stained PVDF membranes provided in Supplementary Material 1, we observe that the CobB and CobQ bands are not easily visible. This aligns with your observations and can be attributed to potential protein loss during the transfer from SDS-PAGE to the PVDF membrane.

      Author response image 7.

      The SDS-PAGE gel displayed the loading amounts of Kac-BSA and CobB/CobQ.

      To enhance the visibility of the CobQ/CobB bands, we increased the loading of CobQ/CobB in a new Western blot experiment, using 2 µg of Kac-BSA in combination with 0.8 µg of CobQ/CobB. As shown in Figure 8, while the increasing amounts of Kac-BSA resulted in a more blurred signal, the bands for the recombinant CobQ and CobB proteins were clearly detectable. This indicates that both proteins were indeed involved in the in vitro protein deacetylation assay.

      Author response image 8.

      Western blot verified the deacetylase activity assay of AhCobQ and AhCobB on Kac-BSA.

      Furthermore, we conducted a mass spectrometry analysis comparing Kac-BSA and Kac-BSA incubated with CobQ, as well as BSA without acetylation, against the A. hydrophila database with a cut-off of unique matched peptides >1. It is challenging to completely avoid contaminant detection during protein purification, especially when using high-resolution mass spectrometry. Our findings revealed that CobQ has the highest number of unique matched peptides (Author response table 1), while contaminants such as AHA_3036, AHA_0497, AHA_1279, and valS could be excluded, as they were present in Kac-BSA or BSA samples. Additionally, Tuf1, RplQ, GroEL, RpsF, RpsU, RpsB, RpsO, and RpsJ are known ribosomal subunits or chaperonins that are abundantly expressed in cells and may interact with various proteins, leading to contaminant detection.

      Author response table 1.

      LC MS/MS results of selected peptide quantification among Kac-BSA and Kac-BSA incubated with CobQ and BSA without acetylation against A. hydrophila database (unique matched peptides>1).

      Although AceE, a pyruvate dehydrogenase E1 component, theoretically possesses deacetylase activity, this possibility is low. First, in the SDS-PAGE gel of the purified recombinant protein, CobQ is the major band, with other proteins present at very low levels (less than 1/10 of CobQ). This suggests that significant deacetylation by contaminants is unlikely. Second, we purified His-tagged AhCobQ and GST-fused AhCobQ separately and tested their deacetylase activities. As shown in Figure S4 of the updated manuscript, both purified AhCobQ proteins exhibited deacetylase activity, while the negative control (purified GST protein only) did not, further supporting our conclusion that enzyme activity is not attributable to contaminating proteins (Figure S5).

      (2) Without the CobB and CobQ bands, it is impossible to say the function of CobQ is a new deacetylase. To avoid this confusion, it is easy to run a new gel and stain it with anti-His antibody to show these deacetylases.

      Thank you very much for your suggestion. We have performed the experiment in the comment (1) as your suggestion.

      (3) The explanation about the CobB/CobQ bands are not visible is not acceptable. Because the molecular weight of the CobB and CobQ is smaller than that of BSA, it is impossible that these bands will be loss during membrane transfer.

      Thank you for your valuable feedback. I completely agree that the loss of CobB and CobQ proteins during membrane transfer is unlikely due to their smaller molecular weight compared to BSA. As shown in Figure 7, the bands for CobB and CobQ are detectable in the SDS-PAGE gel but not visible on the Coomassie R-350 stained PVDF membrane.

      Several factors could contribute to this issue. One possibility is that the detection sensitivity of Coomassie R-350 may be lower than that of Coomassie R-250 used in the gel. Additionally, the Western blot results using an anti-His antibody further indicate low loading amounts of CobB and CobQ proteins on the PVDF membrane (Figure 8). This suggests that the observed low levels may indeed be due to protein loss during the membrane transfer process, despite their relatively small size.

      Reviewer #3 (Recommendations for the authors):

      (1) I found Tables S1 and S2 in the revised manuscript. It is strange to me that the intensity of Kac-BSA+CobQ is zero, completely nothing. Typically, a portion of the acetylated peptide remains after the deacetylation reaction.

      Thank you for your observation. When we report an intensity of zero, it does not imply a complete absence of signal; rather, it indicates that the signal for the target peptide is below the detectable threshold. This is likely due to the minimum cut-off setting in the MaxQuant (MQ) software, which is determined by parameters like "peptide_mass_tolerance" (as discussed in MQ user groups online, though it may not be explicitly listed in the parameters file).

      In our study, we performed a deacetylase assay that demonstrated CobQ's rapid activity; for instance, it can deacetylate ICD-K388ac within just four minutes. This leads me to hypothesize that the CobQ + Kac-BSA sample may have undergone near-complete enzymatic hydrolysis during the reaction.

      Furthermore, Table S1 in manuscript presents only a selection of the mass spectrometry results to illustrate CobQ's activity. In addition to the 15 acetylated peptides shown, there are many more (27 peptides) that exhibit significantly reduced acetylation levels without reaching zero intensity. The overall acetylation level of BSA peptides incubated with CobQ is calculated to be only 0.13 times that of Kac-BSA (Diagnostic peak: yes, peptide score: >100, Localization probability: >0.95) (Author response image 9).

      Based on these findings, we believe our mass spectrometry results are reliable and effectively support our conclusions. Thank you for your understanding.

      Author response image 9.

      The intensities of all Kac peptides of Kac-BSA with or without AhCobQ incubation in LC MS/MS.

      (2) It would be better to provide the information about ArcA and ArcA-2 as mentioned in the authors' response. It would be helpful for readers to understand that they are different proteins.

      Thank you for your suggestion. In the A. hydrophila ATCC 7966 dataset, there are indeed two distinct proteins referred to as ArcA: ArcA-1, which functions as an aerobic respiration control protein, and ArcA-2, which acts as an arginine deiminase. Importantly, these two proteins do not share any sequence homology; they are only similarly named due to their acronyms. While we believe this distinction does not require extensive explanation in the current study, we appreciate your input. Additionally, in response to Reviewer 2’s feedback, we have decided to remove the Western blot result for ArcA-2 due to its poor quality in the updated manuscript.

      (3) Line 409-416. Despite my comment, the citation of related papers on ICD acetylation in E. coli is still missing.

      Thank you for your suggestion. It has been added and highlighted in red. (Venkat S, et al, 2018, 430(13): 1901-1911)

      (4) The image resolution of Figure 3C and 3D is still bad. I could not evaluate that Kac was exactly incorporated at the target site.

      Thank you for your feedback regarding the image resolution of Figures 3C and 3D. We have now displayed these figures with improved clarity, as you suggested.

      To further validate the reliability of our MS2 data, we employed Proteome Discoverer 2.4 (Thermo) to analyze the raw data and provide theoretical mass information. As shown in Author response images 10-13, the MS2 spectra and fragment match lists for both unmodified and acetylated peptides offer additional confirmation of the reliability of our mass spectrometry results.

      Author response image 10.

      MS2 spectrum of unmodified peptide using PD v2.4 software.

      Author response image 11.

      The theoretical mass of unmodified peptide by PD 2.4

      Author response image 12.

      MS2 spectrum of acetylated peptide using PD v2.4 software.

      Author response image 13.

      The theoretical mass of acetylated peptide by PD 2.4.

      (5) Again, in Figure 8D, it should be shown the significance between ICD-Kac388 and ICD-Kac388+AhCobB to support the authors' conclusion that AhCobQ activates ICD by deacetylation at K388.

      Thanks for your suggestion, we have updated the figure in Figure 8D in updated manuscript.

      (6) It was nice that the authors presented the mass spectrum data of ICD-K388 acetylation (Figure 2 in responding letter). However, the data did not convince me that K388 is acetylated. In the figure, two b-ion peaks are detected, 285.1557 and 386.2034, which may correspond to NK (theoretical mass, 260.15) and NKT (theoretical mass, 361.20) peptides, respectively. If K388 is acetylated, an increase in the mass of 42 should be observed, but the difference between the detected and theoretical mass is 25. I also could not understand what the peak of 126.0913 mass is, indicated with acK* in red.

      Thank you for your detailed observation. The data presented in the MS2 spectrum for ICD-K388 acetylation in Figure 2 of the previous response letter were generated using Proteome Discoverer 2.4 (PD, Thermo) to ensure accurate mass calculations. Similar to the results from MaxQuant, ICD-K388 was identified again (Author response image 14).

      Regarding the b-ion peaks you mentioned, the values 285.1557 and 386.2034 correspond to NK<sup>ac</sup> and NK<sup>ac</sup>T peptides, respectively. The theoretical masses for these peptides are as follows: NK<sup>ac</sup> (285.15 = 115.05020 + 128.095 + 42.01) and NK<sup>ac</sup>T (386.20 = NK<sup>ac</sup> + 101.04768). The differences between the theoretical and detected masses for the relevant b-ions (b2*-NK, b52+-NH3, and b3) are minimal, at 0.00 Da and 2.1 ppm, respectively, which is consistent with the incorporation of an NH3 group (Author response image 15).

      Author response image 14.

      The MS2 of ICD-K388 peptide by PD 2.4.

      Author response image 15.

      The theoretical mass of ICD-K388 peptide by PD 2.4.

      The peak at 126.0913 m/z, indicated as acK*, represents immonium ions of ε-N-acetyllysine, which are generated during the fragmentation of acetyllysine. This diagnostic ion is widely recognized as a marker for identifying acetylated peptides (Nakayasu, et al,. A method to determine lysine acetylation stoichiometries. International journal of proteomics. 2014;2014(1):730725; Trelle et al., Utility of immonium ions for assignment of ε-N-acetyllysine-containing peptides by tandem mass spectrometry. Analytical chemistry. 2008;80(9):3422-30). Additionally, it is a default parameter in MaxQuant for identifying Kac peptides (Author response image 16).

      Based on these findings, we believe the evidence supporting ICD-K388 acetylation is robust.

      Author response image 16.

      The default parameter in Kac peptide identification in Maxquant v1.6 software

      (7) As mentioned by other reviewers, some of the figures and tables are incomplete. Some panels (ex. Figure 7C and 7D) and explanations (ex. What are lanes 1, 2, and 3 in Figure S3) are still missing.

      Thank you for your suggestion. It has been added.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public Review): 

      The authors of the study investigated the generalization capabilities of a deep learning brain age model across different age groups within the Singaporean population, encompassing both elderly individuals aged 55 to 88 years and children aged 4 to 11 years. The model, originally trained on a dataset primarily consisting of Caucasian adults, demonstrated a varying degree of adaptability across these age groups. For the elderly, the authors observed that the model could be applied with minimal modifications, whereas for children, significant fine-tuning was necessary to achieve accurate predictions. Through their analysis, the authors established a correlation between changes in the brain age gap and future executive function performance across both demographics. Additionally, they identified distinct neuroanatomical predictors for brain age in each group: lateral ventricles and frontal areas were key in elderly participants, while white matter and posterior brain regions played a crucial role in children. These findings underscore the authors' conclusion that brain age models hold the potential for generalization across diverse populations, further emphasizing the significance of brain age progression as an indicator of cognitive development and aging processes.

      Strengths: 

      (1) The study tackles a crucial research gap by exploring the adaptability of a brain age model across Asian demographics (Chinese, Malay, and Indian Singaporeans), enriching our knowledge of brain aging beyond Western populations.

      (2) It uncovers distinct anatomical predictors of brain aging between elderly and younger individuals, highlighting a significant finding in the understanding of age-related changes and ethnic differences.

      Weaknesses: 

      (1) Clarity in describing the fine-tuning process is essential for improved comprehension.

      (2) The analysis often limits its findings to p-values, omitting the effect sizes crucial for understanding the relationship with cognition.

      (3) Employing a predictive framework for cognition using brain age could offer more insight than mere statistical correlations.

      (4) Expanding the study's scope to evaluate the model's generalisability to unseen Caucasian samples is vital for establishing a comparative baseline.

      In summary, this paper underscores the critical need to include diverse ethnicities in model testing and estimation.

      Reviewer #1 (Recommendations for the authors): 

      Comment #1 - Fine-Tuning Process Clarity: Enhanced clarity in the fine-tuning process documentation is crucial for understanding how models are adapted to new datasets. This involves explaining parameter adjustments and choices, which facilitates replication and application in further research.

      We thank Reviewer #1 for this pertinent point. As advised, we have added a Supplementary Methods section with more details on the finetuning process. This includes the addition of Supplementary Figure S6, which shows examples of learning curves that helped inform our parameter adjustments and choices. We have added a reference to this section in Section 5.2 of the Methods.

      Comment #2 - Effect Sizes Reporting: The emphasis on reporting effect sizes alongside p-values addresses the need to quantify the strength of observed effects, particularly the relationship between brain age and cognition. Effect sizes provide insights into the practical significance of findings, crucial for clinical and practical applications.

      We thank Reviewer #1 for raising this important comment. As suggested, we have added standardized regression coefficients (as measures of effect size) alongside p-values in Figures 3 – 4, Supplementary Figures S2 – S4, Supplementary Tables S4 – S15, and the text of Sections 2.2 – 2.3 of the Results. We have additionally added 95% confidence intervals to Supplementary Tables S4 – S15.

      Comment #3 - Predictive Framework for Cognition: Adopting a predictive framework for cognition using brain age moves the research from mere correlation to actionable prediction, offering potentials based on predictive analytics.

      We thank Reviewer #1 for this insightful suggestion. Adopting a predictive framework would certainly be a useful and exciting avenue for the application of brain age. However, we note that the current study was primarily interested in the generalizability and interpretability of brain age in Asian children and older adults, as well as the added value of longitudinal measures of brain age. Thus, we believe our correlation-based analysis effectively demonstrated that deviations of brain age from chronological age were not merely random errors, but were informative of cognition. Furthermore, ongoing changes to these deviations were informative of future cognition. This helps to establish the brain age gap as a biomarker for aging, independent of chronological age. Additionally, we expect that the accurate prediction of future cognition would require a multitude of factors, in addition to T1-based brain age, as well as a large sample size to train and test. We believe such a dataset would be a promising avenue for future work, but it is outside the scope of the current study.

      Nonetheless, we were able to conduct a preliminary analysis using the current longitudinal data from SLABS and GUSTO. We extracted the same variables used in the original analyses of future cognition, corresponding to Figures 3D and 4B in the main text. To implement a predictive framework, we split the data into 10 stratified cross-validation folds. We also used kernel ridge regression (KRR) as the predictive model, as it has previously shown promising performance in behavioral and cognitive prediction [1]. We used a cosine kernel and nested 5-fold cross-validation to pick the optimal regularization strength (alpha).

      To investigate the added value of BAG and longitudinal changes in BAG, we compared 3 predictive models for each cognitive domain. The baseline model consisted of the demographic covariates used in the original analyses (i.e. chronological age, sex, and years of education for older adults). A second model combined demographics with baseline BAG, and the third model incorporated demographics, baseline BAG, and the (early) annual rate of change in BAG. Predictions were extracted from each test fold, and performance was measured by the correlation between test predictions and actual values of future cognition (or change in cognition). Models were statistically compared using the corrected resampled t-test for machine learning models [1], [2], [3]. The Benjamini-Hochberg procedure was used to correct for multiple comparisons.

      Author response image 1 shows the prediction results for SLABS and GUSTO. Notably, adding the early change in BAG significantly improves the prediction of future change in executive function in SLABS. There is also an improvement in predicting the future inhibition score in GUSTO, but this is not significant after multiple comparison correction. Encouragingly, these are the same domains that showed significant associations with the change in BAG in the original analyses. This suggests that longitudinal brain age continues to contribute information, independent of baseline factors, in a predictive framework. We hope that future work can expand on this analysis with, for instance, larger sample sizes, more varied and informative predictors, and state-of-the-art prediction methods, in order to establish actionable predictions of future cognition.

      Author response image 1.

      Predictive framework for cognition similarly suggests value of longitudinal change in BAG. Prediction performance (Pearson's correlation) of KRR across future cognitive outcomes. Each boxplot shows the distribution of performance over cross-validation folds. Model performances are statistically compared for each outcome. Significant outcomes from the original analyses are bolded. (A) Results for SLABS using the early change in BAG and future change in cognitive scores (non-overlapping). Early change in BAG again shows benefit for predicting future change in executive function. (B) Results for GUSTO using the early change in BAG (from 4.5-7.5 years old) and future cognitive score (at 8.5 years old). Early change in BAG again shows benefit for predicting future inhibition, but it is not significant after multiple comparison correction. Key - **: p < 0.01; * (ns): p < 0.05 but p<sub>corr</sub> > 0.05 after multiple comparison correction; ns: p > 0.05

      Comment #4 - Generalizability to Unseen Caucasian Samples: Evaluating the model's performance on unseen (longitudinal) Caucasian samples is important for benchmarking.

      We thank Reviewer #1 for this important comment. We agree that generalizability should be benchmarked against performance on unseen Caucasian samples. In the SFCN model paper [4], they conducted an out-of-sample test on unseen Caucasian samples from ages 13 to 95. In this age range, they reported a high correlation (r = 0.975) and low MAE (MAE = 3.90). This favorable generalization performance was verified in adults by independent evaluations [5], [6]. This is also in line with what we observed in Asian older adults, taking into account the different age ranges and sample sizes involved [7].

      However, this also highlights the difficulty in evaluating on younger ages in the range of GUSTO (4.5 – 10.5 years old). Most accessible developmental datasets (e.g. HBN, PING) were already included in model training, preventing an unbiased evaluation on these samples. Datasets such as PNC and ABCD were not included in training, but they primarily consist of an older age range than GUSTO. Holm et al. [8] previously tested the SFCN model in ABCD and reported satisfactory performance (low MAE) from 9 – 13 years old. However, to the best of our knowledge, there are no reported generalization results (for any ethnicity) from 4.5 – 7.5 years old, which is where we found the most performance degradation in GUSTO. We are also not aware of any datasets in this age range we could access to test this, unfortunately, but it would be an important area for future work.

      While benchmarking in Caucasian children is difficult, we were able to conduct a preliminary analysis with older adults using the ADNI dataset (which was not included in the model training [4]). We selected a longitudinal subset with cognitive data available and no dementia at baseline (N = 137). We used composite cognitive scores covering memory, executive function, language, and visuospatial function [9], [10], [11]. We followed the same methodology (e.g. preprocessing, finetuning, statistical analysis) as the main analyses on EDIS, SLABS, and GUSTO. To maximize the data available, we tested associations with future cognition (taken at the last available time point), similar to GUSTO. We again included chronological age, sex, and years of education as demographic covariates.

      Author response image 2 shows the brain age predictions for the pretrained and finetuned models on ADNI. Similar to Singaporean older adults, the pretrained model performs well, producing a high correlation (r = 0.8053; compared to r = 0.7389 for EDIS and r = 0.8136 for SLABS) and somewhat low MAE (MAE = 4.9735; compared to MAE = 3.9895 for EDIS and MAE = 3.4668 for SLABS). After finetuning, the MAE improves (MAE = 3.6837; compared to MAE = 3.3232 for EDIS and MAE = 3.2653 for SLABS) with a similar correlation (r = 0.7854; compared to r = 0.7445 for EDIS and r = 0.8138 for SLABS). This suggests that generalization to unseen Singaporean older adults is in line with the generalization to unseen Caucasian older adults.

      Author response image 2. 

      Brain age predictions on unseen Caucasian sample of older adults. Predictions from the A) pretrained and B) finetuned brain age models on ADNI participants. Compare to Figure 2 of the main text.

      For the associations with future cognition, we again find that baseline BAG does not associate with future cognition (Author response tables 1 and 2). However, encouragingly, we find that the early annual rate of change in BAG does associate with future memory, which is significant after multiple comparison correction for the finetuned model (Author response tables 2 and 3). This suggests  a degree of replicability to the original results, but interestingly, in a different domain (memory vs. executive function). In contrast to SLABS, which consists of healthy older adults recruited from the community, ADNI consists of participants at risk of AD recruited from memory clinics. Thus, this difference in domain could be due to factors such as a stronger signal for memory in the testing battery or greater variations in memory function and decline. However, it could also reflect other population differences between ADNI and SLABS. This is an intriguing area for future study, ideally with larger sample sizes and more diverse populations included.

      Author response table 1.

      Linear relationship between pretrained baseline BAG and future cognitive score in ADNI. Compare to Supplementary Tables S4 – S15 of the original text.

      Author response table 2. 

      Linear relationship between finetuned baseline BAG and future cognitive score in ADNI. Compare to Supplementary Tables S4 – S15 of the original text.

      Author response table 3.

      Linear relationship between pretrained change in BAG and future cognitive score in ADNI. Compare to Supplementary Tables S4 – S15 of the original text.

      Author response table 4. 

      Linear relationship between finetuned change in BAG and future cognitive score in ADNI. Compare to Supplementary Tables S4 – S15 of the original text.

      References

      (1) L. Q. R. Ooi et al., “Comparison of individualized behavioral predictions across anatomical, diffusion and functional connectivity MRI,” NeuroImage, vol. 263, p. 119636, Nov. 2022, doi: 10.1016/j.neuroimage.2022.119636.

      (2) C. Nadeau and Y. Bengio, “Inference for the Generalization Error,” Mach. Learn., vol. 52, no. 3, pp. 239–281, Sep. 2003, doi: 10.1023/A:1024068626366.

      (3) R. R. Bouckaert and E. Frank, “Evaluating the Replicability of Significance Tests for Comparing Learning Algorithms,” in Advances in Knowledge Discovery and Data Mining, H. Dai, R. Srikant, and C. Zhang, Eds., Berlin, Heidelberg: Springer, 2004, pp. 3–12. doi: 10.1007/978-3-540-24775-3_3.

      (4) E. H. Leonardsen et al., “Deep neural networks learn general and clinically relevant representations of the ageing brain,” NeuroImage, vol. 256, p. 119210, Aug. 2022, doi: 10.1016/j.neuroimage.2022.119210.

      (5) R. P. Dörfel et al., “Prediction of brain age using structural magnetic resonance imaging: A comparison of accuracy and test-retest reliability of publicly available software packages,” Neuroscience, preprint, Jan. 2023. doi: 10.1101/2023.01.26.525514.

      (6) J. L. Hanson, D. J. Adkins, E. Bacas, and P. Zhou, “Examining the reliability of brain age algorithms under varying degrees of participant motion,” Brain Inform., vol. 11, no. 1, p. 9, Apr. 2024, doi: 10.1186/s40708-024-00223-0.

      (7) A.-M. G. de Lange et al., “Mind the gap: Performance metric evaluation in brain-age prediction,” Hum. Brain Mapp., vol. 43, no. 10, pp. 3113–3129, Jul. 2022, doi: 10.1002/hbm.25837.

      (8) M. C. Holm et al., “Linking brain maturation and puberty during early adolescence using longitudinal brain age prediction in the ABCD cohort,” Dev. Cogn. Neurosci., vol. 60, p. 101220, Feb. 2023, doi: 10.1016/j.dcn.2023.101220.

      (9) P. K. Crane et al., “Development and assessment of a composite score for memory in the Alzheimer’s Disease Neuroimaging Initiative (ADNI),” Brain Imaging Behav., vol. 6, no. 4, pp. 502–516, Dec. 2012, doi: 10.1007/s11682-012-9186-z.

      (10) L. E. Gibbons et al., “A composite score for executive functioning, validated in Alzheimer’s Disease Neuroimaging Initiative (ADNI) participants with baseline mild cognitive impairment,” Brain Imaging Behav., vol. 6, no. 4, pp. 517–527, Dec. 2012, doi: 10.1007/s11682-012-9176-1.

      (11) S.-E. Choi et al., “Development and validation of language and visuospatial composite scores in ADNI,” Alzheimers Dement. Transl. Res. Clin. Interv., vol. 6, no. 1, p. e12072, 2020, doi: 10.1002/trc2.12072.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      Dong et al here have studied the impact of the small Ras-like GTPase Rab10 on the exocytosis of dense core vesicles (DVC), which are important mediators of neuropeptide signaling in the brain. They use optical imaging to show that lentiviral depletion of Rab10 in mouse hippocampal neurons in culture independent of the established defects in neurite outgrowth hamper DCV exocytosis. They further demonstrate that such defects are paralleled by changes in ER morphology and defective ER-based calcium buffering as well as reduced ribosomal protein expression in Rab10-depleted neurons. Re-expression of Rab10 or supplementation of exogenous L-leucine to restore defective neuronal protein synthesis rescues impaired DCV secretion. Based on these results they propose that Rab10 regulates DCV release by maintaining ER calcium homeostasis and neuronal protein synthesis.

      Strengths:

      This work provides interesting and potentially important new insights into the connection between ER function and the regulated secretion of neuropeptides via DCVs. The authors combine advanced optical imaging with light and electron microscopy, biochemistry, and proteomics approaches to thoroughly assess the effects of Rab10 knockdown at the cellular level in primary neurons. The proteomic dataset provided may be valuable in facilitating future studies regarding Rab10 function. This work will thus be of interest to neuroscientists and cell biologists.

      We appreciate the positive evaluation of our manuscript.

      Weaknesses:

      While the main conclusions of this study are comparably well supported by the data, I see three major weaknesses:

      (1) For some of the data the statistical basis for analysis remains unclear. I.e. is the statistical assessment based on N= number of experiments or n = number of synapses, images, fields of view etc.? As the latter cannot be considered independent biological replicates, they should not form the basis of statistical testing.

      This is an important point and we agree that multiple samples from the same biological replicate are not independent observations. We reanalyzed all nested data using a linear mixed model and indicated this in the Methods section and the relevant figure legends (Brunner et al., 2022). In brief, biological replicates (individual neuronal cultures) were used as a linear predictor. Outliers were identified and excluded using the ROUT method in GraphPad. A fixed linear regression model was then fitted to the data using the lm() function in R. A one-way anova (analysis of variance) was used to assess whether including the experimental group as a second linear predictor (formula = y ~ Group + Culture) statistically improved the fit of a model without group information (formula = y ~ 1 + Culture). Post-hoc analysis was performed using the emmeans() function with Tukey’s adjustment when more than two experimental groups were present. Importantly, our conclusions remain unchanged.

      (2) As it stands the paper reports on three partially independent phenotypic observations, the causal interrelationship of which remains unclear. Based on prior studies (e.g. Mercan et al 2013 Mol Cell Biol; Graves et al JBC 1997) it is conceivable that defective ER-based calcium signaling and the observed reduction in protein synthesis are causally related. For example, ER calcium release is known to promote pS6K1 phosphorylation, a major upstream regulator of protein synthesis and ribosome biogenesis. Conversely, L-leucine supplementation is known to trigger calcium release from ER stores via IP3Rs. Given the reported impact of Rab10 on axonal transport of autophagosomes and, possibly, lysosomes via JIP3/4 or other mediators (see e.g. Cason and Holzbaur JCB 2023) and the fact that mTORC1, the alleged target of leucine supplementation, is located on lysosomes, which in turn form membrane contacts with the ER, it seems worth analyzing whether the various phenotypes observed are linked at the level of mTORC1 signaling.

      This is great suggestion that could indeed further clarify the potential interplay between ER-based Ca2+ signaling and protein synthesis. To address this, we assessed the phosphorylation level of pS6K1 in control and Rab10 knockdown (KD) neurons with or without leucine treatment. These data are included in the new Figure 8—figure supplement 1 in the revised manuscript. Our results indicate that pS6K1 phosphorylation was not upregulated in Rab10 KD neurons, suggesting that the level of mTORC1 signaling is not different between wild-type or KD neurons. Furthermore, leucine treatment increased the pS6K1 phosphorylation level, as expected, but this effect was similar in both groups. Hence, we conclude that differences in mTORC1 signaling induced by Rab10 loss is not a major factor in the observed impairment in protein synthesis.

      Author response image 1.

      Rab10 depletion does not upregulate mTORC1 pathway. (A)Typical immunoblot showing pS6K1 levels in each condition. (B) Quantification of relative pS6K1 levels in each condition. All Data are plotted as mean±s.e.m. (C) Control, Control + Leu: N = 2, n = 2, Rab10 KD, Rab10 KD + Leu: N = 2, n = 4.

      (3) The claimed lack of effect of Rab10 depletion on SV exocytosis is solely based on very strong train stimulation with 200 Aps, a condition not very well suited to analyze defects in SV fusion. The conclusion that Rab10 loss does not impact SV fusion thus seems premature.

      We agree that 200 APs stimulation might be too strong to detect specific effects on evoked synaptic vesicle release, although this stimulation pattern is an established pattern in hundreds of studies (Emperador-Melero et al., 2018; Granseth et al., 2006; Ivanova et al., 2021; Kwon and Chapman, 2011; Reshetniak et al., 2020). We have toned down our conclusions and clarified in the revised manuscript that Rab10 is dispensable for SV exocytosis evoked by intense stimulations. The corresponding statements in the text have been modified accordingly (p. 5, l. 98, 124) and in figure legend (p. 17, 490).

      Reviewer #2 (Public Review):

      Summary:<br /> In this paper, the authors assess the function of Rab10 in dense core vesicle (DCV) exocytosis using RNAi and cultured neurons. The author provides evidence that their knockdown (KD) is effective and provides evidence that DCV is compromised. They also perform proteomic analysis to identify potential pathways that are affected upon KD of Rab10 that may be involved in DCV release. Upon focusing on ER morphology and protein synthesis, the authors conclude that defects in protein synthesis and ER Ca2+ homeostasis contributes to the DVC release defect upon Rab10 KD. The authors claim that Rab10 is not involved in synaptic vesicle (SV) release and membrane homeostasis in mature neurons.

      Strengths:

      The data related to Rab10's role in DCV release seems to be strong and carried out with rigor. While the paper lacks in vivo evidence that this gene is indeed involved in DCV in a living mammalian organism, I feel the cellular studies have value. The identification of ER defect in Rab10 manipulation is not truly novel but it is a good conformation of studies performed in other systems. The finding that DCV release defect and protein synthesis defect seen upon Rab10 KD can be significantly suppressed by Leucine supplementation is also a strength of this work.

      We appreciate the positive evaluation of our manuscript.

      Weaknesses:

      The data showing Rab10 is NOT involved in SV exocytosis seems a bit weak to me. Since the proteomic analysis revealed so many proteins that are involved in SV exo/encodytosis to be affected upon Rab10, it is a bit strange that they didn't see an obvious defect. Perhaps this could have been because of the protocol that the authors used to trigger SV release (I am not an E-phys expert but perhaps this could have been a 'sledge-hammer' manipulation that may mask any subtle defects)? Perhaps the authors can claim that DCV is more sensitive to Rab10 KD than SV, but I am not sure whether the authors should make a strong claim about Rab10 not being important for SV exocytosis.

      We agree that 200 APs stimulation might be too strong to see specific effects on evoked synaptic vesicle release, although this stimulation pattern is an established pattern in hundreds of studies. We have toned down our conclusions and clarified in the revised manuscript that Rab10 is dispensable for SV exocytosis evoked by intense stimulations. The corresponding statements in the text have been modified accordingly (p. 5, l. 98, 124) and in figure legend (p. 17, 490).

      Also, the authors mention "Rab10 does not regulate membrane homeostasis in mature neurons" but I feel this is an overstatement. Since the authors only performed KD experiments, not knock-out (KO) experiments, I believe they should not make any conclusion about it not being required, especially since there is some level of Rab10 present in their cells. If they want to make these claims, I believe the authors will need to perform conditional KO experiments, which are not performed in this study.

      This is a valid point. We have changed the statement to “membrane homeostasis in mature neurons was unaffected by Rab10 knockdown” (p. 13, l.376-377).

      Finally, the authors show that protein synthesis and ER Ca2+ defects seem to contribute to the defect but they do not discuss the relationship between the two defects. If the authors treat the Rab10 KD cells with both ionomycin and Leucine, do they get a full rescue? Or is one defect upstream of the other (e.g. can they see rescue of ER morphology upon Leucine treatment)? While this is not critical for the conclusions of the paper, several additional experiments could be performed to clarify their model, especially considering there is no clear model that explains how Rab10, protein synthesis, ER homeostasis, and Ca2+ are related to DCV (but not SV) exocytosis.

      This is an important point and a great suggestion. We have now tested the rescue effects of leucine treatment on ER morphology, as suggested. These data are included in the new Figure 8—figure supplement 2 in the revised manuscript. Our results indicate that the same dose of leucine that rescues DCV fusion and protein translation failed to rescue ER morphology. Hence, the defects in ER morphology appear to be independent of the impaired protein translation.

      Author response image 2.

      Leucine supplementation does not rescue ER morphological deficiency in Rab10 KD neurons. (A) Typical examples showing the KDEL signals in each condition. (B) Quantification of RTN4 intensity in MAP2-positive dendrites. (C) The ratio of neuritic to somatic RTN4 intensity (N/S). All Data are plotted as mean±s.e.m. (B, C) Control: N = 3, n = 10; Rab10 KD: N = 3, n = 11; Rab10 KD + Leu: N = 3; n = 11. A one-way ANOVA tested the significance of adding experimental group as a predictor. **** = p<0.0001, ns = not significant.

      Reviewer #3 (Public Review):

      In the submitted manuscript, Dong and colleagues set out to dissect the role of the Rab10 small GTPase on the intracellular trafficking and exocytosis of dense core vesicles (DCVs). While the authors have already shown that Rab3 plays a central role in the exocytosis of DVC in mammalian neurons, the roles of several other Rab-members have been identified genetically, but their precise mechanism of action in mammalian neurons remains unclear. In this study, the authors use a carefully designed and thoroughly executed series of experiments, including live-cell imaging, functional calcium-imaging, proteomics, and electron microscopy, to identify that DCV secretion upon Rab10 depletion in adult neurons is primarily a result of dysregulated protein synthesis and, to a lesser extent, disrupted intracellular calcium buffering. Given that the full deletion of Rab10 has a deleterious effect on neurons and that Rab10 has a major role in axonal development, the authors cautiously employed the knock-down strategy from 7 DIV, to focus on the functional impact of Rab10 in mature neurons. The experiments in this study were meticulously conducted, incorporating essential controls and thoughtful considerations, ensuring rigorous and comprehensive results.

      We are grateful for the positive evaluation of our manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      The work by Dong et al provides interesting and potentially important new insights into the connection between ER function and the regulated secretion of neuropeptides via DCVs. I suggest that the authors address the following points experimentally to increase the impact of this potentially important study.

      Major points:

      (1) As alluded to above, for some of the data the statistical basis for analysis remains unclear (examples are Figures 1C-F, J,K; Figure 2 1B-D,I-K; Figure 2 - Supplement 1D-F; Figure 2 - Supplement 2J,K, etc). I.e. is the statistical assessment based on N = number of experiments or n = number of synapses, images, fields of view etc.? As the latter cannot be considered independent biological replicates, they should not form the basis of statistical testing. The Ms misses also misses a dedicated paragraph on statistics in the methods section.

      See reply to reviewer 1 above. We fully agree and solved this point.

      (2) A main weakness of the paper is the missing connection between neuronal protein synthesis, and the observed structural and signaling defects at the level of the ER. I suggest that the authors analyze mTORC1 signaling in Rab10 depleted neurons and under rescue conditions (+Leu or re-expression of Rab10) as ribosome biogenesis is a major downstream target of mTORC1 and mTORC1 activity is related to lysosome position, which may be affected upon rab10 loss -either directly or via effects on the ER that forms tight contacts with lysosomes.

      See reply to reviewer 1 above. We agreed and followed up experimentally.

      (3) Related to the above: Does overexpression of SERCA2 restore normal DCV exocytosis in Rab10-depleted neurons? This would help to distinguish whether calcium storage and release at the level of the ER indeed contribute to the exocytosis defect.

      This is an important point and a great suggestion. We have now tested the rescue effects of overexpression of SERCA2 on DCV fusion. These data are included in the new Figure 8—figure supplement 3 in the revised manuscript. SERCA2 OE failed to rescue the DCV fusion defects in Rab10 KD neurons.

      Author response image 3.

      Overexpression of SERCA2 does not rescue DCV fusion deficits in Rab10 KD neurons. (A) Typical examples showing the SERCA2 signals in each condition. (B) Cumulative plot of DCV fusion events per cell. (C) Summary graph of DCV fusion events per cell. (A) Total number of DCVs (total pool) per neuron, measured as the number of NPY-pHluorin puncta upon NH4Cl perfusion. (B) Fraction of NPY-pHluorin-labeled DCVs fusing during stimulation. All Data are plotted as mean±s.e.m. (C-E) Control: N = 2, n = 10; Rab10 KD: N = 2, n = 13; SERCA2 OE: N = 2; n = 15. A one-way ANOVA tested the significance of adding experimental group as a predictor. *** = p<0.001, ** = p<0.01, ns = not significant.

      (4) The claimed lack of effect of Rab10 depletion on SV exocytosis is solely based on very strong train stimulation with 200 Aps, a condition not very well suited to analyze defects in SV fusion. The conclusion that Rab10 loss does not impact SV fusion thus seems premature. The authors should conduct additional experiments under conditions of single or few Aps (e.g. 4 or 10 Aps) to really assess whether or not Rab10 depletion alters SV exocytosis at the level of pHluorin analysis in cultured neurons.

      See reply to reviewer 2 above. Agreed to and made textual adjustments to solve this

      (5) Related to the above: I am puzzled by the data shown in Figure 1H-J: From the pHluorin traces shown I would estimate a tau value of about 20-30 s (e.g. decay to 1/e = 37% of the peak value). The bar graph in Figure 1K claims 3-4 s, clearly clashing with the data shown. Were these experiments conducted at RT (where expected tau values are in the range of 30s) or at 37{degree sign}C (one would expect taus of around 10 s in this case for Syp-pH)? I ask the authors to carefully check and possibly re-analyze their datasets.

      This is indeed a mistake. We thank the reviewer for flagging this miscalculation. Our original Matlab script used for calculating the tau value contained an error and the datasets were normalized twice by mistake. We now reanalyzed the data and the corresponding figures and texts have been updated. Our conclusion that Rab10 KD does not affect SV endocytosis remains unchanged since the difference in tau between the control (28.5 s) and Rab10 KD (32.8 s) suffered from the same systematic error and were/are not significantly different.

      (6) How many times was the proteomics experiment shown in Figure 3 conducted? I noticed that the data in panel H missed statistical analysis and error bars. Given the typical variation in these experiments, I suggest to only include data for proteins identified in at least 3 out of 4 experimental replicates.

      We agree that this information has not been clear. We have now explained replication in the Methods section (p. 42, l. 879-885). In brief, the proteomics experiment presented in Fig 3 was conducted with two independent cultures (‘biological replicates’), hence, formally only two independent observations. For each biological replicate, we performed four technical replicates. For our analysis, we only included peptides that were consistently detected across all samples (not only three as this reviewer suggests). Proteins in Panel H are ER-related proteins that are significantly different from control neurons with an adjusted FDR ≤ 0.01 and Log2 fold change ≥ 0.56. The primary purpose of our proteomics experiments was to generate hypotheses and guide subsequent experiments and the main findings were corroborated by other experiments presented in the manuscript.

      Minor:

      (7) Figure 2 - supplement 3 and Figure 4 - supplement 3 are only mentioned in the discussion. The authors should consider referring to these data in the results section.

      This is a valid point. We have now added a new statement “Moreover, only 10% of DCVs co-transport with Rab10” in the Results (p. 6-7, l. 162-164).

      (8) Where is the pHluorin data shown in Figure 1 bleach-corrected? If so, this should be stated somewhere in the Ms. Moreover, the timing of the NH4Cl pulse should be indicated in the scheme in panel I.

      We thank the reviewer for pointing these omissions out. We have now included information about the timing of NH4Cl pulse in panel I. We did not do bleach-correction for the pHluorin data shown in Figure 1. It has been shown that pHluorin is very stable with a bleaching rate in the alkaline state of 0.06% per second and 0.0024% per second in the quenched state (Balaji and Ryan, 2007). Indeed, we did not observe obvious photobleaching in the first 30s during our imaging as indicated by the average trace of pHluorin intensity in panel I.

      (9) Page 3/ lines 59-60: "...strongest inhibition of neuropeptide accumulation...". What is probably meant is "...strongest inhibition of neuropeptide release".

      We agree this statement is unclear. Sasidharan et al used a coelomocyte uptake assay as an indirect readout for DCV release. The ‘strongest inhibition of neuropeptide accumulation’ in coelomocytes in Rab10 mutant indicates DCV fusion deficits. We have now replaced the text with “Rab10 deficiency produces the strongest inhibition of neuropeptide release in C. elegans” to make it more clear.

      Reviewer #3 (Recommendations For The Authors):

      I strongly recommend the publishing of this study as a VOR with minor comments directed to the authors.

      (1) In Figure 4, the authors should include examples of tubular ER at the synapse, especially as this is an interesting point discussed in ln 226-229. Are there noticeable changes in the ER-mitochondria contacts at the synaptic boutons?

      We agree that examples of tubular ER at the synapse would improve the manuscript. We have now replaced the Figure 4A with such examples. We found it challenging to quantify ER-mitochondria contacts based on the electron microscopy (EM) images we currently have. The ER-mitochondria contact sites are quite rare in the cross-sections of our samples, making it difficult to perform a reliable quantitative analysis.

      (2) The limited impairment of calcium-ion homeostasis in Rab10 KD neurons is very interesting. Would the overexpression of Rab10T23N mimic the effect of a KD scenario? Is there a separation of function for Rab10 in calcium homeostasis vs. the regulation of protein synthesis?

      This is an interesting possibility. We tested this and expressed Rab10T23N in a new series of experiments. These data are presented as a new Figure 5 in the revised manuscript (p. 29). We observed that Ca2+ refilling after caffeine treatment was delayed to a similar extent in Rab10T23N-expressing and Rab10 KD neurons. While impaired Ca2+ homeostasis may affect protein synthesis through ER stress or mTORC1 activation, our findings indicate otherwise in Rab10 KD neurons. First, ATF4 levels, a marker of ER stress, were unaffected in Rab10 KD neurons. This indicates that any ER stress present is minimal or insufficient to significantly impact protein synthesis through this pathway. Second, we did not observe significant changes in mTORC1 activation in Rab10 KD neurons as indicated by a normal pS6K1 phosphorylation (see above). Based on these observations, we conclude that Rab10's roles in calcium homeostasis and protein synthesis are most likely separate.

      (3) The authors indicate that the internal release of calcium ions from the ER has no effect on DCV trafficking and fusion without showing the data. It is important to include this data as the major impact of the study is the dissecting of the calcium effects in mammalian neurons from the previous studies in invertebrates.

      We agree this is an important aspect in our reasoning. We are submitting the related manuscript on internal calcium stores to BioRVix. The link will be added to the consolidated version of our manuscript

      (4) The distinction between Rab3 and Rab10 co-trafficking on DCVs should be reported in the Results (currently, Figure 2 - supplement 3 is only mentioned in the Discussion) as it helps to understand the effects on DCV fusion.

      We agree. We now added a new statement “Moreover, only 10% of DCVs co-transport with Rab10” in the Results (p. 6, l. 162-163).

      Reference:

      Balaji, J., Ryan, T.A., 2007. Single-vesicle imaging reveals that synaptic vesicle exocytosis and endocytosis are coupled by a single stochastic mode. Proceedings of the National Academy of Sciences 104, 20576–20581. https://doi.org/10.1073/pnas.0707574105

      Brunner, J.W., Lammertse, H.C.A., Berkel, A.A. van, Koopmans, F., Li, K.W., Smit, A.B., Toonen, R.F., Verhage, M., Sluis, S. van der, 2022. Power and optimal study design in iPSC-based brain disease modelling. Molecular Psychiatry 28, 1545. https://doi.org/10.1038/s41380-022-01866-3

      Emperador-Melero, J., Huson, V., van Weering, J., Bollmann, C., Fischer von Mollard, G., Toonen, R.F., Verhage, M., 2018. Vti1a/b regulate synaptic vesicle and dense core vesicle secretion via protein sorting at the Golgi. Nat Commun 9, 3421. https://doi.org/10.1038/s41467-018-05699-z

      Granseth, B., Odermatt, B., Royle, S.J., Lagnado, L., 2006. Clathrin-Mediated Endocytosis Is the Dominant Mechanism of Vesicle Retrieval at Hippocampal Synapses. Neuron 51, 773–786. https://doi.org/10.1016/j.neuron.2006.08.029

      Ivanova, D., Dobson, K.L., Gajbhiye, A., Davenport, E.C., Hacker, D., Ultanir, S.K., Trost, M., Cousin, M.A., 2021. Control of synaptic vesicle release probability via VAMP4 targeting to endolysosomes. Science Advances 7, eabf3873. https://doi.org/10.1126/sciadv.abf3873

      Kwon, S.E., Chapman, E.R., 2011. Synaptophysin Regulates the Kinetics of Synaptic Vesicle Endocytosis in Central Neurons. Neuron 70, 847–854. https://doi.org/10.1016/j.neuron.2011.04.001

      Reshetniak, S., Fernández-Busnadiego, R., Müller, M., Rizzoli, S.O., Tetzlaff, C., 2020. Quantitative Synaptic Biology: A Perspective on Techniques, Numbers and Expectations. International Journal of Molecular Sciences 21, 7298. https://doi.org/10.3390/ijms21197298

    1. Author response:

      To Reviewer #1:

      Thank you for your thorough review and comments on our work, which you described as “the role of neuritin in T cell biology studied here is new and interesting.”.  We have summarized your comments into two categories: biology and investigation approach, experimental rigor, and data presentation.

      Biology and Investigation approach comments:

      (1) Questions regarding the T cell anergy model:

      Major point “(4) Figure 1E-H. The authors assume that this immunization protocol induces anergic cells, but they provide no experimental evidence for this. It would be useful to show that T cells are indeed anergic in this model, especially those that are OVA-specific. The lack of IL-2 production by Cltr cells could be explained by the presence of fewer OVA-specific cells, rather than by an anergic status.”

      T cell anergy is a well-established concept first described by Schwartz’s group. It refers to the hyporesponsive T cell functional state in antigen-experienced CD4 T cells (Chappert and Schwartz, 2010; Fathman and Lineberry, 2007; Jenkins and Schwartz, 1987; Quill and Schwartz, 1987).  Anergic T cells are characterized by their inability to expand and to produce IL2 upon subsequent antigen re-challenge. In this paper, we have borrowed the existing in vivo T cell anergy induction model used by Mueller’s group for T cell anergy induction (Vanasek et al., 2006).  Specifically, Thy1.1+ Ctrl or Nrn1-/- TCR transgenic OTII cells were co-transferred with the congenically marked Thy1.2+ WT polyclonal Treg cells into TCR-/- mice.  After anergy induction, the congenically marked TCR transgenic T cells were recovered by sorting based on Thy1.1+ congenic marker, and subsequently re-stimulation ex vivo with OVA323-339 peptide. We evaluated the T cell anergic state based on OTII cell expansion in vivo and IL2 production upon OVA323-339 restimulation ex vivo.  

      “The authors assume that this immunization protocol induces anergic cells, but they provide no experimental evidence for this.”

      Because the anergy model by Mueller's group is well established (Vanasek et al., 2006), we did not feel that additional effort was required to validate this model as the reviewer suggested. Moreover, the limited IL2 production among the control cells upon restimulation confirms the validity of this model.

      “The lack of IL-2 production by Cltr cells could be explained by the presence of fewer OVAspecific cells, rather than by an anergic status”.

      Cells from Ctrl and Nrn1-/- mice on a homogeneous TCR transgenic (OTII) background were used in these experiments. The possibility that substantial variability of TCR expression or different expression levels of the transgenic TCR could have impacted IL2 production rather than anergy induction is unlikely.

      Overall, we used this in vivo anergy model to evaluate the Nrn1-/- T cell functional state in comparison to Ctrl cells under the anergy induction condition following the evaluation of Nrn1 expression, particularly in anergic T cells.  Through studies using this anergy model, we observed a significant change in Treg induction among OTII cells. We decided to pursue the role of Nrn1 in Treg cell development and function rather than the biology of T cell anergy as evidenced by subsequent experiments.

      Minor points “(6) On which markers are anergic cells sorted for RNAseq analysis?”

      Cells were sorted out based on their congenic marker marking Ctrl or Nrn1-/- OTII cells transferred into the host mice.  We did not specifically isolate anergic cells for sequencing.

      (2) Question regarding the validity of iTreg differentiation model.

      Major point: “(5) Figure 2A-C and Figure 3. The use of iTregs to try to understand what is happening in vivo is problematic. iTregs are cells that have probably no equivalent in vivo, and so may have no physiological relevance. In any case, they are different from pTreg cells generated in vivo. Working with pTreg may be challenging, that is why I would suggest generating data with purified nTreg. Moreover, it was shown in the article of Gonzalez-Figueroa 2021 that Nrn1-/- nTreg retained a normal suppressive function, which would not be what is concluded by the authors of this manuscript. Moreover, we do not even know what the % of Foxp3 cells is in the iTreg used (after differentiation and 20h of re-stimulation) and whether this % is the same between Ctlr and Nrn1 KO cells.”.

      We thank Reviewer #1 for their feedback. While it is true that iTregs made in vitro and in vivo generated pTregs display several distinctions (e. g., differences in Foxp3 expression stability, for example), we strongly disagree with this statement by Revieweer#1 “The use of iTregs to try to understand what is happening in vivo is problematic. iTregs are cells that have probably no equivalent in vivo, and so may have no physiological relevance.” The induced Treg cell (iTreg) model was established over 20 years ago (Chen et al., 2003; Zheng et al., 2002), and the model is widely adopted with over 2000 citations. Further, it has been instrumental in understanding different aspects of regulatory T cell biology (Hurrell et al., 2022; John et al., 2022; Schmitt and Williams, 2013; Sugiura et al., 2022).   

      Because we have observed reduced pTreg generation in vivo, we choose to use the in vitro iTreg model system to understand the mechanistic changes involved in Treg cell differentiation and function, specifically, neuritin’s role in this process. We have made no claim that iTreg cell biology is identical to pTreg generated in vivo or nTreg cells. However, the iTreg culture system has proved to be a good in vitro system for deciphering molecular events involved in complex processes. As such, it remains a commonly used approach by many research groups in the Treg cell field (Hurrell et al., 2022; John et al., 2022; Sugiura et al., 2022). Moreover, applying the iTreg in vitro culture system has been instrumental in helping us identify the cell electrical state change in Nrn1-/- CD4 cells and revealed the biological link between Nrn1 and the ionotropic AMPA receptor (AMPAR), which we will discuss in the subsequent discussion. It is technically challenging to use nTreg cells for T cell electrical state studies due to their heterogeneous nature from development in an in vivo environment and the effect of manipulation during the nTreg cell isolation process, which can both affect the T cell electrical state.   

      “Moreover, it was shown in the article of Gonzalez-Figueroa 2021 that Nrn1-/- nTreg retained a normal suppressive function, which would not be what is concluded by the authors of this manuscript.” 

      We have also carried out nTreg studies in vitro in addition to iTreg cells. Similar to Gonzalez-Figueroa et al.'s findings, we did not observe differences in suppression function between Nrn1-/- and WT nTreg using the in vitro suppression assay. However, Nrn1-/- nTreg cells revealed reduced suppression function in vivo (Fig. 2D-L). In fact, Gonzalez-Figueroa et al. observed reduced plasma cell formation after OVA immunization in Treg-specific Nrn1-/- mice, implicating reduced suppression from Nrn1-/- follicular regulatory T (Tfr) cells. Thus, our observation of the reduced suppression function of Nrn1-/- nTreg toward effector T cell expansion, as presented in Fig. 2D-L, does not contradict the results from Gonzalez-Figueroa et al. Rather, the conclusions of these two studies agree that Nrn1 can play important roles in immune suppression observable in vivo that are not captured readily by the in vitro suppression assay.

      “Moreover, we do not even know what the % of Foxp3 cells is in the iTreg used (after differentiation and 20h of re-stimulation) and whether this % is the same between Ctlr and Nrn1 KO cells.”

      We have stated in the manuscript on page 7 line 208 that “Similar proportions of Foxp3+ cells were observed in Nrn1-/- and Ctrl cells under the iTreg culture condition, suggesting that Nrn1 deficiency does not significantly impact Foxp3+ cell differentiation”. In the revised manuscript, we will include the data on the proportion of Foxp3+ cells before iTreg restimulation.

      (3) Confirmation of transcriptomic data regarding amino acids or electrolytes transport change

      Minor point“(3) Would not it be possible to perform experiments showing the ability of cells to transport amino acids or electrolytes across the plasma membrane? This would be a more interesting demonstration than transcriptomic data.”

      We appreciate Review# 1’s suggestion regarding “perform experiments showing the ability of cells to transport amino acids or electrolytes across the plasma membrane”.  We have indeed already performed such experiments corroborating the transcriptomics data on differential amino acid and nutrient transporter expression. Specifically, we loaded either iTreg or Th0 cells with membrane potential (MP) dye and measured MP level change after adding the complete set of amino acids (complete AA).  Upon entry, the charge carried by AAs may transiently affect cell membrane potential. Different AA transporter expression patterns may show different MP change patterns upon AA entry, as we showed in Author response image 1. We observed reduced MP change in Nrn1-/- iTreg compared to the Ctrl, whereas in the context of Th0 cells, Nrn1-/- showed enhanced MP change than the Ctrl. We can certainly include these data in the revised manuscript.

      Author response image 1.

      Membrane potential change induced by amino acids entry. a. Nrn1-/- or WT iTreg cells loaded with MP dye and MP change was measured upon the addition of a complete set of AAs. b. Nrn1-/- or WT Th0 cells loaded with MP dye and MP change was measured upon the addition of a complete set of AAs.

      (4) EAE experiment data assessment

      Minor point ”(5) Figure 5F. How are cells re-stimulated? If polyclonal stimulation is used, the experiment is not interesting because the analysis is done with lymph node cells. This analysis should either be performed with cells from the CNS or with MOG restimulation with lymph node cells.”

      In the EAE study, the Nrn1-/- mice exhibit similar disease onset but a protracted non-resolving disease phenotype compared to the WT control mice.  Several reasons may contribute to this phenotype: 1. Enhanced T effector cell infiltration/persistence in the central nervous system (CNS); 2. Reduced Treg cell-mediated suppression to the T effector cells in the CNS; 3. Protracted non-resolving inflammation at the immunization site has the potential to continue sending T effector cells into CNS, contributing to persistent inflammation. Based on this reasoning, we examined the infiltrating T effector cell number and Treg cell proportion in the CNS.  We also restimulated cells from draining lymph nodes close to the inflammation site, looking for evidence of persistent inflammation.  When mice were harvested around day 16 after immunization, the inflammation at the local draining lymph node should be at the contraction stage.  We stimulated cells with PMA and ionomycin intended to observe all potential T effector cells involved in the draining lymph node rather than only MOG antigen-specific cells.  We disagree with Reviewer #1’s assumption that “This analysis should either be performed with cells from the CNS or with MOG restimulation with lymph node cells.”. We think the experimental approach we have taken has been appropriately tailored to the biological questions we intended to answer.

      Experimental rigor and data presentation.

      (1) Data labeling and additional supporting data

      Major points (2) The authors use Nrn1+/+ and Nrn1+/- cells indiscriminately as control cells on the basis of similar biology between Nrn1+/+ and Nrn1+/- cells at homeostasis. However, it is quite possible that the Nrn1+/- cells have a phenotype in situations of in vitro activation or in vivo inflammation (cancer, EAE). It would be important to discriminate Nrn1+/- and Nrn1+/+ cells in the data or to show that both cell types have the same phenotype in these conditions too.

      (3) Figure 1A-D. Since the authors are using the Nrp1 KO mice, it would be important to confirm the specificity of the anti-Nrn1 mAb by FACS. Once verified, it would be important to add FACS results with this mAb in Figures 1A-C to have single-cell and quantitative data as well.

      Minor points  

      (1) Line 119, 120 of the text. It is said that one of the most up-regulated genes in anergic cells is Nrn1 but the data is not shown.

      (2) For all figures showing %, the titles of the Y axes are written in an odd way. For example, it is written "Foxp3% CD4". It would be more conventional and clearer to write "% Foxp3+ / CD4+" or "% Foxp3+ among CD4+".

      (4) For certain staining (Figure 3E, H) it would be important to show the raw data, in addition to MFI or % values.

      We can adapt the labeling and provide additional data, including Nrn1 staining on Treg cells and flow graphs for pmTOR and pS6 staining (Fig. 3H), as requested by Reviewer #1.

      (2) Experimental rigor:

      General comments:

      “However, it is disappointing that reading this manuscript leaves an impression of incomplete work done too quickly.”

      We were discouraged to receive the comment, “this manuscript leaves an impression of incomplete work done too quickly.” Our study of this novel molecule began without any existing biological tools such as antibodies, knockout mice, etc.  Over the past several years, we have established our own antibodies for Nrn1 detection, obtained and characterized Nrn1 knockout mice, and utilized multiple approaches to identify the molecular mechanism of Nrn1 function. Through the use of the in vitro iTreg system described in this manuscript, we identified the association of Nrn1 deficiency with cell electrical state change, potentially connected to AMPAR function. We have further corroborated our findings by generating Nrn1 and AMPAR T cell specific double knockout mice and confirmed that T cell specific AMPAR deletion could abrogate the phenotype caused by the Nrn1 deficiency (see Author response image 2).  We did not include the double knockout data in the current manuscript because AMPAR function has not yet been studied thoroughly in T cell biology, and we feel this topic warrants examination in its own right.  However, the unpublished data support the finding that Nrn1 modulates the T cell electrical state and, consequently, metabolism, ultimately influencing tolerance and immunity.  In its current form, the manuscript represents the first characterization of the novel molecule Nrn1 in anergic cells, Tregs, and effector T cells. While this work has led to several exciting additional questions, we disagree that the novel characterization we have presented Is incomplete. We feel that our present data set, which squarely highlights Nrn1’s role as an important immune regulator while shedding unprecedented light on the molecular events involved, will be of considerable interest to a broad field of researchers.

      “Multiple models have been used, but none has been studied thoroughly enough to provide really conclusive and unambiguous data. For example, 5 different models were used to study T cells in vivo. It would have been preferable to use fewer, but to go further in the study of mechanisms.”

      We have indeed used multiple in vivo models to reveal Nrn1's function in Treg differentiation, Treg suppression function, T effector cell differentiation and function, and the overall impact on autoimmune disease. Because the impact of ion channel function is often context-dependent, we examined the biological outcome of Nrn1 deficiency in several in vivo contexts.  We would appreciate it if Reviewer#1 would provide a specific example, given the Nrn1 phenotype, of how to proceed deeper to investigate the electrical change in the in vivo models.

      “Major points (1) A real weakness of this work is the fact that in most of the results shown, there are few biological replicates with differences that are often small between Ctrl and Nrn1 -/-. The systematic use of student's t-test may lead to thinking that the differences are significant, which is often misleading given the small number of samples, which makes it impossible to know whether the distributions are Gaussian and whether a parametric test can be used. RNAseq bulk data are based on biological duplicates, which is open to criticism.”

      We respectfully disagree with Reviewer #1 on the question of statistical power and significance to our work. We have used 5-8 mice/group for each in vivo model and 3-4 technical replicates for the in vitro studies, with a minimum of 2-3 replicate experiments. These group sizes and replication numbers are in line with those seen in high-impact publications. While some differences between Ctrl and Nrn1-/- appear small, they have significant biological consequences, as evidenced by the various Nrn1-/- in vivo phenotypes. Furthermore, we believe we have subjected our data to the appropriate statistical tests to ensure rigorous analysis and representation of our findings.

      To Reviewer #2.

      We thank Reviewer #2 for the careful review of the manuscript. We especially appreciate the comments that “The characterizations of T cell Nrn1 expression both in vitro and in vivo are comprehensive and convincing. The in vivo functional studies of anergy development, Treg suppression, and EAE development are also well done to strengthen the notion that Nrn1 is an important regulator of CD4 responsiveness.”

      “The major weakness of this study stems from a lack of a clear molecular mechanism involving Nrn1. “  

      We fully understand this comment from Reviewer #2. The main mechanism we identified contributing to the functional defect of Nrn1-/- T cells involves novel effects on the electric and metabolic state of the cells. Although we referenced neuronal studies that indicate Nrn1 is the auxiliary protein for the ionotropic AMPA-type glutamate receptor (AMPAR) and may affect AMPAR function, we did not provide any evidence in this manuscript as the topic requires further in-depth study.   

      For the benefit of this discussion, we include our preliminary Nrn1 and AMPAR double knockout data (Author response image 2), which indicates that abrogating AMPAR expression can compensate for the defect caused by Nrn1 deficiency in vitro and in vivo. This preliminary data supports the notion that Nrn1 modulates AMPAR function, which causes changes in T cell electric and metabolic state, influencing T cell differentiation and function.  

      Author response image 2.

      Deletion of AMPAR expression in T cells compensates for the defect caused by Nrn1 deficiency. Nrn1-/- mice were crossed with T cell-specific AMPAR knockout mice (AMPARfl/flCD4Cre+) mice. The following mice were generated and used in the experiment: T cell specific AMPAR-knockout and Nrn1 knockout mice (AKONKO), Nrn1 knockout mice (AWTNKO), Ctrl mice (AWTNWT). a. Deletion of AMPAR compensates for the iTreg cell defect observed in Nrn1-/- CD4 cells. iTreg live cell proportion, cell number, and Ki67 expression among Foxp3+ cells 3 days after aCD3 restimulation. b. Deletion of AMPAR in T cells abrogates the enhanced autoimmune response in Nrn1-/- Mouse in the EAE disease model. Mouse relative weight change and disease score progression after EAE disease induction.  

      Ion channels can influence cell metabolism through multiple means (Vaeth and Feske, 2018; Wang et al., 2020). First, ion channels are involved in maintaining cell resting membrane potential. This electrical potential difference across the cell membrane is essential for various cellular processes, including metabolism (Abdul Kadir et al., 2018; Blackiston et al., 2009; Nagy et al., 2018; Yu et al., 2022). Second, ion channels facilitate the movement of ions across cell membranes. These ions are essential for various metabolic processes. For example, ions like calcium (Ca2+), potassium (K+), and sodium (Na+) play crucial roles in signaling pathways that regulate metabolism (Kahlfuss et al., 2020). Third, ion channel activity can influence cellular energy balance due to ATP consumption associated with ion transport to maintain ion balances (Erecińska and Dagani, 1990; Gerkau et al., 2019). This, in turn, can impact processes like ATP production, which is central to cellular metabolism. Thus, ion channel expression and function determine the cell’s bioelectric state and contribute to cell metabolism (Levin, 2021).

      Because the AMPAR function has not been thoroughly studied using a genetic approach in T cells, we do not intend to include the double knockout data in this manuscript before fully characterizing the T cell-specific AMPAR knockout mice.  

      “Although the biochemical and informatics studies are well-performed, it is my opinion that these results are inconclusive in part due to the absence of key "naive" control groups. This limits my ability to understand the significance of these data.

      Specifically, studies of the electrical and metabolic state of Nrn1-/- inducible Treg cells (iTregs) would benefit from similar data collected from wild-type and Nrn1-/- naive CD4 T cells.”

      We appreciate the reviewer’s comments. This comment reflects two concerns in data interpretation:

      (1) Are Nrn1-/- naïve T cells fundamentally different from WT cells? Does this fundamental difference contribute to the observed electrical and metabolic phenotype in iTreg or Th0 cells? This is a very good question we will perform the experiments as the reviewer suggested. While Nrn1 is expressed at a basal (low) level in naïve T cells, deletion of Nrn1 may cause changes in naïve T cell phenotype.   

      (2) Is the Nrn1-/- phenotype caused by Nrn1 functional deficiency or due to the secondary effect of Nrn1 deletion, such as non-physiological cell membrane structure changes?

      We have done the following experiment to address this concern.  We have cultured WT T cells in the presence of Nrn1 antibody and compared the outcome with Nrn1-/- iTreg cells (Author response image 3). WT iTreg cells under antibody blockade exhibited similar changes as Nrn1-/- iTreg cells, confirming the physiological relevance of the Nrn1-/- phenotype.

      Author response image 3.

      Nrn1 antibody blockade in WT iTreg cell culture caused similar phenotypic change as in Nrn1-/- iTreg cells. Nrn1-/- and WT CD4 cells were differentiated under iTreg condition in the presence of anti-Nrn1 (aNrn1) antibody or isotype control for 3 days. Cells were restimulated with anti-CD3 and in the presence of aNrn1 or isotype. a. MP measured 18hr after anti-CD3 restimulation. b. live CD4 cell number and proportion of Ki67 expression among live cells three days after restimulation. c. The proportion of Foxp3+ cells among live cells three days after restimulation.  

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    1. Author response:

      Reviewer #1 (Public Review):

      Summary:

      Li et al investigated how adjuvants such as MPLA and CpG influence antigen presentation at the level of the Antigen-presenting cell and MHCII : peptide interaction. They found that the use of MPLA or CpG influences the exogenous peptide repertoire presented by MHC II molecules. Additionally, their observations included the finding that peptides with low-stability peptide:MHC interactions yielded more robust CD4+ T cell responses in mice. These phenomena were illustrated specifically for 2 pattern recognition receptor activating adjuvants. This work represents a step forward for how adjuvants program CD4+ Th responses and provides further evidence regarding the expected mechanisms of PRR adjuvants in enhancing CD4+ T cell responses in the setting of vaccination.

      Strengths:

      The authors use a variety of systems to analyze this question. Initial observations were collected in an H pylori model of vaccination with a demonstration of immunodominance differences simply by adjuvant type, followed by analysis of MHC:peptide as well as proteomic analysis with comparison by adjuvant group. Their analysis returns to peptide immunization and analysis of strength of relative CD4+ T cell responses, through calculation of IC:50 values and strength of binding. This is a comprehensive work. The logical sequence of experiments makes sense and follows an unexpected observation through to trying to understand that process further with peptide immunization and its impact on Th responses. This work will premise further studies into the mechanisms of adjuvants on T cells.

      Weaknesses:

      Comment 1. While MDP has a different manner of interaction as an adjuvant compared to CpG and MPLA, it is unclear why MDP has a different impact on peptide presentation and it should be further investigated, or at minimum highlighted in the discussion as an area that requires further investigation.

      Thank you for the suggestion. We investigated the reasons for the different effects of MDP on peptide presentation compared with those of CpG and MPLA. We found that the expression of some proteins involved in antigen processing and presentation, such as CTSS, H2-DM, Ifi30, and CD74, was substantially lower in the MDP-treated group than in the CpG- and MPLA-treated groups. To further confirm whether these proteins play a key role during adjuvant modification of peptide presentation, we knocked down them using shRNA and then performed immunopeptidomics. The original mass spectra and peptide spectrum matches have been deposited in the public proteomics repository iProX (https://www.iprox.cn/page/home.html) under accession number IPX0007611000. Unfortunately, the expected results for peptide presentation repertoires were not observed. Thus, we hypothesized that the different effects of MDP on peptide presentation might not result from differences in protein expression. We cannot exclude the possibility that some other proteins that may be important in this process were overlooked. We are still working on the mechanisms and do not have an exact conclusion. Thus, we did not present related data in this manuscript.

      The related statements were added in the Discussion section on page 13, lines 292–299: “In this study, we found that the peptide repertoires presented by APCs were significantly affected by the adjuvants CpG and MPLA, but not MDP. All three adjuvants belong to the PRR ligand adjuvant family. CpG and MPLA bind to TLRs and MDP is recognized by NOD2. Although the receptors are different, many common molecules are involved both in TLR and NLD pathway activation. Unfortunately, we did not demonstrate why the MDP had different impacts on peptide presentation compared with other adjuvants. Further investigation is required to clarify the mechanism by which MPLA, CpG, and MDP adjuvants modulate the presentation of peptides with different stabilities.”

      Comment 2. It is alluded by the authors that TLR activating adjuvants mediate selective, low affinity, exogenous peptide binding onto MHC class II molecules. However, this was not demonstrated to be related specifically to TLR binding. I wonder if some work with TLR deficient mice (TLR 4KO for example) could evaluate this phenomenon more specifically.

      Thank you for the suggestion. This is an important point that was overlooked in this study. Based on published research on the mechanisms of PRR adjuvants, CpG and MPLA, we believe that the effect of CpG and MPLA on APCs-selective epitope presentation needs to be bound to the corresponding receptor, although we did not give a definitive conclusion in the manuscript.

      To confirm the TLR-activating adjuvants affecting peptides presented on MHC molecules specifically through TLR binding, we have used CRISPR-cas9 to knock out TLR4 and TLR9 of A20 cells and repeated the experiments, as suggested. We chose TLR4- and TLR9- knockout A20 cell lines instead of TLR-deficient mice because a large number of APCs are required for immunopeptidomics. Moreover, the data observed in this study were based on the A20 cell line. However, these experiments are time-consuming. Unfortunately, we were unable to provide timely data. In addition, we believe that elucidating the downstream molecular mechanisms of TLR activation is necessary, as mentioned in comment 1. All these data will be combined and reported in our upcoming publications.

      Comment 3. It is unclear to me if this observation is H pylori model/antigen-specific. It may have been nice to characterize the phenomenon with a different set of antigens as supplemental. Lastly, it is unclear if the peptide immunization experiment reveals a clear pattern related to high and low-stability peptides among the peptides analyzed.

      Q1: It is unclear to me if this observation is H. pylori model/antigen-specific. It may have been nice to characterize the phenomenon with a different set of antigens as supplemental.

      Thank you for the comment. To confirm the effect of the adjuvant on the exogenous peptide repertoire presented by MHC II molecules, a set of antigens from another bacterium, Pseudomonas aeruginosa, was used, and the experiments were repeated. The A20 cells were treated with CpG and pulsed with Pseudomonas aeruginosa antigens. Twelve hours later, MHC-II–peptide complexes were immunoprecipitated, and immunopeptidomics were performed. The data are shown below (Author response image 1). Information on the MHC-peptides from Pseudomonas aeruginosa is given in the Supplementary Table named “Table S3 Response to comment3”. A total of 713 and 205 bacterial peptides were identified in the PBS and CpG groups (Author response image 1A). The number of exogenous peptides in the CpG-treated group was significantly lower than that in the PBS-treated control group (Author response image 1B). A total of 568 bacterial peptides were presented only in the PBS group; 60 bacterial peptides were presented in the CpG-treated group, and 145 bacterial peptides were presented in both groups (Author response image 1C). We then analyzed the MHC-binding stability of the peptides present in the adjuvant-treated group and that of the peptide-deficient after adjuvant stimulation using the IEDB website. We found that the IC50 of the peptides in the adjuvant-treated group were much higher than those of the deficient peptides, which indicated that the peptides presented in the CpG-treated groups have lower binding stability for MHC-II (Author response image 1D). These results indicate that CpG adjuvant affects the presentation of exogenous peptides with high binding stability, which is consistent with the data reported in our manuscript. Using another set of antigens, we confirmed that our observations were not H. pylori model- or antigen-specific.

      Author response image 1.

      MHC-II peptidome measurements in adjuvant-treated APCs pulsed with Pseudomonas aeruginosa antigens. (A) Total number of bacterial peptides identified in the PBS- and CpG-treated groups. (B) The number and length distribution of bacterial peptides in different groups were compared. (C) Venn diagrams showing the distribution of bacterial peptides in different groups. (D) IC50 of the presented, deficient, and co-presented peptides post-adjuvant stimulation from immunopeptidome binding to H2-IA and H2-IE were predicted using the IEDB website. High IC50 means low binding stability. *p<0.05, **p<0.01.

      Q2: Lastly, it is unclear if the peptide immunization experiment reveals a clear pattern related to high and low-stability peptides among the peptides analyzed.

      In this study, we used a peptide immunization experiment to evaluate the responses induced by the screened peptides with different stabilities. In addition to this method, tetramer staining and ELISA have been used to assess epitope-specific T-cell proliferation and cytokine secretion. Among these, tetramer staining is often used in studies involving model antigens. However, as many peptides were screened in our study, synthesizing a sufficient number of tetramers was difficult. However, we believe that the experimental data obtained in this study support the conclusion. Nevertheless, we agree that more methods applied will make the pattern more clearly.

      Reviewer #2 (Public Review):

      Adjuvants boost antigen-specific immune responses to vaccines. However, whether adjuvants modulate the epitope immunodominance and the mechanisms involved in adjuvant's effect on antigen processing and presentation are not fully characterized. In this manuscript, Li et al report that immunodominant epitopes recognized by antigen-specific T cells are altered by adjuvants.

      Using MPLA, CpG, and MDP adjuvants and H. pylori antigens, the authors screened the dominant epitopes of Th1 responses in mice post-vaccination with different adjuvants and found that adjuvants altered antigen-specific CD4+ T cell immunodominant epitope hierarchy. They show that adjuvants, MPLA and CpG especially, modulate the peptide repertoires presented on the surface of APCs. Surprisingly, adjuvant favored the presentation of low-stability peptides rather than high-stability peptides by APCs. As a result, the low stability peptide presented in adjuvant groups elicits T cell response effectively.

      Thanks a lot for your comments.

      Reviewer #1 (Recommendations For The Authors):

      Recommendation 1. Figure 6: The peptides considered low affinity- it would be helpful to specify from which adjuvant they were collected from. When they are pooled it is unclear if we are analyzing peptides collected from adjuvanting with any of the three adjuvants studied.

      Thank you for the suggestion. The related description in Figure 6 has been modified in the revised manuscript. Data for the peptides identified from the adjuvants MPLA- and CpG-treated groups are shown separately.

      Recommendation 2. It is unclear to me why the A20 cell line is less preferred to the J774 line for the immunopeptidome analysis - can the authors expand on this?

      We apologize for not clearly explaining this in the original manuscript. In fact, the A20 cell line is better than J774A.1 cell line for immunopeptidomics experiments. Compared to J774A.1 cells, more MHC-II peptides were obtained from a smaller number of A20 cells using immunopeptidomics. At the beginning of this study, we chose the J774A.1 cell line as it is a macrophage cell line. J774A.1 cells (up to 5×108) were pulsed with the antigens, and MHC-II–peptide complexes were eluted from the cell surface for immunopeptidomics. Unfortunately, only a few hundred peptides from the host were detected and no exogenous peptides were detected. Next, we tested the A20 cell line. In total, 108 A20 cells were used in this study. More than 3500 host peptides and approximately 50 exogenous peptides have been identified. These data indicate that the A20 cell line was better.

      To investigate the reasons for this, we detected MHC-II expression on cell surfaces using FACS. Our purpose was to elute peptides from MHC–peptide complexes present on the cell surface. Low MHC expression resulted in the elution of a few peptides. We found the MFI of MHC-II molecules on J774A.1 cell is about 500; however, the MFI of MHC-II molecules on A20 cells is more than 300,000. These data indicate that MHC-II expression on A20 cells was much higher than that on J774A.1 cells. J774A.1 cell is a macrophage cell line. Macrophages have excellent antigen phagocytic capabilities; however, their ability to present antigens is relatively weak. MHC molecules on the macrophage cell surface can be upregulated in the stimulation of some cytokines, for example, IFN-γ. In this study, we used adjuvants as stimulators and did not want to use additional cytokine stimulators. Thus, J774A.1 cells were not used in the present study.

      The related statements are reflected on page 6 lines 120–128 “We also selected another H-2d cell J774A.1, a macrophage cell line, for immunopeptidome analysis in this study. Briefly, 5×108 J774A.1 cells were used for immunopeptidomics. Moreover, fewer than 350 peptides were observed at a peptide spectrum match (PSM) level of < 1.0% false discovery rate (FDR). However, more than 5500 peptides were detected in 108 A20 cells at FDR < 1.0% (Figure S2A). CD86 and MHC-II molecule expression on J774A.1 cells was substantially lower than that on A20 cells (Figure S2B). Low MHC-II expression on J774A.1 cells could be the reason for the lack of peptides identified by LC–MS/MS. Thus, A20 cells instead of J774A.1 cells were used for the subsequent experiments.”

      Recommendation 3. Lines 172-177, can more details be provided about the whole proteome analysis? The plots are shown for relative representation of protein expression to PBS, but it is unclear to me what examples of these proteins are (IFN pathway, Ubiquitination pathway). Could these be confirmed by protein expression analyses in supplemental?

      Thank you for the suggestion. In this study, we conducted whole proteome analysis to investigate changes in protein expression across different pathways in the adjuvant groups. Through KEGG enrichment analysis, we compared the differential expression of MHC presentation pathway proteins (such as H2-M, Ifi30, CD74, CTSS, proteasome, and peptidase subunits) between the PBS- and adjuvant-treated groups using our proteome data. In addition, we focused on IFN and ubiquitination pathways that play crucial roles in antigen presentation modification and immune response. The proteins and their relative expression in these pathways are shown in Figure S4B. Details regarding the protein names and expressions are provided in Supplemental Table S2 of the revised manuscript.

      The original statements in the results “Then, we analyzed the whole proteome data to determine whether the proteins involved in antigen presentation and processing were altered. We found that proteins involved in antigen processing, peptidase function, ubiquitination pathway, and interferon (IFN) signaling were altered post adjuvants treatment, especially in MPLA and CpG groups (Figure 5C; Figure S4B and S4C). These data suggest that adjuvants MPLA and CpG may affect the antigen processing of APCs, resulting in fewer peptides presentation.” This has been revised on page 8 lines 172–182 as “We then investigated whole-proteome data to determine the evidence of adjuvant modification of antigen presentation. We focused on the proteins involved in antigen processing, peptidase function, ubiquitination pathway, and IFN signaling. The ubiquitination pathway and IFN signaling play crucial roles in the modification of antigen presentation and immune responses. Through KEGG enrichment analysis, we found that many proteins involved in antigen processing, peptidase function, ubiquitination pathways, and IFN signaling were altered after adjuvant treatment, particularly in the MPLA- and CpG-treated groups (Figure 5C; Figure S4B). The expression of each protein is shown in Figure S4C and Supplementary Table 2. These data suggest that MPLA and CpG adjuvants may affect the antigen processing of APCs, resulting in fewer peptide presentations.”

      Recommendation 4. Lines 212-218: I think there needs to be more discussion of interpretation here. Only one of the low-stability peptides required low concentrations for CD4+ T cell responses in vitro. What about the other peptides in the analysis? Perhaps if the data is taken together there is not a clear pattern?

      Thank you for the comment. In this study, epitope-specific CD4+ T-cells were expanded in vitro from the spleens of peptide-pool-immunized mice. T-cell responses to individual peptides were detected using ICS and FACS. Only one peptide, recA #23, with low binding stability, and one high-stability peptide, ureA #2, induced effective T-cell responses. Peptide ureA #3 with high stability induces low Th1 responses. The other peptides cannot induce CD4+ T-cell secreting IFN-γ (Data are shown in Author response image 2). Thus, we compared the strength of IFN-γ responses induced by these three peptides at a set of low concentrations. Data for other peptides without any response could not be taken together.

      Author response image 2.

      The expanded CD4+T cells from peptides immunized mice were screened for their response to the peptides in an ICS assay.

      In this study, we used a peptide pool containing four low-stability peptides to vaccinate mice; however, only one peptide induced an effective CD4+ T-cell response. We speculate that the possible reasons are as follows. First, the number of peptides used for vaccination is too small. Only four low-stability peptides were synthesized and used to immunize mice. Three of these could not induce an effective T-cell response, possibly because of their low immunogenicity. If more peptides are synthesized and used, more peptides that induce T-cell responses may be observed. Second, epitope-specific T-cell responses are variable. Responses to the subdominant peptides can be inhibited by the dominant peptide. The subdominant peptide can become dominant by changing the peptide dose or in the absence of the dominant peptide. Thus, we believe that responses to the other three peptides may be detected if mice are immunized with a peptide pool that does not contain a response epitope.

      The corresponding statements have been added to the Discussion section on page 13 lines 287–291 as “Unfortunately, only one peptide, recA #23, with low binding stability and induced significant Th1 responses, was identified in this study. To further confirm that low-stability peptides can induce stronger and higher TCR-affinity antigen-specific T-cell clonotype responses than high-stability peptides, further studies should monitor more peptides with different stabilities.”

      Recommendation 5. There are some areas where additional editing to text would be beneficial due to grammar (eg lines 122-126; line 116, etc).

      The manuscript has been edited by a professional language editing company.

      Reviewer #2 (Recommendations For The Authors):

      Recommendation 1. It is interesting that there was no difference in IFNg responses induced by different adjuvants.

      Thank you for the comment. Possible reasons for the lack of difference in IFN-γ responses could be as follows. First, all adjuvants used in this study have been confirmed to effectively induce Th1 responses. Second, in this study, IFN-γ responses were examined using expanded antigen-specific T cells in vitro. The in vitro cell expansion efficiency may have affected these results.

      Recommendation 2. The data to support the claim that changes in exogenous peptide presentation among adjuvant groups were not due to differences in antigen phagocytosis is insufficient.

      Thank you for the comment. In this study, proteomics of A20 cells pulsed with antigens in different adjuvant-treated groups were used to determine exogenous antigens phagocytosed by cells. In addition, we used fluorescein isothiocyanate (FITC)-labeled OVA to pulse APCs and detected antigen phagocytosis by APCs after treatment with different adjuvants. The MFI of FITC was detected by FACS at different time points. The data are shown below (Author response image 3). No obvious differences in FITC MFI were detected after adjuvant stimulation, indicating that antigen phagocytosis among the adjuvant groups was almost the same.

      A20 cells, used as APCs, are the B-cell line. Antigen recognition and phagocytosis by B-cells depends on the B-cell receptor (BCR) on the cell surface. The ability of BCRs to bind to different antigens varies, leading to significant differences in the phagocytosis of different antigens by B-cells. Therefore, detecting the phagocytosis of a single antigen may not reflect the overall phagocytic state of the B-cells. Thus, in this study, we used proteomics to detect exogenous proteins in B-cells pulsed with H. pylori antigens, which contain thousands of components, to evaluate their overall phagocytic capacity. Only the proteomic data are presented in our manuscript.

      Author response image 3.

      Antigen phagocytosis of A20 cells were measured using FITC-labeled OVA. (A) A20 cells were pulsed with FITC-labeled OVA. MFI of FITC was measured after 1 h. (B) MFI of FITC was examined post the stimulation of adjuvants at different time points.

      Recommendation 3. It is not clear how MPLA, CpG, and MDP adjuvants modulate the presentation of low vs high stability peptides.

      Thank you for pointing this out. We acknowledge that we did not clarify the mechanisms by which adjuvants affect the stability of the peptide presentations of APCs.

      We performed experiments to detect the expression of proteins involved in antigen processing and presentation in the different adjuvant-treated groups. Furthermore, shRNAs were used to knock down the expression of key molecules. Immunopeptidomics was used to detect peptide presentation. Unfortunately, the expected results for peptide presentation repertoires were not observed. We are still working on the mechanisms.

      Please also see our response to comment 1 of reviewer 1

      The related statements were added in the Discussion section on page 13, lines 292–299: “In this study, we found that the peptide repertoires presented by APCs were significantly affected by the adjuvants CpG and MPLA, but not MDP. All three adjuvants belong to the PRR ligand adjuvant family. CpG and MPLA bind to TLRs and MDP is recognized by NOD2. Although the receptors are different, many common molecules are involved both in TLR and NLD pathway activation.  Unfortunately, we did not demonstrate why the MDP had different impacts on peptide presentation compared with other adjuvants. Further investigation is required to clarify the mechanism by which MPLA, CpG, and MDP adjuvants modulate the presentation of peptides with different stabilities.”

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Reviewer #1 (Public Review): 

      The reviewer retained most of their comments from the previous reviewing round. In order to meet these comments and to further examine the dynamic nature of threat omission-related fMRI responses, we now re-analyzed our fMRI results using the single trial estimates. The results of these additional analyses are added below in our response to the recommendations for the authors of reviewer 1. However, we do want to reiterate that there was a factually incorrect statement concerning our design in the reviewer’s initial comments. Specifically, the reviewer wrote that “25% of shocks are omitted, regardless of whether subjects are told that the probability is 100%, 75%, 50%, 25%, or 0%.” We want to repeat that this is not what we did. 100% trials were always reinforced (100% reinforcement rate); 0% trials were never reinforced (0% reinforcement rate). For all other instructed probability levels (25%, 50%, 75%), the stimulation was delivered in 25% of the trials (25% reinforcement rate). We have elaborated on this misconception in our previous letter and have added this information more explicitly in the previous revision of the manuscript (e.g., lines 125-129; 223-224; 486-492).   

      Reviewer #1 (Recommendations For The Authors): 

      I do not have any further recommendations, although I believe an analysis of learning-related changes is still possible with the trial-wise estimates from unreinforced trials. The authors' response does not clarify whether they tested for interactions with run, and thus the fact that there are main effects does not preclude learning. I kept my original comments regarding limitations, with the exception of the suggestion to modify the title. 

      We thank the reviewer for this recommendation. In line with their suggestion, we have now reanalyzed our main ROI results using the trial-by-trial estimates we obtained from the firstlevel omission>baseline contrasts. Specifically, we extracted beta-estimates from each ROI and entered them into the same Probability x Intensity x Run LMM we used for the relief and SCR analyses. Results from these analyses (in the full sample) were similar to our main results. For the VTA/SN model, we found main effects of Probability (F = 3.12, p = .04), and Intensity (F = 7.15, p < .001) (in the model where influential outliers were rescored to 2SD from mean). There was no main effect of Run (F = 0.92, p = .43) and no Probability x Run interaction (F = 1.24, p = .28). If the experienced contingency would have interfered with the instructions, there should have been a Probability x Run interaction (with the effect of Probability only being present in the first runs). Since we did not observe such an interaction, our results indicate that even though some learning might still have taken place, the main effect of Probability remained present throughout the task.  

      There is an important side note regarding these analyses: For the first level GLM estimation, we concatenated the functional runs and accounted for baseline differences between runs by adding run-specific intercepts as regressors of no-interest. Hence, any potential main effect of run was likely modeled out at first level. This might explain why, in contrast to the rating and SCR results (see Supplemental Figure 5), we found no main effect of Run. Nevertheless, interaction effects should not be affected by including these run-specific intercepts.

      Note that when we ran the single-trial analysis for the ventral putamen ROI, the effect of intensity became significant (F = 3.89, p = .02). Results neither changed for the NAc, nor the vmPFC ROIs.  

      Reviewer #2 (Public Review): 

      Comments on revised version: 

      I want to thank the authors for their thorough and comprehensive work in revising this manuscript. I agree with the authors that learning paradigms might not be a necessity when it comes to study the PE signals, but I don't particularly agree with some of the responses in the rebuttal letter ("Furthermore, conditioning paradigms generally only include one level of aversive outcome: the electrical stimulation is either delivered or omitted."). This is of course correct description for the conditioning paradigm, but the same can be said for an instructed design: the aversive outcome was either delivered or not. That being said, adopting the instructed design itself is legitimate in my opinion. 

      We thank the reviewer for this comment. We have now modified the phrasing of this argument to clarify our reasoning (see lines 102-104: “First, these only included one level of aversive outcome: the electrical stimulation was either delivered at a fixed intensity, or omitted; but the intensity of the stimulation was never experimentally manipulated within the same task.”).  

      The reason why we mentioned that “the aversive outcome is either delivered or omitted” is because in most contemporary conditioning paradigms only one level of aversive US is used. In these cases, it is therefore not possible to investigate the effect of US Intensity. In our paradigm, we included multiple levels of aversive US, allowing us to assess how the level of aversiveness influences threat omission responding. It is indeed true that each level was delivered or not. However, our data clearly (and robustly across experiments, see Willems & Vervliet, 2021) demonstrate that the effects of the instructed and perceived unpleasantness of the US (as operationalized by the mean reported US unpleasantness during the task) on the reported relief and the omission fMRI responses are stronger than the effect of instructed probability.  

      My main concern, which the authors spent quite some length in the rebuttal letter to address, still remains about the validity for different instructed probabilities. Although subjects were told that the trials were independent, the big difference between 75% and 25% would more than likely confuse the subjects, especially given that most of us would fall prey to the Gambler's fallacy (or the law of small numbers) to some degree. When the instruction and subjective experience collides, some form of inference or learning must have occurred, making the otherwise straightforward analysis more complex. Therefore, I believe that a more rigorous/quantitative learning modeling work can dramatically improve the validity of the results. Of course, I also realize how much extra work is needed to append the computational part but without it there is always a theoretical loophole in the current experimental design. 

      We agree with the reviewer that some learning may have occurred in our task. However, we believe the most important question in relation to our study is: to what extent did this learning influence our manipulations of interest?  

      In our reply to reviewer 1, we already showed that a re-analysis of the fMRI results using the trial-by-trial estimates of the omission contrasts revealed no Probability x Run interaction, suggesting that – overall – the probability effect remained stable over the course of the experiment. However, inspired by the alternative explanation that was proposed by this reviewer, we now also assessed the role of the Gambler’s fallacy in a separate set of analyses. Indeed, it is possible that participants start to expect a stimulation more after more time has passed since the last stimulation was experienced. To test this alternative hypothesis, we specified two new regressors that calculated for each trial of each participant how many trials had passed since the last stimulation (or since the beginning of the experiment) either overall (across all trials of all probability types; hence called the overall-lag regressor) or per probability level (across trials of each probability type separately; hence called the lag-per-probability regressor). For both regressors a value of 0 indicates that the previous trial was either a stimulation trial or the start of experiment, a value of 1 means that the last stimulation trial was 2 trials ago, etc.  

      The results of these additional analyses are added in a supplemental note (see supplemental note 6), and referred to in the main text (see lines 231-236: “Likewise, a post-hoc trial-by-trial analysis of the omission-related fMRI activations confirmed that the Probability effect for the VTA/SN activations was stable over the course of the experiment (no Probability x Run interaction) and remained present when accounting for the Gambler’s fallacy (i.e., the possibility that participants start to expect a stimulation more when more time has passed since the last stimulation was experienced) (see supplemental note 6). Overall, these post-hoc analyses further confirm the PE-profile of omission-related VTA/SN responses”.  

      Addition to supplemental material (pages 16-18)

      Supplemental Note 6: The effect of Run and the Gambler’s Fallacy 

      A question that was raised by the reviewers was whether omission-related responses could be influenced by dynamical learning or the Gambler’s Fallacy, which might have affected the effectiveness of the Probability manipulation.  

      Inspired by this question, we exploratorily assessed the role of the Gambler’s Fallacy and the effects of Run in a separate set of analyses. Indeed, it is possible that participants start to expect a stimulation more when more time has passed since the last stimulation was experienced. To test this alternative hypothesis, we specified two new regressors that calculated for each trial of each participant how many trials had passed since the last stimulation (or since the beginning of the experiment) either overall (across all trials of all probability types; hence called the overall-lag regressor) or per probability level (across trials of each probability type separately; hence called the lag-per-probability regressor). For both regressors a value of 0 indicates that the previous trial was either a stimulation trial or the start of experiment, a value of 1 means that the last stimulation trial was 2 trials ago, etc.  

      The new models including these regressors for each omission response type (i.e., omission-related activations for each ROI, relief, and omission-SCR) were specified as follows:   

      (1) For the overall lag:

      Omission response ~ Probability * Intensity * Run + US-unpleasantness + Overall-lag + (1|Subject).  

      (2) For the lag per probability level:

      Omission response ~ Probability * Intensity * Run + US-unpleasantness + Lag-perprobability : Probability + (1|Subject).  

      Where US-unpleasantness scores were mean-centered across participants; “*” represents main effects and interactions, and “:” represents an interaction (without main effect). Note that we only included an interaction for the lag-per-probability model to estimate separate lag-parameters for each probability level.  

      The results of these analyses are presented in the tables below. Overall, we found that adding these lag-regressors to the model did not alter our main results. That is: for the VTA/SN, relief and omission-SCR, the main effects of Probability and Intensity remained. Interestingly, the overall-lag-effect itself was significant for VTA/SN activations and omission SCR, indicating that VTA/SN activations were larger when more time had passed since the last stimulation (beta = 0.19), whereas SCR were smaller when more time had passed (beta = -0.03). This pattern is reminiscent of the Perruchet effect, namely that the explicit expectancy of a US increases over a run of non-reinforced trials (in line with the gambler’s fallacy effect) whereas the conditioned physiological response to the conditional stimulus declines (in line with an extinction effect, Perruchet, 1985; McAndrew, Jones, McLaren, & McLaren, 2012). Thus, the observed dissociation between the VTA/SN activations and omission SCR might similarly point to two distinctive processes where VTA/SN activations are more dependent on a consciously controlled process that is subjected to the gambler’s fallacy, whereas the strength of the omission SCR responses is more dependent on an automatic associative process that is subjected to extinction. Importantly, however, even though the temporal distance to the last stimulation had these opposing effects on VTA/SN activations and omission SCRs, the main effects of the probability manipulation remained significant for both outcome variables. This means that the core results of our study still hold.   

      Next to the overall-lag effect, the lag-per-probability regressor was only significant for the vmPFC. A follow-up of the beta estimates of the lag-per-probability regressors for each probability level revealed that vmPFC activations increased with increasing temporal distance from the stimulation, but only for the 50% trials (beta = 0.47, t = 2.75, p < .01), and not the 25% (beta = 0.25, t = 1.49, p = .14) or the 75% trials (beta = 0.28, t = 1.62, p = .10).

      Author response table 1.

      F-statistics and corresponding p-values from the overall lag model. (*) F-test and p-values were based on the model where outliers were rescored to 2SD from the mean. Note that when retaining the influential outliers for this model, the p-value of the probability effect was p = .06. For all other outcome variables, rescoring the outliers did not change the results. Significant effects are indicated in bold.

      Author response table 2.

      F-statistics and corresponding p-values from the lag per probability level model. (*) F-test and p-values were based on the model where outliers were rescored to 2SD from the mean. Note that when retaining the influential outliers for this model, the p-value of the Intensity x Run interaction was p = .05. For all other outcome variables, rescoring the outliers did not change the results. Significant effects are indicated in bold.

      As the authors mentioned in the rebuttal letter, "selecting participants only if their anticipatory SCR monotonically increased with each increase in instructed probability 0% < 25% < 50% < 75% < 100%, N = 11 participants", only ~1/3 of the subjects actually showed strong evidence for the validity of the instructions. This further raises the question of whether the instructed design, due to the interference of false instruction and the dynamic learning among trials, is solid enough to test the hypothesis .  

      We agree with the reviewer that a monotonic increase in anticipatory SCR with increasing probability instructions would provide the strongest evidence that the manipulation worked. However, it is well known that SCR is a noisy measure, and so the chances to see this monotonic increase are rather small, even if the underlying threat anticipation increases monotonically. Furthermore, between-subject variation is substantial in physiological measures, and it is not uncommon to observe, e.g., differential fear conditioning in one measure, but not in another (Lonsdorf & Merz, 2017). It is therefore not so surprising that ‘only’ 1/3 of our participants showed the perfect pattern of monotonically increasing SCR with increasing probability instructions. That being said, it is also important to note that not all participants were considered for these follow-up analyses because valid SCR data was not always available.

      Specifically, N = 4 participants were identified as anticipation non-responders (i.e. participant with smaller average SCR to the clock on 100% than on 0% trials; pre-registered criterium) and were excluded from the SCR-related analyses, and N = 1 participant had missing data due to technical difficulties. This means that only 26 (and not 31) participants were considered for the post hoc analyses. Taking this information into account, this means that 21 out of 26 participants (approximately 80%) showed stronger anticipatory SCR following 75% instructions compared to 25% instructions and that  11 out of 26 participants (approximately 40%) even showed the monotonical increase in their anticipatory SCR (see supplemental figure 4). Furthermore, although anticipatory SCR gradually decreased over the course of the experiment, there was no Run x Probability interaction, indicating that the instructions remained stable throughout the task (see supplemental figure 3).  

      Reviewer #2 (Recommendations For The Authors):

      A more operational approach might be to break the trials into different sections along the timeline and examine how much the results might have been affected across time. I expect the manipulation checks would hold for the first one or two runs and the authors then would have good reasons to focus on the behavioral and imaging results for those runs. 

      This recommendation resembles the recommendation by reviewer 1. In our reply to reviewer 1, we showed the results of a re-analysis of the fMRI data using the trial-by-trial estimates of the omission contrasts, which revealed no Probability x Run interaction, suggesting that – overall - the probability effect remained (more or less) stable over the course of the experiment.  For a more in depth discussion of the results of this additional analysis, we refer to our answer to reviewer 1.  

      Reviewer #3 (Public Review): 

      Comments on revised version: 

      The authors were extremely responsive to the comments and provided a comprehensive rebuttal letter with a lot of detail to address the comments. The authors clarified their methodology, and rationale for their task design, which required some more explanation (at least for me) to understand. Some of the design elements were not clear to me in the original paper. 

      The initial framing for their study is still in the domain of learning. The paper starts off with a description of extinction as the prime example of when threat is omitted. This could lead a reader to think the paper would speak to the role of prediction errors in extinction learning processes. But this is not their goal, as they emphasize repeatedly in their rebuttal letter. The revision also now details how using a conditioning/extinction framework doesn't suit their experimental needs. 

      We thank the reviewer for pointing out this potential cause of confusion. We have now rewritten the starting paragraph of the introduction to more closely focus on prediction errors, and only discuss fear extinction as a potential paradigm that has been used to study the role of threat omission PE for fear extinction learning (see lines 40-55). We hope that these adaptations are sufficient to prevent any false expectations. However, as we have mentioned in our previous response letter, not talking about fear extinction at all would also not make sense in our opinion, since most of the knowledge we have gained about threat omission prediction errors to date is based on studies that employed these paradigms.  

      Adaptation in the revised manuscript (lines 40-55):  

      “We experience pleasurable relief when an expected threat stays away1. This relief indicates that the outcome we experienced (“nothing”) was better than we expected it to be (“threat”). Such a mismatch between expectation and outcome is generally regarded as the trigger for new learning, and is typically formalized as the prediction error (PE) that determines how much there can be learned in any given situation2. Over the last two decades, the PE elicited by the absence of expected threat (threat omission PE) has received increasing scientific interest, because it is thought to play a central role in learning of safety. Impaired safety learning is one of the core features of clinical anxiety4. A better understanding of how the threat omission PE is processed in the brain may therefore be key to optimizing therapeutic efforts to boost safety learning. Yet, despite its theoretical and clinical importance, research on how the threat omission PE is computed in the brain is only emerging.  

      To date, the threat omission PE has mainly been studied using fear extinction paradigms that mimic safety learning by repeatedly confronting a human or animal with a threat predicting cue (conditional stimulus, CS; e.g. a tone) in the absence of a previously associated aversive event (unconditional stimulus, US; e.g., an electrical stimulation). These (primarily non-human) studies have revealed that there are striking similarities between the PE elicited by unexpected threat omission and the PE elicited by unexpected reward.”

      It is reasonable to develop a new task to answer their experimental questions. By no means is there a requirement to use a conditioning/extinction paradigm to address their questions. As they say, "it is not necessary to adopt a learning paradigm to study omission responses", which I agree with.  But the authors seem to want to have it both ways: they frame their paper around how important prediction errors are to extinction processes, but then go out of their way to say how they can't test their hypotheses with a learning paradigm.

      Part of their argument that they needed to develop their own task "outside of a learning context" goes as follows: 

      (1) "...conditioning paradigms generally only include one level of aversive outcome: the electrical stimulation is either delivered or omitted. As a result, the magnitude-related axiom cannot be tested." 

      (2) "....in conditioning tasks people generally learn fast, rendering relatively few trials on which the prediction is violated. As a result, there is generally little intra-individual variability in the PE responses" 

      (3) "...because of the relatively low signal to noise ratio in fMRI measures, fear extinction studies often pool across trials to compare omission-related activity between early and late extinction, which further reduces the necessary variability to properly evaluate the probability axiom" 

      These points seem to hinge on how tasks are "generally" constructed. However, there are many adaptations to learning tasks:

      (1) There is no rule that conditioning can't include different levels of aversive outcomes following different cues. In fact, their own design uses multiple cues that signal different intensities and probabilities. Saying that conditioning "generally only include one level of aversive outcome" is not an explanation for why "these paradigms are not tailored" for their research purposes. There are also several conditioning studies that have used different cues to signal different outcome probabilities. This is not uncommon, and in fact is what they use in their study, only with an instruction rather than through learning through experience, per se.

      (2) Conditioning/extinction doesn't have to occur fast. Just because people "generally learn fast" doesn't mean this has to be the case. Experiments can be designed to make learning more challenging or take longer (e.g., partial reinforcement). And there can be intra-individual differences in conditioning and extinction, especially if some cues have a lower probability of predicting the US than others. Again, because most conditioning tasks are usually constructed in a fairly simplistic manner doesn't negate the utility of learning paradigms to address PEaxioms.

      (3) Many studies have tracked trial-by-trial BOLD signal in learning studies (e.g., using parametric modulation). Again, just because other studies "often pool across trials" is not an explanation for these paradigms being ill-suited to study prediction errors. Indeed, most computational models used in fMRI are predicated on analyzing data at the trial level. 

      We thank the reviewer for these remarks. The “fear conditioning and extinction paradigms” that we were referring to in this paragraph were the ones that have been used to study threat omission PE responses in previous research (e.g., Raczka et al., 2011; Thiele et al. 2021; Lange et al. 2020; Esser et al., 2021; Papalini et al., 2021; Vervliet et al. 2017). These studies have mainly used differential/multiple-cue protocols where either one (or two) CS+  and one CS- are trained in an acquisition phase and extinguished in the next phase. Thus, in these paradigms: (1) only one level of aversive US is used; and (2) as safety learning develops over the course of extinction, there are relatively few omission trials during which “large” threat omission PEs can be observed (e.g. from the 24 CS+ trials that were used during extinction in Esser et al., the steepest decreases in expectancy – and thus the largest PE – were found in first 6 trials); and (3) there was never absolute certainty that the stimulation will no longer follow. Some of these studies have indeed estimated the threat omission PE during the extinction phase based on learning models, and have entered these estimates as parametric modulators to CS-offset regressors. This is very informative. However, the exact model that was used differed per study (e.g. Rescorla-Wagner in Raczka et al. and Thiele et al.; or a Rescorla- Wagner–Pearce- Hall hybrid model in Esser et al.). We wanted to analyze threat omission-responses without commitment to a particular learning model. Thus, in order to examine how threat omissionresponses vary as a function of probability-related expectations, a paradigm that has multiple probability levels is recommended (e.g. Rutledge et al., 2010; Ojala et al., 2022)

      The reviewer rightfully pointed out that conditioning paradigms (more generally) can be tailored to fit our purposes as well. Still, when doing so, the same adaptations as we outlined above need to be considered: i.e. include different levels of US intensity; different levels of probability; and conditions with full certainty about the US (non)occurrence. In our attempt to keep the experimental design as simple and straightforward as possible, we decided to rely on instructions for this purpose, rather than to train 3 (US levels) x 5 (reinforcement levels) = 15 different CSs. It is certainly possible to train multiple CSs of varying reinforcement rates (e.g. Grings et al. 1971, Ojala et al., 2022). However, given that US-expectation on each trial would primarily depend on the individual learning processes of the participants, using a conditioning task would make it more difficult to maintain experimental control over the level of USexpectation elicited by each CS. As a result, this would likely require more extensive training, and thus prolong the study procedure considerably. Furthermore, even though previous studies have trained different CSs for different reinforcement rates, most of these studies have only used one level of US. Thus, in order to not complexify our task to much, we decided to rely on instructions rather than to train CSs for multiple US levels (in addition to multiple reinforcement rates).

      We have tried to clarify our reasoning in the revised version of the manuscript (see introduction, lines 100-113):  

      “The previously discussed fear conditioning and extinction studies have been invaluable for clarifying the role of the threat omission PE within a learning context. However, these studies were not tailored to create the varying intensity and probability-related conditions that are required to systematically evaluate the threat omission PE in the light of the PE axioms. First, these only included one level of aversive outcome: the electrical stimulation was either delivered or omitted; but the intensity of the stimulation was never experimentally manipulated within the same task. As a result, the magnitude-related axiom could not be tested. Second, as safety learning progressively developed over the course of extinction learning, the most informative trials to evaluate the probability axiom (i.e. the trials with the largest PE) were restricted to the first few CS+ offsets of the extinction phase, and the exact number of these informative trials likely differed across participants as a result of individually varying learning rates. This limited the experimental control and necessary variability to systematically evaluate the probability axiom. Third, because CS-US contingencies changed over the course of the task (e.g. from acquisition to extinction), there was never complete certainty about whether the US would (not) follow. This precluded a direct comparison of fully predicted outcomes. Finally, within a learning context, it remains unclear whether brain responses to the threat omission are in fact responses to the violation of expectancy itself, or whether they are the result of subsequent expectancy updating.”

      Again, the authors are free to develop their own task design that they think is best suited to address their experimental questions. For instance, if they truly believe that omission-related responses should be studied independent of updating. The question I'm still left puzzling is why the paper is so strongly framed around extinction (the word appears several times in the main body of the paper), which is a learning process, and yet the authors go out of their way to say that they can only test their hypotheses outside of a learning paradigm. 

      As we have mentioned before, the reason why we refer to extinction studies is because most evidence on threat omission PE to date comes from fear extinction paradigms.  

      The authors did address other areas of concern, to varying extents. Some of these issues were somewhat glossed over in the rebuttal letter by noting them as limitations. For example, the issue with comparing 100% stimulation to 0% stimulation, when the shock contaminates the fMRI signal. This was noted as a limitation that should be addressed in future studies, bypassing the critical point. 

      It is unclear to us what the reviewer means with “bypassing the critical point”. We argued in the manuscript that the contrast we initially specified and preregistered to study axiom 3 (fully predicted outcomes elicit equivalent activation) could not be used for this purpose, as it was confounded by the delivery of the stimulation. Because 100% trials aways included the stimulation and 0% trials never included stimulation, there was no way to disentangle activations related to full predictability from activations related to the stimulation as such.   

      Reviewer #3 (Recommendations For The Authors): 

      I'm not sure the new paragraph explaining why they can't use a learning task to test their hypotheses is very convincing, as I noted in my review. Again, it is not a problem to develop a new task to address their questions. They can justify why they want to use their task without describing (incorrectly in my opinion) that other tasks "generally" are constructed in a way that doesn't suit their needs. 

      For an overview of the changes we made in response to this recommendation, we refer to our reply to the public review.   

      We look forward to your reply and are happy to provide answers to any further questions or comments you may have.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      The study describes a new computational method for unsupervised (i.e., non-artificial intelligence) segmentation of objects in grayscale images that contain substantial noise, to differentiate object, no object, and noise. Such a problem is essential in biology because they are commonly confronted in the analysis of microscope images of biological samples and recently have been resolved by artificial intelligence, especially by deep neural networks. However, training artificial intelligence for specific sample images is a difficult task and not every biological laboratory can handle it. Therefore, the proposed method is particularly appealing to laboratories with little computational background. The method was shown to achieve better performance than a threshold-based method for artificial and natural test images. To demonstrate the usability, the authors applied the method to high-power confocal images of the thalamus for the identification and quantification of immunostained potassium ion channel clusters formed in the proximity of large axons in the thalamic neuropil and verified the results in comparison to electron micrographs.

      Strengths:

      The authors claim that the proposed method has higher pixel-wise accuracy than the threshold-based method when applied to gray-scale images with substantial noises.

      Since the method does not use artificial intelligence, training and testing are not necessary, which would be appealing to biologists who are not familiar with machine learning technology.

      The method does not require extensive tuning of adjustable parameters (trying different values of "Moran's order") given that the size of the object in question can be estimated in advance.

      We appreciate the positive assessment of our approach.

      Weaknesses:

      It is understood that the strength of the method is that it does not depend on artificial intelligence and therefore the authors wanted to compare the performance with another non-AI method (i.e. the threshold-based method; TBM). However, the TBM used in this work seems too naive to be fairly compared to the expensive computation of "Moran's I" used for the proposed method. To provide convincing evidence that the proposed method advances object segmentation technology and can be used practically in various fields, it should be compared to other advanced methods, including AI-based ones, as well.

      Protein localization studies revealed that protein distributions are frequently inhomogeneous in a cell. This is very common in neurons which are highly polarized cell types with distinct axo-somato-dendritic functions. Moreover, due to the nature of the cell-to-cell interactions among neurons (e.g. electrical and chemical synapses) the cell membrane includes highly variable microdomains with unique protein assemblies (i.e. clusters). Protein clusters are defined as membrane segments with higher protein densities compared to neighboring membrane regions. However, protein density can continuously change between “clusters” and “non-clusters”. As a consequence, differentiating proteins involved vs not involved in clusters is a challenging task.  Indeed, our analysis showed that the boundaries of protein clusters varied remarkably when 23 human experts delineated them.

      Despite the fact the protein clusters can only be vaguely defined numerous studies have demonstrated the functional relevance of inhomogeneous protein distribution. Thus, there is a high relevance and need for an observer independent, “operative” segmentation method that can be accomplished and compared among different conditions and specimens. The strength of the Moran’s I analysis we propose here, as pointed out by our reviewers and editors, is that it can extract the relevant signals from an image generated in different, often noisy condition using a simple algorithm that allows quantitative characterization and identification of changes in many biological and non-biological samples.

      In AI based analysis the ground truth is known by an observer and using a large training set AI learns to extract the relevant information for image segmentation. As outlined above the “ground truth”, however, cannot be unequivocally defined for protein clusters. There is no doubt, that with sufficient resource investment there would be an AI based analysis of the same problem. In our view, however, in an average laboratory setting generating a training set using hundreds of images examined by many experts may not be plausible. Moreover, generalization of one training set to another set of cluster, resistance to noise or different levels of background could also not be guaranteed.

      This method was claimed to be better than the TBM when the noise level was high. Related to the above, TBMs can be used in association with various denoising methods as a preprocess. It is questionable whether the claim is still valid when compared to the methods with adequate complexity used together with denoising. Consider for example, Weigert et al. (2018) https://doi.org/10.1038/s41592-018-0216-7; or Lehtinen et al (2018) https://doi.org/10.48550/arXiv.1803.04189.

      In Weigert et al. AI was trained with high-quality images of the same object obtained with extreme photon exposure in confocal microscope. As delineated above without training AI systems cannot be used for such purposes. The Lehtinen paper is unfortunately no longer available at this doi.

      We must emphasize that in our work we did not intend to compare the image segmentation method based on local Moran’s I with all other available segmentation techniques. Rather we wanted to demonstrate a straightforward method of grouping pixels with similar intensities and in spatial proximity which does not require a priori knowledge of the objects. We used TBM to benchmark the method. We agree that with more advanced TBM methods the difference between Moran’s and TBM might have been smaller. The critical component here is, however, that even with most advanced TBM an artificial threshold is needed to be defined. The optimal threshold may change from sample to sample depending on the experimental conditions which makes quantification questionable. Moran’s method overcomes this problem and allows more objective segmentation of images even if the exact conditions (background labeling, noise, intensity etc) are not identical among the samples.

      The computational complexity of the method, determined by the convolution matrix size (Moran's order), linearly increases as the object size increases (Fig. S2b). Given that the convolution must be run separately for each pixel, the computation seems quite demanding for scale-up, e.g. when the method is applied for 3D image volumes. It will be helpful if the requirement for computer resources and time is provided.

      Here we provide the required data concerning the hardware and the computational time:

      Hardware used for performing the analysis:

      Intel(R) Xeon(R) Silver 4112 CPU @ 2.60GHz, 2594 Mhz, 4 kernel CPU, 64GB RAM, NVIDIA GeForce GTX 1080 graphic card.

      MATLAB R2021b software was used for implementation.

      Author response table 1.

      Computation times:

      Reviewer #2 (Public Review):

      Summary:

      The manuscript by David et al. describes a novel image segmentation method, implementing Local Moran's method, which determines whether the value of a datapoint or a pixel is randomly distributed among all values, in differentiating pixel clusters from the background noise. The study includes several proof-of-concept analyses to validate the power of the new approach, revealing that implementation of Local Moran's method in image segmentation is superior to threshold-based segmentation methods commonly used in analyzing confocal images in neuroanatomical studies.

      Strengths:

      Several proof-of-concept experiments are performed to confirm the sensitivity and validity of the proposed method. Using composed images with varying levels of background noise and analyzing them in parallel with the Local Moran's or a Threshold-Based Method (TBM), the study is able to compare these approaches directly and reveal their relative power in isolating clustered pixels.     

      Similarly, dual immuno-electron microscopy was used to test the biological relevance of a colocalization that was revealed by Local Moran's segmentation approach on dual-fluorescent labeled tissue using immuno-markers of the axon terminal and a membrane-protein (Figure 5). The EM revealed that the two markers were present in terminals and their post-synaptic partners, respectively. This is a strong approach to verify the validity of the new approach for determining object-based colocalization in fluorescent microscopy. 

      The methods section is clear in explaining the rationale and the steps of the new method (however, see the weaknesses section). Figures are appropriate and effective in illustrating the methods and the results of the study. The writing is clear; the references are appropriate and useful.

      We are grateful for the constructive assessment of our results.

      Weaknesses:

      While the steps of the mathematical calculations to implement Local Moran's principles for analyzing high-resolution images are clearly written, the manuscript currently does not provide a computation tool that could facilitate easy implementation of the method by other researchers. Without a user-friendly tool, such as an ImageJ plugin or a code, the use of the method developed by David et al by other investigators may remain limited.

      The code for the analysis is now available online as a user-friendly MATLAB script at: https://github.com/dcsabaCD225/Moran_Matlab/blob/main/moran_local.m

      Recommendations for the authors:

      Summary of reviews:

      Both reviewers acknowledge the potential significance and practicality of the newly proposed image segmentation method. This method uses Local Moran's principles, offering an advantage over traditional intensity thresholding approaches by providing more sensitivity, particularly in reducing background noise and preserving biologically relevant pixels.

      Strengths Highlighted:

      • The proposed method can provide more accurate results, especially for grayscale images with significant noise.

      • The method is not dependent on artificial intelligence, making it appealing for researchers with minimal computational background.    

      • The approach can operate without the need for extensive tuning, given that the size of the object is known.

      • Several proof-of-concept experiments were carried out, revealing the effectiveness of the method in comparison with the threshold-based segmentation methods.

      • The manuscript is clear in terms of methodology, and the results are supported by effective illustrations and references.

      Weaknesses Noted:

      • The study lacked a comparative analysis with advanced segmentation methods, especially those that employ artificial intelligence.

      See our response above to the same question of Reviewer 1.

      • There are concerns about computational complexity, especially when dealing with larger data sets or 3D image volumes.

      See our response about the calculations of computation times above to the similar question of Reviewer 1.

      • Both reviewers noted the absence of a data/code availability statement in the manuscript, which might restrict the method's adoption by other researchers.

      The code availability is provided now.

      • Reviewer 2 suggested that some results, particularly related to Kv4.2 in the thalamus, might be better presented in a separate study due to their significance.

      We thank our reviewers for this suggestion. We carefully evaluated the pros and cons of publishing the Kv4.2 data separately. We finally decided to keep the segmentation and experimental data together due to the following reason. We believe that the ultrastructural localization provides strong experimental proof for the relevance of our novel segmentation method. In order to make the potassium channel data more visible we added a subsentence to the title. In this manner we think scientist interested in the imaging method as well as the neurobiology will be both find and cite the paper. The novel title reads now:

      “An image segmentation method based on the spatial correlation coefficient of Local Moran’s I - identification of A-type potassium channel clusters in the thalamus.”

      Reviewer Recommendations:

      (1) Provide details about the data and program code availability.

      See our response above

      (2) Offer practical recommendations and provide clarity on software packages and coding for the proposed method to enhance its adoption.

      Done.

      (3) Consider presenting the findings about Kv4.2 in the thalamus separately as they hold significant importance on their own.

      See our response above

      Given the reviews, the proposed image segmentation method presents a promising advancement in the domain of image analysis. The technique offers tangible benefits, especially for researchers dealing with biological microscopy data. However, for this method to see a broader application, it's imperative to provide clearer practical guidance and make data or code easily accessible. Additionally, while the findings regarding Kv4.2 in the thalamus are intriguing, they might achieve more impact if detailed in a dedicated paper.

      Reviewer #1 (Recommendations For The Authors):

      The availability of data or program code was not stated in the manuscript.

      Reviewer #2 (Recommendations For The Authors):

      (1) While the principles of the method are explained clearly in a step-by-step fashion in the Methods section, the practical aspects of running sequential computations over a large matrix of pixel values are not well described. It would be very useful if the authors could provide recommendations on how to set the data structure and clarify which software and programming package for Local Moran's analysis they used. In addition, providing the code for the sequential implementation described in the Methods section would facilitate the adoption of the method by other researchers, and thus, the impact of the study. Currently, there is no data or code availability statement included in the manuscript.

      See our response above.

      (2) Figure 4 illustrates an experiment in which transmission electron microscopy and freeze-fracture replica labeling approaches were used to demonstrate that a potassium channel marker, Kv4.2 was selective to synapses forming on larger caliber dendrites in the thalamus. As impressive as the EM approaches utilized in this figure are, the results of this experiment have a somewhat tangential bearing on the segmentation method that is the focus of this study. In fact, the experiments illustrated in Figure 5, dual immuno-EM, are more than sufficient to confirm what the dual-confocal imaging coupled with Local Moran's segmentation analysis reveals. Furthermore, the author's findings about the localization and selectivity of Kv4.2 in the thalamus are too important and exciting to bury in a paper focusing on the methodology. Those results may have a wider impact if they are presented and discussed in a separate experimental paper.

      See our response above

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #3 (Public Review):

      The iron manipulation experiments are in the whole animal and it is likely that this affects general feeding behaviour, which is known to affect NB exit from quiescence and proliferative capacity. The loss of ferritin in the gut and iron chelators enhancing the NB phenotype are used as evidence that glia provide iron to NB to support their number and proliferation. Since the loss of NB is a phenotype that could result from many possible underlying causes (including low nutrition), this specific conclusion is one of many possibilities.

      We have investigated the feeding behavior of fly by Brilliant Blue (sigma, 861146)[1]. Our result showed that the amount of dye in the fly body were similar between control group and BPS group, suggesting that BPS almost did not affect the feeding behavior (Figure 3—figure supplement 1A).

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      There was a gap between the Pros nuclear localization and downstream targets of ferritin, particularly NADH dehydrogenase and biosynthesis. Could overexpression of Ndi1 restore Pros localization in NBs?

      Ferritin defect downregulates iron level, which leads to cell cycle arrest of NBs via ATP shortage. And cell cycle arrest of NBs probably results in NB differentiation[2, 3]. We have added the experiment in Figure 5—figure supplement 2. This result showed that overexpression of Ndi1 could significantly restore Pros localization in NBs.

      The abstract requires revision to cover the major findings of the manuscript, particularly the second half.

      We revised the abstract to add more major findings of the manuscript in the second half as follows:

      “Abstract

      Stem cell niche is critical for regulating the behavior of stem cells. Drosophila neural stem cells (Neuroblasts, NBs) are encased by glial niche cells closely, but it still remains unclear whether glial niche cells can regulate the self-renewal and differentiation of NBs. Here we show that ferritin produced by glia, cooperates with Zip13 to transport iron into NBs for the energy production, which is essential to the self-renewal and proliferation of NBs. The knockdown of glial ferritin encoding genes causes energy shortage in NBs via downregulating aconitase activity and NAD+ level, which leads to the low proliferation and premature differentiation of NBs mediated by Prospero entering nuclei. More importantly, ferritin is a potential target for tumor suppression. In addition, the level of glial ferritin production is affected by the status of NBs, establishing a bicellular iron homeostasis. In this study, we demonstrate that glial cells are indispensable to maintain the self-renewal of NBs, unveiling a novel role of the NB glial niche during brain development.”

      In Figure 2B Mira appeared to be nuclear in NBs, which is inconsistent with its normal localization. Was it Dpn by mistake?

      In Figure 2B, we confirmed that it is Mira. Moreover, we also provide a magnified picture in Figure 2B’, showing that the Mira mainly localizes to the cortex or in the cytoplasm as previously reported.

      Figure 2C, Fer1HCH-GFP/mCherry localization was non-uniform in the NBs revealing 1-2 regions devoid of protein localization potentially corresponding to the nucleus and Mira crescent enrichment. It is important to co-label the nucleus in these cells and discuss the intracellular localization pattern of Ferritin.

      We have revised the picture with nuclear marker DAPI in Figure 2C. The result showed that Fer1HCH-GFP/Fer2LCH-mCherry was not co-localized with DAPI, which indicated that Drosophila ferritin predominantly distributes in the cytosol[4, 5]. As for the concern mentioned by this reviewer, GFP/mCherry signal in NBs was from glial overexpressed ferritin, which probably resulted in non-uniform signal.

      In Figure 3-figure supplement 3F, glial cells in Fer1HCH RNAi appeared to be smaller in size. This should be quantified. Given the significance of ferritin in cortex glial cells, examining the morphology of cortex glial cells is essential.

      In Figure 3—figure supplement 3F, we did not label single glial cells so it was difficult to determine whether the size was changed. However, it seems that the chamber formed by the cellular processes of glial cells becomes smaller in Fer1HCH RNAi. The glial chamber will undergo remodeling during neurogenesis, which responses to NB signal to enclose the NB and its progeny[6]. Thus, the size of glial chamber is regulated by NB lineage size. In our study, ferritin defect leads to the low proliferation, inducing the smaller lineage of each NB, which likely makes the chamber smaller.

      Since the authors showed that the reduced NB number was not due to apoptosis, a time-course experiment for glial ferritin KD is recommended to identify the earliest stage when the phenotype in NB number /proliferation manifests during larval brain development.

      We observed brains at different larval stages upon glial ferritin KD. The result showed that NB proliferation decreased significantly, but NB number declined slightly at the second-instar larval stage (Figure 5—figure supplement 1E and F), suggesting that brain defect of glial ferritin KD manifests at the second-instar larval stage.

      Transcriptome analysis on ferritin glial KD identified genes in mitochondrial functions, while the in vivo EM data suggested no defects in mitochondria morphology. A short discussion on the inconsistency is required.

      For the observation of mitochondria morphology via the in vivo EM data, we focused on visible cristae in mitochondria, which was used to determine whether the ferroptosis happens[7]. It is possible that other details of mitochondria morphology were changed, but we did not focus on that. To describe this result more accurately, we replaced “However, our observation revealed no discernible defects in the mitochondria of NBs after glial ferritin knockdown” with the “However, our result showed that the mitochondrial double membrane and cristae were clearly visible whether in the control group or glial ferritin knockdown group, which suggested that ferroptosis was not the main cause of NB loss upon glial ferritin knockdown” in line 207-209.

      The statement “we found no obvious defects of brain at the first-instar larval stage (0-4 hours after larval hatching) when knocking down glial ferritin (Figure 5-figure supplement 1C).” lacks quantification of NB number and proliferation, making it challenging to conclude.

      We have provided the quantification of NB number and proliferation rate of the first-instar larval stage in Figure 5—figure supplement 1C and D. The data showed that there is no significant change in NB number and proliferation rate when knocking down ferritin, suggesting that no brain defect manifests at the first-instar larval stage.

      A wild-type control is necessary for Figure 6A-C as a reference for normal brain sizes.

      We have added Insc>mCherry RNAi as a reference in Figure 6A-D, which showed that the brain size of tumor model is larger than normal brain. Moreover, we removed brat RNAi data from Figure 6A-D to Figure 6—figure supplement 1A-D for the better layout.

      In Figures 6B, D, “Tumor size” should be corrected to “Larval brain volume”.

      Here, we measured the brain area to assess the severity of the tumor via ImageJ instead of 3D data of the brain volume. So we think it would be more appropriate to use the “Larval brain size” than “Larval brain volume” here. Thus, we have corrected “Tumor size” to “Larval brain size” in Figure 6B and D to Figure 6—figure supplement 1B and D.

      Considering that asymmetric division defects in NBs may lead to premature differentiation, it is advisable to explore the potential involvement of ferritin in asymmetric division.

      aPKC is a classic marker to determine the asymmetric division defect of NB. We performed the aPKC staining and found it displayed a crescent at the apical cortex based on the daughter cell position whether in control or glial ferritin knockdown (Figure 5—figure supplement 3A). This result indicated that there was no obvious asymmetric defect after glial ferritin knockdown.

      In the statement "Secondly, we examined the apoptosis in glial cells via Caspase-3 or TUNEL staining, and found the apoptotic signal remained unchanged after glial ferritin knockdown (Figure 3-figure supplement 3A-D).", replace "the apoptosis in glial cells" with "the apoptosis in larval brain cells".

      We have replaced "the apoptosis in glial cells" with "the apoptosis in larval brain cells" in line 216.

      Include a discussion on the involvement of ferritin in mammalian brain development and address the limitations associated with considering ferritin as a potential target for tumor suppression.

      We have added the discussion about ferritin in mammalian brain development in line 428-430 and limitation of ferritin for suppressing tumor in line 441-444.

      Indicate Insc-GAL4 as BDSC#8751, even if obtained from another source. Additionally, provide information on the extensively used DeRed fly stock used in this study within the methods section.

      We provided the stock information of Insc-GAL4 and DsRed in line 673-674.

      Reviewer #2 (Recommendations For The Authors):

      Major points:

      The number of NBs differs a lot between experiments. For example, in Fig 1B and 1K controls present less than 100 NBs whereas in Figure 1 Supplementary 2B it can be seen that controls have more than 150. Then, depending on which control you compare the number of NBs in flies silencing Fer1HCH or Fer2LCH, the results might change. The authors should explain this.

      Figure 1 Supplementary 2B (Figure 1 Supplementary 3B in the revised version) shows NB number in VNC region while Fig 1B and 1K show NB number in CB region. At first, we described the general phenotype showing the NB number in CB and VNC respectively (Fig 1 and Fig 1-Supplementary 1 and 3 in the revised version). And the NB number is consistent in each region. After then, we focused on NB number in CB for the convenience.

      This reviewer encourages the authors to use better Gal4 lines to describe the expression patterns of ferritins and Zip13 in the developing brain. On the one hand, the authors do not state which lines they are using (including supplementary table). On the other hand, new Trojan GAL4 (or at least InSite GAL4) lines are a much better tool than classic enhancer trap lines. The authors should perform this experiment.

      All stock source and number were documented in Table 2. Ferritin GAL4 and Zip13 GAL4 in this study are InSite GAL4. In addition, we also used another Fer2LCH enhancer trapped GAL4 to verify our result (DGRC104255) and provided the result in Figure 2—figure supplement 1. Our data showed that DsRed driven by Fer2LCH-GAL4 was co-localized with the glia nuclear protein Repo, instead of the NB nuclear protein Dpn, which was consistent with the result of Fer1HCH/Fer2LCH GAL4. In addition, we will try to obtain the Trojan GAL4 (Fer1HCH/Fer2LCH GAL4 and Zip13 GAL4) and validate this result in the future.

      The authors exclude very rapidly the possibility of ferroptosis based only on some mitochondrial morphological features without analysing the other hallmarks of this iron-driven cell death. The authors should at least measure Lipid Peroxidation levels in their experimental scenario either by a kit to quantify by-products of lipid peroxidation such as Malonaldehide (MDA) or using an anti 4-HNE antibody.

      We combined multiple experiments to exclude the possibility of ferroptosis. Firstly, ferroptosis can be terminated by iron chelator. And we fed fly with iron chelator upon glial ferritin knockdown, but NB number and proliferation were not restored, which suggested that ferroptosis probably was not the cause of NB loss induced by glial ferritin knockdown (Figure 3B and C). Secondly, Zip13 transports iron into the secretary pathway and further out of the cells in Drosophila gut[8]. Our data showed that knocking down iron transporter Zip13 in glia resulted in the decline of NB number and proliferation, which was consistent with the phenotype upon glial ferritin knockdown (Figure 3E-G). More importantly, the knockdown of Zip13 and ferritin simultaneously aggravated the phenotype in NB number and proliferation (Figure 3E-G). These results suggested that the phenotype was induced by iron deficiency in NB, which excluded the possibility of iron overload or ferroptosis to be the main cause of NB loss upon glial ferritin knockdown. Finally, we observed mitochondrial morphology on double membrane and the cristae that are critical hallmarks of ferroptosis, but found no significant damage (Figure 3-figure supplement 2E and F).

      In addition, we have added the 4-HNE determination in Figure 3—figure supplement 2G and H. This result showed that 4-HNE level did not change significantly, suggesting that lipid peroxidation was stable, which supported to exclude the possibility that the ferroptosis led to the NB loss upon glial ferritin knockdown.

      All of the above results together indicate that ferroptosis is not the cause of NB loss after ferritin knockdown.

      A major flaw of the manuscript is related to the chapter Glial ferritin defects result in impaired Fe-S cluster activity and ATP production and the results displayed in Figure 4. The authors talk about the importance of FeS clusters for energy production in the mitochondria. Surprisingly, the authors do not analyse the genes involved in this process such as but they present the interaction with the cytosolic FeS machinery that has a role in some extramitochondrial proteins but no role in the synthesis of FeS clusters incorporated in the enzymes of the TCA cycle and the respiratory chain. The authors should repeat the experiments incorporating the genes NSF1 (CG12264), ISCU(CG9836), ISD11 (CG3717), and fh (CG8971) or remove (or at least rewrite) this entire section.

      Thanks for this constructive advice and we have revised this in Figure 4B and C. We repeated the experiment with blocking mitochondrial Fe-S cluster biosynthesis by knocking down Nfs1 (CG12264), ISCU(CG9836), ISD11 (CG3717), and fh (CG8971), respectively. Nfs1 knockdown in NB led to a low proliferation, which was consistent with CIA knockdown. However, we did not observe the obvious brain defect in ISCU(CG9836), ISD11 (CG3717), and fh (CG8971) knockdown in NB. Our interpretation of these results is that Nfs1 probably is a necessary core component in Fe-S cluster assembly while others are dispensable[9].

      The presence and aim of the mouse model Is unclear to this reviewer. On the one hand, It Is not used to corroborate the fly findings regarding iron needs from neuroblasts. On the other hand, and without further explanation, authors migrate from a fly tumor model based on modifying all neuroblasts to a mammalian model based exclusively on a glioma. The authors should clarify those issues.

      Although iron transporter probably is different in Drosophila and mammal, iron function is conserved as an essential nutrient for cell growth and proliferation from Drosophila to mammal. The data of fly suggested that iron is critical for brain tumor growth and thus we verified this in mammalian model. Glioma is the most common form of central nervous system neoplasm that originates from neuroglial stem or progenitor cells[10]. Therefore, we validated the effect of iron chelator DFP on glioma in mice and found that DFP could suppress the glioma growth and further prolong the survival of tumor-bearing mice.

      Minor points

      Although referred to adult flies, the authors did not include either in the introduction or in the discussion existing literature about expression of ferritins in glia or alterations of iron metabolism in fly glia cells (PMID: 21440626 and 25841783, respectively) or usage of the iron chelator DFP in drosophila (PMID: 23542074). The author should check these manuscripts and consider the possibility of incorporating them into their manuscript.

      Thanks for your remind. We have incorporated all recommended papers into our manuscript line 65-67 and 168.

      The number of experiments in each figure is missing.

      All experiments were repeated at least three times. And we revised this in Quantifications and Statistical Analysis of Materials and methods.

      If graphs are expressed as mean +/- sem, it is difficult to understand the significance stated by the authors in Figure 2E.

      We apologize for this mistake and have revised this in Quantifications and Statistical Analysis. All statistical results were presented as means ± SD.

      When authors measure aconitase activity, are they measuring all (cytosolic and mitochondrial) or only one of them? This is important to better understand the experiments done by the authors to describe any mitochondrial contribution (see above in major points).

      In this experiment, we were measuring the total aconitase activity. We also tried to determine mitochondrial aconitase but it failed, which was possibly ascribed to low biomass of tissue sample.

      In this line, why do controls in aconitase and atp lack an error bar? Are the statistical tests applied the correct ones? It is not the same to have paired or unpaired observations.

      It is the normalization. We repeated these experiments at least three times in different weeks respectively, because the whole process was time-consuming and energy-consuming including the collection of brains, protein determination and ATP or aconitase determination. And the efficiency of aconitase or ATP kit changed with time. We cannot control the experiment condition identically in different batches. Therefore, we performed normalization every time to present the more accurate result. The control group was normalized as 1 via dividing into itself and other groups were divided by the control. This normalized process was repeated three times. Therefore, there is no error bar in the control group. We think it is appropriate to apply ANOVA with a Bonferroni test in the three groups.

      In some cases, further rescue experiments would be appreciated. For example, expression of Ndi restores control NAD+ levels or number of NBs, it would be interesting to know if this is accompanied by restoring mitochondrial integrity and its ability to produce ATP.

      We have determined ATP production after overexpressing Ndi1 and provided this result in Figure 4—figure supplement 1B. The data showed that expression of Ndi1 could restore ATP production upon glial Fer2LCH knockdown, which was consistent with our conclusion.

      Lines 293-299 on page 7 are difficult to understand.

      According to our above results, the decrease of NB number and proliferation upon glial ferritin knockdown (KD) was caused by energy deficiency. As shown in the schematic diagram (Author response image 1), “T” represented the total energy which was used for NB maintenance and proliferation. “N” indicated the energy for maintaining NB number. “P” indicated the energy for NB proliferation. “T” is equal to “N” plus “P”. When ferritin was knocked down in glia, “T”, “N” and “P” declined in “Ferritin KD” compared to “wildtype (WT)”. Knockdown of pros can prevent the differentiation of NB, but it cannot supply the energy for NB, which probably results in the rescue of NB number but not proliferation. Specifically, NB number increased significantly in “Ferritin KD Pros KD” compared to “Ferritin KD”, which resulted in consuming more energy for NB maintenance in “Ferritin KD Pros KD”. As shown in the schematic diagram, “T” was not changed between “Ferritin KD Pros KD” and “Ferritin KD”, whereas ”N” was increased in “Ferritin KD Pros KD” compared to “Ferritin KD”. Thus, “P” was decreased, which suggested that less energy was remained for proliferation, leading to the failure of rescue in NB proliferation. It seemed that the level of proliferation in “Ferritin KD Pros KD” was even lower than “Ferritin KD”.

      Author response image 1.

      The schematic diagram of relationship between energy and NB function in different groups. “T” represents total energy for NB maintenance and proliferation. “N” represents the energy for NB maintenance. “P” represents the energy for NB proliferation. T=N+P 

      Line 601 should indicate that Tables 2 and 3 are part of the supplementary material.

      We have revised this in line 678.

      Figure 4-supplement 1. Only validation of 2 genes from a RNAseq seems too little.

      We dissected hundreds of brains for sorting NBs because of low biomass of fly brain. This is a difficult and energy-consuming work. Most NBs were used for RNA-seq, so we can only use a small amount of sample left for validation which is not enough for more genes.

      Figure 6E, the authors indicate that 10 mg/ml DFP injection could significantly prolong the survival time. Which increase in % is produced by DFP?

      We have provided the bar graph in Author response image 2. The increase is about 16.67% by DFP injection.

      Author response image 2.

      The bar graph of survival time of mice treated with DFP. (The unpaired two-sided Student’s t test was employed to assess statistical significance. Statistical results were presented as means ± SD. n=7,6; *: p<0.05)

      Reviewer #3 (Recommendations For The Authors):

      As I read the initial results that built the story (glia make ferritin>release it> NBs take them up>use it for TCA and ETC) I kept thinking about what it meant for NBs to be 'lost'. This led me to consider alternate possibilities that the results might point to, other than the ones the authors were suggesting. It was only in Figure 5 that the authors ruled out some of those possibilities. I would suggest that they first illustrate how NBs are lost upon glial ferritin loss of function before they delve into the mechanism. This would also be a place to similarly address that glial numbers and general morphology are unchanged upon ferritin loss.

      This recommendation provides a valuable guideline to build this story especially for researchers who are interested in neural stem cell studies. Actually, we tried this logic to present our study but found that there are several gaps in the middle of the manuscript, such as the relationship between glial ferritin and Pros localization in NB, so that the whole story cannot be fluently presented. Therefore, we decided to present this study in the current way.

      More details of the screen would be useful to know. How many lines did they screen, what was the assay? This is not mentioned anywhere in the text.

      We have added this in Screen of Materials and methods. We screened about 200 lines which are components of classical signaling pathways, highly expressed genes in glial cells or secretory protein encoding genes. UAS-RNAi lines were crossed with repo-Gal4, and then third-instar larvae of F1 were dissected. We got the brains from F1 larvae and performed immunostaining with Dpn and PH3. Finally, we observed the brain in Confocal Microscope.

      Many graphs seem to be repeated in the main figures and the supplementary data. This is unnecessary, or at least should be mentioned.

      We appreciate your kind reminder. However, we carefully went through all the figures and did not find the repeated graphs, though some of them look similar.

      The authors mention that they tested which glial subtypes ferritin is needed in, but don't show the data. Could they please show the data? Same with the other iron transport/storage/regulation. Also, in both this and later sections, the authors could mention which Gal4 was used to label what cell types. The assumption is that the reader will know this information.

      We have added the result of ferritin knockdown in glial subpopulations in Figure 1—figure supplement 2. However, considering that the quantity of iron-related genes, we did not take the picture, but we recorded this in Table 3.

      For all their images showing colocalisation, magnified, single-colour images shown in grayscale will be useful. For example, without the magnification, it is not possible to see the NB expression of the protein trap line in Figure 2B. A magnified crop of a few NBs (not a single one like in 2C) would be more useful.

      We have provided Figure 2A’, B’, D’ and Figure 3D’ as suggested.

      There are a lot of very specific assays used to detect ROS, NAD, aconitase activity, among others. It would be nice to have a brief but clear description of how they work in the main text. I found myself having to refer to other sources to understand them. (I believe SoNAR should be attributed to Zhao et al 206 and not Bonnay et al 2020.)

      We have added a brief description about ROS, aconitase activity, NAD in line 198-199, 229-231, and 269 as suggested.

      I did not understand the normalisation done with respect to SoNAR. Is this standard practice? Is the assumption that 'overall protein levels will be higher in slowly proliferating NBs' reasonable? This is why they state the need to normalise.

      The SoNAR normalization is not a standard practice. However, we think that our normalization of SoNar is reasonable. According to our results, the expression level of Dpn and Mira seemed higher in glial ferritin knockdown, so we speculated that some proteins accumulated in slowly proliferating NBs. Thus, we used Insc-GAL4 to drive DsRed for indicating the expression level of Insc and found that DsRed rose after glial ferritin knockdown, suggesting that Insc expression was increased indeed. Therefore, we have to normalize SoNar driven by Insc-GAL4 based on DsRed driven by Insc-Gal4, which eliminates the effect of increased Insc upon glial ferritin knockdown.

      FAC is mentioned as a chelator? But the authors seem to use it oppositely. Is there an error?

      FAC is a type of iron salt, which is used to supply iron. We have also indicated that in line 156 according to your advice. 

      The lack of any cell death in the L3 brain surprised me. There should be plenty of hemilineages that die, as do many NBs, particularly in the abdominal segments. Is the stain working? Related to this, P35 is not the best method for rescuing cell death. H99 might be a better way to go.

      We were also surprised to see this result and repeated this experiment for several times with both negative and positive controls. Moreover, we also used TUNEL to validate this result, which led to the same result. We will try to use H99 to rescue NB loss in the future, because it needs to be integrated and recombined with our current genetic tools.

      It would be nice to see the aconitase activity signal as opposed to just the quantification.

      This method can only determine the absorbance for indicating aconitase activity, so our result is just the quantification.

      Glia are born after NBs are specified. In fact, they arise from NBs (and glioblasts). So, it's unlikely that the knockdown of ferritin in glia can at all affect initial NB specification.

      We completely agree with this statement.

      The section on tumor suppression seems out of place. The fly data on which the authors base this as an angle to chase is weak. Dividing cells will be impaired if they have inadequate energy production. As a therapeutic, this will affect every cell in the body. I'm not sure that cancer therapeutics is pursuing such broadly acting lines of therapies anymore.

      Our data suggested that iron/ferritin is more critical for high proliferative cells. Tumor cells have a high expression of TfR (Transferrin Receptor)[11], which can bind to Transferrin and ferritin[12]. And ferritin specifically targets on the tumor cells[11]. Thus, we think iron/ferritin is extremely essential for tumor cells. If we can find the appropriate dose of iron/ferritin inhibitor, suppressing tumor growth but maintaining normal cell growth, iron/ferritin might be an effective target of tumor treatment.

      The feedback from NB to glial ferritin is also weak data. The increased cell numbers (of unknown identity) could well be contributing to the increase in ferritin. I would omit the last two sections from the MS.

      In brat RNAi and numb RNAi, increased cells are NB-like cells, which cannot undergo further differentiation and are not expected to produce ferritin. More importantly, we used Repo (glia marker) as the reference and quantified the ratio of ferritin level to Repo level, which can exclude the possibility that increased glial cells lead to the increase in ferritin.

      References

      (1) Tanimura T, Isono K, Takamura T, et al. Genetic Dimorphism in the Taste Sensitivity to Trehalose in Drosophila-Melanogaster. J Comp Physiol, 1982,147(4):433-7

      (2) Myster DL, Duronio RJ. Cell cycle: To differentiate or not to differentiate? Current Biology, 2000,10(8):R302-R4

      (3) Dalton S. Linking the Cell Cycle to Cell Fate Decisions. Trends in Cell Biology, 2015,25(10):592-600

      (4) Nichol H, Law JH, Winzerling JJ. Iron metabolism in insects. Annu Rev Entomol, 2002,47:535-59

      (5) Pham DQ, Winzerling JJ. Insect ferritins: Typical or atypical? Biochim Biophys Acta, 2010,1800(8):824-33

      (6) Speder P, Brand AH. Systemic and local cues drive neural stem cell niche remodelling during neurogenesis in Drosophila. Elife, 2018,7

      (7) Mumbauer S, Pascual J, Kolotuev I, et al. Ferritin heavy chain protects the developing wing from reactive oxygen species and ferroptosis. PLoS Genet, 2019,15(9):e1008396

      (8) Xiao G, Wan Z, Fan Q, et al. The metal transporter ZIP13 supplies iron into the secretory pathway in Drosophila melanogaster. Elife, 2014,3:e03191

      (9) Marelja Z, Leimkühler S, Missirlis F. Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the  Life Cycle by Controlling Cell Metabolism. Front Physiol, 2018,9

      (10) Morgan LL. The epidemiology of glioma in adults: a "state of the science" review. Neuro-Oncology, 2015,17(4):623-4

      (11) Fan K, Cao C, Pan Y, et al. Magnetoferritin nanoparticles for targeting and visualizing tumour tissues. Nat Nanotechnol, 2012,7(7):459-64

      (12) Li L, Fang CJ, Ryan JC, et al. Binding and uptake of H-ferritin are mediated by human transferrin receptor-1. Proc Natl Acad Sci U S A, 2010,107(8):3505-10

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      This study sought to reveal the potential roles of m6A RNA methylation in gene dosage regulatory mechanisms, particularly in the context of aneuploid genomes in Drosophila. Specifically, this work looked at the relationships between the expression of m6A regulatory factors, RNA methylation status, classical and inverse dosage effects, and dosage compensation. Using RNA sequencing and m6A mapping experiments, an in-depth analysis was performed to reveal changes in m6A status and expression changes across multiple aneuploid Drosophila models. The authors propose that m6A methylation regulates MOF and, in turn, deposition of H4K16Ac, critical regulators of gene dosage in the context of genomic imbalance.

      Strengths:

      This study seeks to address an interesting question with respect to gene dosage regulation and the possible roles of m6A in that process. Previous work has linked m6A to X-inactivation in humans through the Xist lncRNA, and to the regulation of the Sxl in flies. This study seeks to broaden that understanding beyond these specific contexts to more broadly understand how m6A impacts imbalanced genomes in other contexts.

      Weaknesses:

      The methods being used particularly for analysis of m6A at both the bulk and transcript-specific level are not sufficiently specific or quantitative to be able to confidently draw the conclusions the authors seek to make. MeRIP m6A mapping experiments can be very valuable, but differential methylation is difficult to assess when changes are small (as they often are, in this study but also m6A studies more broadly). For instance, based on the data presented and the methods described, it is not clear that the statement that "expression levels at m6A sites in aneuploidies are significantly higher than that in wildtype" is supported. MeRIP experiments are not quantitative, and since there are far fewer peaks in aneuploidies, it stands to reason that more antibody binding sites may be available to enrich those fewer peaks to a larger extent. But based on the data as presented (figure 2D) this conclusion was drawn from RPKM in IP samples, which may not fully account for changing transcript abundances in absolute (expression level changes) and relative (proportion of transcripts in input RNA sample) terms.

      Methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq) is a commonly used strategy of genome-wide mapping of m6A modification. This method uses anti-m6A antibody to immunoprecipitate RNA fragments, which results in selective enrichment of methylated RNA. Then the RNA fragments were subjected to deep sequencing, and the regions enriched in the immunoprecipitate relative to input samples are identified as m6A peaks using the peak calling algorithm. We identified m6A peaks in different samples by the exomePeak2 program and determined common m6A peaks for each genotype based on the intersection of biological replicates. Figure 2D shows the RPM values of m6A peaks in MeRIP samples for each genotype, indicating that the levels of reads in the m6A peak regions were significantly higher in the aneuploid IP samples than in wildtypes. When the enrichment of IP samples relative to Input samples (RPM.IP/RPM.Input) was taken into account, the statistics for all three aneuploidies were still significantly higher than those of the wildtypes (Mann Whitney U test p-values < 0.001). This analysis is not about changes in the abundance of transcripts, but from the MeRIP perspective, showing that there are relatively more m6A-modified reads mapped to the m6A peaks in aneuploidies than that in wildtypes. In addition, we have added the results of IP/Input in the main text, and revised the description in the manuscript to make it more precise to reduce possible misunderstandings.

      The bulk-level m6A measurements as performed here also cannot effectively support these conclusions, as they are measured in total RNA. The focus of the work is mRNA m6A regulators, but m6A levels measured from total RNA samples will not reflect mRNA m6A levels as there are other abundance RNAs that contain m6A (including rRNA). As a result, conclusions about mRNA m6A levels from these measurements are not supported.

      According to some published articles, m6A levels of purified mRNA or total RNA can be detected by different methods (such as mass spectrometry, 2D thin-layer chromatography, etc.) in Drosophila cells or tissues [1-3].

      Here, we used the EpiQuik m6A RNA Methylation Quantification Kit (Colorimetric) (Epigentek, NY, USA, Cat # P-9005), which is suitable for detecting m6A methylation status directly using total RNA isolated from any species such as mammals, plants, fungi, bacteria, and viruses. This kit has previously been used by researchers to detect the m6A/A ratio in total RNA [4, 5] or purified mRNA [6] from different species.

      In order to compare the m6A levels between the total RNA and mRNA, it was shown that the enrichment of mRNA from total RNA using Dynabeads™mRNA Purification Kit (Invitrogen Cat # 61006) did not show any significantly differences comparing with the results of total RNA (Figure 1). That’s the reason why most of the results of m6A levels in the manuscript were detected in total RNA.

      Author response image 1.

      The m6A levels of total RNA and mRNA

      As suggested, we will try to extract and purify mRNA from different genotypes to verify our conclusion based on the m6A levels of total RNA if necessary. In addition, m6A modification in other types of RNA other than mRNA (e.g., lncRNA, rRNA) is not necessarily meaningless. We will also add discussions of this issue in the manuscript.

      (1) Lence T, et al. (2016) m6A modulates neuronal functions and sex determination in Drosophila. Nature 540(7632):242-247.

      (2) Haussmann IU, et al. (2016) m(6)A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination. Nature 540(7632):301-304.

      (3) Kan L, et al. (2017) The m(6)A pathway facilitates sex determination in Drosophila. Nat Commun 8:15737.

      (4) Zhu C, et al. (2023) RNA Methylome Reveals the m(6)A-mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-withering. Genomics Proteomics Bioinformatics 21(4):769-787.

      (5) Song H, et al. (2021) METTL3-mediated m(6)A RNA methylation promotes the anti-tumour immunity of natural killer cells. Nat Commun 12(1):5522.

      (6) Yin H, et al. (2021) RNA m6A methylation orchestrates cancer growth and metastasis via macrophage reprogramming. Nat Commun 12(1):1394.

      Reviewer #2 (Public Review):

      Summary:

      The authors have tested the effects of partial- or whole-chromosome aneuploidy on the m6A RNA modification in Drosophila. The data reveal that overall m6A levels trend up but that the number of sites found by meRIP-seq trend down, which seems to suggest that aneuploidy causes a subset of sites to become hyper-methylated. Subsequent bioinformatic analysis of other published datasets establish correlations between the activity of the H4K16 acetyltransferase dosage compensation complex (DCC) and the expression of m6A components and m6A abundance, suggesting that DCC and m6A can act in a feedback loop on each other. Overall, this paper uses bioinformatic trends to generate a candidate model of feedback between DCC and m6A. It would be improved by functional studies that validate the effect in vivo.

      Strengths:

      • Thorough bioinformatic analysis of their data.

      • Incorporation of other published datasets that enhance scope and rigor.

      • Finds trends that suggest that a chromosome counting mechanism can control m6A, as fits with pub data that the Sxl mRNA is m6A modified in XX females and not XY males.

      • Suggests this counting mechanism may be due to the effect of chromatin-dependent effects on the expression of m6A components.

      Weaknesses:

      • The linkage between H4K16 machinery and m6A is indirect and based on bioinformatic trends with little follow-up to test the mechanistic bases of these trends.

      We found a set of ChIP-seq data (GSE109901) of H4K16ac in female and male Drosophila larvae from the public database, and analyzed whether H4K16ac is directly associated with m6A regulator genes. ChIP-seq is a standard method to study transcription factor binding and histone modification by using efficient and specific antibodies for immunoprecipitation. The results showed that there were H4K16ac peaks at the 5' region in gene of m6A reader Ythdc1 in both males and females. In addition, most of the genome sites where the other m6A regulator genes located are acetylated at H4K16 in both sexes, except that Ime4 shows sexual dimorphism and only contains H4K16ac peak in females. These results indicate that the m6A regulator gene itself is acetylated at H4K16, so there is a direct relationship between H4K16ac and m6A regulators. We have added these contents to the text.

      Besides the above conclusion from the seq data, we are also going to do some experiments to test the linkage between H4K16 and m6A in the next, such as how about the m6A levels when MOF is over expressed with the increased levels of H4K16Ac, the H4K16 levels when YT521B is knocked down or over expressed and the relative expression levels of important regulatory genes in there.

      • The paper lacks sufficient in vivo validation of the effects of DCC alleles on m6A and vice versa. For example, Is the Ythdc1 genomic locus a direct target of the DCC component Msl-2 ? (see Figure 7).

      In order to study whether Ythdc1 genomic locus is a direct target of DCC component, we first analyzed a published MSL2 ChIP-seq data of Drosophila (GSE58768). Since MSL2 is only expressed in males under normal conditions, this set of data is from male Drosophila. According to the results, the majority (99.1%) of MSL2 peaks are located on the X chromosome, while the MSL2 peaks on other chromosomes are few. This is consistent with the fact that MSL2 is enriched on the X chromosome in male Drosophila [1, 2]. Ythdc1 gene is located on chromosome 3L, and there is no MSL2 peak near it. Similarly, other m6A regulator genes are not X-linked, and there is no MSL2 peak. Then we analyzed the MOF ChIP-seq data (GSE58768) of male Drosophila. It was found that 61.6% of MOF peaks were located on the X chromosome, which was also expected [3, 4]. Although there are more MOF peaks on autosomes than MSL2 peaks, MOF peaks are absent on m6A regulator genes on autosomes. Therefore, at present, there is no evidence that the gene locus of m6A regulators are the direct targets of DCC component MSL2 and MOF, which may be due to the fact that most MSL2 and MOF are tethered to the X chromosome by MSL complex under physiological conditions. Whether there are other direct or indirect interactions between Ythdc1 and MSL2 is an issue worthy of further study in the future.

      (1) Bashaw GJ & Baker BS (1995) The msl-2 dosage compensation gene of Drosophila encodes a putative DNA-binding protein whose expression is sex specifically regulated by Sex-lethal. Development 121(10):3245-3258.

      (2) Kelley RL, et al. (1995) Expression of msl-2 causes assembly of dosage compensation regulators on the X chromosomes and female lethality in Drosophila. Cell 81(6):867-877.

      (3) Kind J, et al. (2008) Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell 133(5):813-828.

      (4) Conrad T, et al. (2012) The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex. Dev Cell 22(3):610-624.

      Quite a bit of technical detail is omitted from the main text, making it difficult for the reader to interpret outcomes.

      (1) Please add the tissues to the labels in Figure 1D.

      Figure 1D shows the subcellular localization of FISH probe signals in Drosophila embryos. Arrowheads indicate the foci of probe signals. The corresponding tissue types are (1) blastoderm nuclei; (2) yolk plasm and pole cells; (3) brain and midgut; (4) salivary gland and midgut; (5) blastoderm nuclei and yolk cortex; (6) blastoderm nuclei and pole cells; (7) blastoderm nuclei and yolk cortex; (8) germ band. We have added these to the manuscript.

      (2) In the main text, please provide detail on the source tissues used for meRIP; was it whole larvae? adult heads? Most published datasets are from S2 cells or adult heads and comparing m6A across tissues and developmental stages could introduce quite a bit of variability, even in wt samples. This issue seems to be what the authors discuss in lines 197-199.

      In this article, the material used to perform MeRIP-seq was the whole third instar larvae. Because trisomy 2L and metafemale Drosophila died before developing into adults, it was not possible to use the heads of adults for MeRIP-seq detection of aneuploidy. For other experiments described here, the m6A abundance was measured using whole larvae or adult heads; material used for RT-qPCR analysis was whole larvae, larval brains, or adult heads; Drosophila embryos at different developmental stages were used for fluorescence in situ hybridization (FISH) experiments. We provide a detailed description of the experimental material for each assay in the manuscript.

      (3) In the main text, please identify the technique used to measure "total m6A/A" in Fig 2A. I assume it is mass spec.

      We used the EpiQuik m6A RNA Methylation Quantification Kit (Colorimetric) (Epigentek, NY, USA, Cat # P-9005) to measure the m6A/A ratio in RNA samples. This kit is commercially available for quantification of m6A RNA methylation, which used colorimetric assay with easy-to-follow steps for convenience and speed, and is suitable for detecting m6A methylation status directly using total RNA isolated from any species such as mammals, plants, fungi, bacteria, and viruses.

      (4) Line 190-191: the text describes annotating m6A sites by "nearest gene" which is confusing. The sites are mapped in RNAs, so the authors must unambiguously know the identity of the gene/transcript, right?

      When the m6A peaks were annotated using the R package ChIPseeker, it will include two items: "genomic annotation" and "nearest gene annotation". "Genomic annotation" tells us which genomic features the peak is annotated to, such as 5’UTR, 3’UTR, exon, etc. "Nearest gene annotation" indicates which specific gene/transcript the peak is matched to. We modified the description in the main text to make it easier to understand.

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Reviewer #3:

      Comments on current version:

      As mentioned in my first review, this work is significantly underpowered for the following reasons: 1) n=4 for each treatment group.; 2) no randomization of the surgical sites receiving treatments; 3) implants surgically inserted without precision/guided surgery. The authors have not addressed these concerns.

      On a minor note: not sure why the authors present a methodology to evaluate the dynamic bone formation (line 272) but do not present results (i.e. by means of histomorphometrical analyses) utilizing this methodology.

      We sincerely appreciate your thorough review and valuable feedback. We have carefully considered your comments and would like to address them as follows:

      As mentioned in my first review, this work is significantly underpowered for the following reasons:

      (1) n=4 for each treatment group.;

      We acknowledge your concern regarding the limited sample size (n=4 per group). While we understand this may affect statistical power, our choice was influenced by ethical considerations in animal experimentation and resource constraints. Increasing the sample size would undoubtedly strengthen the statistical power of our study. However, the logistical and ethical constraints associated with using a larger number of animals in such invasive procedures were significant limiting factors. Specifically, increasing the number of medium to large experimental animals could raise ethical issues, so we used the minimum number possible. Additionally, our study design was reviewed and approved by the animal IRB, which dictated the minimum number of animals we could use. Nevertheless, we conducted power analysis to ensure that our sample size, although limited, was sufficient to detect significant differences given the high variability typically observed in biological responses. The results obtained from our n=4 samples showed consistent trends and significant differences between groups, indicating the robustness of our findings. I will include this point in the limitations section of the discussion. Thank you.

      (2) no randomization of the surgical sites receiving treatments;

      Thank you for pointing out this issue. We agree that randomization is essential when considering individual differences and the anatomical variations of the jawbone, such as those found in humans. However, this study is an animal experiment where other conditions were controlled, and the interventions were applied after complete bone healing following tooth extraction. Therefore, the impact of randomization of surgical sites was likely minimal, and it is challenging to determine whether it significantly influenced the experimental results. Of course, twelve female OVX beagles were randomly designated into three groups. (Methods section, line 298) However regarding your concern, we would like to present the robustness of histological results from different surgical sites as shown below. Also we will include this point in the limitations section of the discussion.

      Histologic analysis of the different surgical sites showed significant differences in bone formation and osseointegration among the three treatment groups: vehicle control, rhPTH(1-34), and dimeric Cys25PTH(1-34). Goldner trichrome staining (Figure A-C) showed enhanced bone formation in both the rhPTH(1-34) and dimeric Cys25PTH(1-34) groups compared to the vehicle control group. The rhPTH(1-34) group showed the most pronounced bone mass gain around the implant. Both treatment groups showed improved bone-to-implant contact compared to the control group, as indicated by the red arrows.

      Masson trichrome staining (Figure D-F) further confirmed these results, showing an increase in bone matrix (blue staining) in the rhPTH(1-34) and dimeric Cys25PTH(1-34) groups, with the dimeric rhPTH(1-34) group showing the most extensive and dense bone formation.

      TRAP staining (Figure G-I and G'-I') was used to assess osteoclast activity. Interestingly, both the rhPTH(1-34) and dimeric Cys25PTH(1-34) groups showed an increase in TRAP-positive cells compared to the vehicle control, suggesting enhanced bone remodeling activity. The highest number of TRAP-positive cells was observed in the rhPTH(1-34) group and the highest trabecular number, indicating the most active bone remodeling.

      To summarize the results, histological analyses revealed that both rhPTH(1-34) and dimeric Cys25PTH(1-34) treatments significantly enhanced osseointegration and bone formation around titanium implants in a postmenopausal osteoporosis model compared to the control. The rhPTH(1-34) group demonstrated superior outcomes, exhibiting the most substantial increase in bone volume, bone-to-implant contact, and osteoclastic activity, indicating its greater efficacy in promoting bone regeneration and implant integration in this experimental context.

      Author response image 1.

      Histological analysis using Goldner trichrome, Masson trichrome, and TRAP staining

      (3) implants surgically inserted without precision/guided surgery. The authors have not addressed these concerns.

      The primary purpose of precision guides is to prevent damage to various anatomical structures and to ensure perfect placement at the desired location. Even disregarding the potential inaccuracies of precision guides in actual clinical settings, the primary goal of this animal experiment was not to achieve perfect placement or prevent damage to anatomical structures. Instead, the objective was to histologically measure the integrity of the bone surrounding titanium fixture's platform after pharmacological intervention, ensuring it was fully seated in the alveolar bone. To this end, we secured sufficient visibility through periosteal dissection to confirm the perfect placement of the implant and adhered to the principle of maintaining sufficient mesiodistal distance between each fixture. Using such precision guides in this animal experiment, which is not an evaluation of 'implant precision guides,' could potentially introduce inaccuracies and contradict the experimental objectives. Furthermore, since this experiment was conducted on an edentulous ridge where all teeth had been extracted, achieving the same placement as in the presurgical simulation would be impossible, even with the use of precision guides. Thank you once again for your constructive feedback. We will include this point in the limitations section of the discussion.

      On a minor note: not sure why the authors present a methodology to evaluate the dynamic bone formation (line 272) but do not present results (i.e. by means of histomorphometrical analyses) utilizing this methodology.

      As the reviewer mentioned, we confirmed that the sentence was included in the Methods section despite the analysis not actually being performed. We sincerely apologize for this oversight and will make the necessary corrections immediately. Thank you very much for your keen observation.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      This paper presents a compelling and comprehensive study of decision-making under uncertainty. It addresses a fundamental distinction between belief-based (cognitive neuroscience) formulations of choice behaviour with reward-based (behavioural psychology) accounts. Specifically, it asks whether active inference provides a better account of planning and decision-making, relative to reinforcement learning. To do this, the authors use a simple but elegant paradigm that includes choices about whether to seek both information and rewards. They then assess the evidence for active inference and reinforcement learning models of choice behaviour, respectively. After demonstrating that active inference provides a better explanation of behavioural responses, the neuronal correlates of epistemic and instrumental value (under an optimised active inference model) are characterised using EEG. Significant neuronal correlates of both kinds of value were found in sensor and source space. The source space correlates are then discussed sensibly, in relation to the existing literature on the functional anatomy of perceptual and instrumental decision-making under uncertainty.

      Strengths:

      The strengths of this work rest upon the theoretical underpinnings and careful deconstruction of the various determinants of choice behaviour using active inference. A particular strength here is that the experimental paradigm is designed carefully to elicit both information-seeking and reward-seeking behaviour; where the information-seeking is itself separated into resolving uncertainty about the context (i.e., latent states) and the contingencies (i.e., latent parameters), under which choices are made. In other words, the paradigm - and its subsequent modelling - addresses both inference and learning as necessary belief and knowledge-updating processes that underwrite decisions.

      The authors were then able to model belief updating using active inference and then look for the neuronal correlates of the implicit planning or policy selection. This speaks to a further strength of this study; it provides some construct validity for the modelling of belief updating and decision-making; in terms of the functional anatomy as revealed by EEG. Empirically, the source space analysis of the neuronal correlates licences some discussion of functional specialisation and integration at various stages in the choices and decision-making.

      In short, the strengths of this work rest upon a (first) principles account of decision-making under uncertainty in terms of belief updating that allows them to model or fit choice behaviour in terms of Bayesian belief updating - and then use relatively state-of-the-art source reconstruction to examine the neuronal correlates of the implicit cognitive processing.

      Response: We are deeply grateful for your careful review of our work and for the thoughtful feedback you have provided. Your dedication to ensuring the quality and clarity of the work is truly admirable. Your comments have been invaluable in guiding us towards improving the paper, and We appreciate your time and effort in not just offering suggestions but also providing specific revisions that I can implement. Your insights have helped us identify areas where I can strengthen the arguments and clarify the methodology.

      Comment 1:

      The main weaknesses of this report lies in the communication of the ideas and procedures. Although the language is generally excellent, there are some grammatical lapses that make the text difficult to read. More importantly, the authors are not consistent in their use of some terms; for example, uncertainty and information gain are sometimes conflated in a way that might confuse readers. Furthermore, the descriptions of the modelling and data analysis are incomplete. These shortcomings could be addressed in the following way.

      First, it would be useful to unpack the various interpretations of information and goal-seeking offered in the (active inference) framework examined in this study. For example, it will be good to include the following paragraph:

      "In contrast to behaviourist approaches to planning and decision-making, active inference formulates the requisite cognitive processing in terms of belief updating in which choices are made based upon their expected free energy. Expected free energy can be regarded as a universal objective function, specifying the relative likelihood of alternative choices. In brief, expected free energy can be regarded as the surprise expected following some action, where the expected surprise comes in two flavours. First, the expected surprise is uncertainty, which means that policies with a low expected free energy resolve uncertainty and promote information seeking. However, one can also minimise expected surprise by avoiding surprising, aversive outcomes. This leads to goal-seeking behaviour, where the goals can be regarded as prior preferences or rewarding outcomes.

      Technically, expected free energy can be expressed in terms of risk plus ambiguity - or rearranged to be expressed in terms of expected information gain plus expected value, where value corresponds to (log) prior preferences. We will refer to both decompositions in what follows; noting that both decompositions accommodate information and goal-seeking imperatives. That is, resolving ambiguity and maximising information gain have epistemic value, while minimising risk or maximising expected value have pragmatic or instrumental value. These two kinds of values are sometimes referred to in terms of intrinsic and extrinsic value, respectively [1-4]."

      Response 1: We deeply thank you for your comments and corresponding suggestions about our interpretations of active inference. In response to your identified weaknesses and suggestions, we have added corresponding paragraphs in the Methods section (The free energy principle and active inference, line 95-106):

      “Active inference formulates the necessary cognitive processing as a process of belief updating, where choices depend on agents' expected free energy. Expected free energy serves as a universal objective function, guiding both perception and action. In brief, expected free energy can be seen as the expected surprise following some policies. The expected surprise can be reduced by resolving uncertainty, and one can select policies with lower expected free energy which can encourage information-seeking and resolve uncertainty. Additionally, one can minimize expected surprise by avoiding surprising or aversive outcomes (oudeyer et al., 2007; Schmidhuber et al., 2010). This leads to goal-seeking behavior, where goals can be viewed as prior preferences or rewarding outcomes.

      Technically, expected free energy can also be expressed as expected information gain plus expected value, where the value corresponds to (log) prior preferences. We will refer to both formulations in what follows. Resolving ambiguity, minimizing risk, and maximizing information gain has epistemic value while maximizing expected value have pragmatic or instrumental value. These two types of values can be referred to in terms of intrinsic and extrinsic value, respectively (Barto et al., 2013; Schwartenbeck et al., 2019).”

      Oudeyer, P. Y., & Kaplan, F. (2007). What is intrinsic motivation? A typology of computational approaches. Frontiers in neurorobotics, 1, 108.

      Schmidhuber, J. (2010). Formal theory of creativity, fun, and intrinsic motivation (1990–2010). IEEE transactions on autonomous mental development, 2(3), 230-247.

      Barto, A., Mirolli, M., & Baldassarre, G. (2013). Novelty or surprise?. Frontiers in psychology, 4, 61898.

      Schwartenbeck, P., Passecker, J., Hauser, T. U., FitzGerald, T. H., Kronbichler, M., & Friston, K. J. (2019). Computational mechanisms of curiosity and goal-directed exploration. elife, 8, e41703.

      Comment 2:

      The description of the modelling of choice behaviour needs to be unpacked and motivated more carefully. Perhaps along the following lines:

      "To assess the evidence for active inference over reinforcement learning, we fit active inference and reinforcement learning models to the choice behaviour of each subject. Effectively, this involved optimising the free parameters of active inference and reinforcement learning models to maximise the likelihood of empirical choices. The resulting (marginal) likelihood was then used as the evidence for each model. The free parameters for the active inference model scaled the contribution of the three terms that constitute the expected free energy (in Equation 6). These coefficients can be regarded as precisions that characterise each subjects' prior beliefs about contingencies and rewards. For example, increasing the precision or the epistemic value associated with model parameters means the subject would update her beliefs about reward contingencies more quickly than a subject who has precise prior beliefs about reward distributions. Similarly, subjects with a high precision over prior preferences or extrinsic value can be read as having more precise beliefs that she will be rewarded. The free parameters for the reinforcement learning model included..."

      Response 2: We deeply thank you for your comments and corresponding suggestions about our description of the behavioral modelling. In response to your identified weaknesses and suggestions, we have added corresponding content in the Results section (Behavioral results, line 279-293):

      “To assess the evidence for active inference over reinforcement learning, we fit active inference (Eq.9), model-free reinforcement learning, and model-based reinforcement learning models to the behavioral data of each participant. This involved optimizing the free parameters of active inference and reinforcement learning models. The resulting likelihood was used to calculate the Bayesian Information Criterion (BIC) (Vrieze 2012) as the evidence for each model. The free parameters for the active inference model (AL, AI, EX, prior, and α) scaled the contribution of the three terms that constitute the expected free energy in Eq.9. These coefficients can be regarded as precisions that characterize each participant's prior beliefs about contingencies and rewards. For example, increasing α means participants would update their beliefs about reward contingencies more quickly, increasing AL means participants would like to reduce ambiguity more, and increasing AI means participants would like to learn the hidden state of the environment and avoid risk more. The free parameters for the model-free reinforcement learning model are the learning rate α and the temperature parameter γ and the free parameters for the model-based are the learning rate α, the temperature parameter γ and prior (the details for the model-free reinforcement learning model can be seen in Eq.S1-11 and the details for the model-based reinforcement learning model can be seen Eq.S12-23 in the Supplementary Method). The parameter fitting for these three models was conducted using the `BayesianOptimization' package in Python (Frazire 2018), first randomly sampling 1000 times and then iterating for an additional 1000 times.”

      Vrieze, S. I. (2012). Model selection and psychological theory: a discussion of the differences between the Akaike information criterion (AIC) and the Bayesian information criterion (BIC). Psychological methods, 17(2), 228.

      Frazier, P. I. (2018). A tutorial on Bayesian optimization. arXiv preprint arXiv:1807.02811.

      Comment 3:

      In terms of the time-dependent correlations with expected free energy - and its constituent terms - I think the report would benefit from overviewing these analyses with something like the following:

      "In the final analysis of the neuronal correlates of belief updating - as quantified by the epistemic and intrinsic values of expected free energy - we present a series of analyses in source space. These analyses tested for correlations between constituent terms in expected free energy and neuronal responses in source space. These correlations were over trials (and subjects). Because we were dealing with two-second timeseries, we were able to identify the periods of time during decision-making when the correlates were expressed.

      In these analyses, we focused on the induced power of neuronal activity at each point in time, at each brain source. To illustrate the functional specialisation of these neuronal correlates, we present whole-brain maps of correlation coefficients and pick out the most significant correlation for reporting fluctuations in selected correlations over two-second periods. These analyses are presented in a descriptive fashion to highlight the nature and variety of the neuronal correlates, which we unpack in relation to the existing EEG literature in the discussion. Note that we did not attempt to correct for multiple comparisons; largely, because the correlations observed were sustained over considerable time periods, which would be almost impossible under the null hypothesis of no correlations."

      Response 3: We deeply thank you for your comments and corresponding suggestions about our description of the regression analysis in the source space. In response to your suggestions, we have added corresponding content in the Results section (EEG results at source level, line 331-347):

      “In the final analysis of the neural correlates of the decision-making process, as quantified by the epistemic and intrinsic values of expected free energy, we presented a series of linear regressions in source space. These analyses tested for correlations over trials between constituent terms in expected free energy (the value of avoiding risk, the value of reducing ambiguity, extrinsic value, and expected free energy itself) and neural responses in source space. Additionally, we also investigated the neural correlate of (the degree of) risk, (the degree of) ambiguity, and prediction error. Because we were dealing with a two-second time series, we were able to identify the periods of time during decision-making when the correlates were expressed. The linear regression was run by the "mne.stats.linear regression" function in the MNE package (Activity ~ Regressor + Intercept). Activity is the activity amplitude of the EEG signal in the source space and regressor is one of the regressors that we mentioned (e.g., expected free energy, the value of reducing ambiguity, etc.).

      In these analyses, we focused on the induced power of neural activity at each time point, in the brain source space. To illustrate the functional specialization of these neural correlates, we presented whole-brain maps of correlation coefficients and picked out the brain region with the most significant correlation for reporting fluctuations in selected correlations over two-second periods. These analyses were presented in a descriptive fashion to highlight the nature and variety of the neural correlates, which we unpacked in relation to the existing EEG literature in the discussion. Note that we did not attempt to correct for multiple comparisons; largely, because the correlations observed were sustained over considerable time periods, which would be almost impossible under the null hypothesis of no correlations.”

      Comment 4:

      There was a slight misdirection in the discussion of priors in the active inference framework. The notion that active inference requires a pre-specification of priors is a common misconception. Furthermore, it misses the point that the utility of Bayesian modelling is to identify the priors that each subject brings to the table. This could be easily addressed with something like the following in the discussion:

      "It is a common misconception that Bayesian approaches to choice behaviour (including active inference) are limited by a particular choice of priors. As illustrated in our fitting of choice behaviour above, priors are a strength of Bayesian approaches in the following sense: under the complete class theorem [5, 6], any pair of choice behaviours and reward functions can be described in terms of ideal Bayesian decision-making with particular priors. In other words, there always exists a description of choice behaviour in terms of some priors. This means that one can, in principle, characterise any given behaviour in terms of the priors that explain that behaviour. In our example, these were effectively priors over the precision of various preferences or beliefs about contingencies that underwrite expected free energy."

      Response 4: We deeply thank you for your comments and corresponding suggestions about the prior of Bayesian methods. In response to your suggestions, we have added corresponding content in the Discussion section (The strength of the active inference framework in decision-making, line 447-453):

      “However, it may be the opposite. As illustrated in our fitting results, priors can be a strength of Bayesian approaches. Under the complete class theorem (Wald 1947; Brown 1981), any pair of behavioral data and reward functions can be described in terms of ideal Bayesian decision-making with particular priors. In other words, there always exists a description of behavioral data in terms of some priors. This means that one can, in principle, characterize any given behavioral data in terms of the priors that explain that behavior. In our example, these were effectively priors over the precision of various preferences or beliefs about contingencies that underwrite expected free energy.”

      Wald, A. (1947). An essentially complete class of admissible decision functions. The Annals of Mathematical Statistics, 549-555.

      Brown, L. D. (1981). A complete class theorem for statistical problems with finite sample spaces. The Annals of Statistics, 1289-1300.

      Reviewer #2 (Public Review):

      Summary:

      Zhang and colleagues use a combination of behavioral, neural, and computational analyses to test an active inference model of exploration in a novel reinforcement learning task.

      Strengths:

      The paper addresses an important question (validation of active inference models of exploration). The combination of behavior, neuroimaging, and modeling is potentially powerful for answering this question.

      Response: We want to express our sincere gratitude for your thorough review of our work and for the valuable comments you have provided. Your attention to detail and dedication to improving the quality of the work are truly commendable. Your feedback has been invaluable in guiding us towards revisions that will strengthen the work. We have made targeted modifications based on most of the comments. However, due to factors such as time and energy constraints, we have not added corresponding analyses for several comments.

      Comment 1:

      The paper does not discuss relevant work on contextual bandits by Schulz, Collins, and others. It also does not mention the neuroimaging study of Tomov et al. (2020) using a risky/safe bandit task.

      Response 1:

      We deeply thank you for your suggestions about the relevant work. We now discussion and cite these representative papers in the Introduction section (line 42-55):

      “The decision-making process frequently involves grappling with varying forms of uncertainty, such as ambiguity - the kind of uncertainty that can be reduced through sampling, and risk - the inherent uncertainty (variance) presented by a stable environment. Studies have investigated these different forms of uncertainty in decision-making, focusing on their neural correlates (Daw et al., 2006; Badre et al., 2012; Cavanagh et al., 2012).

      These studies utilized different forms of multi-armed bandit tasks, e.g the restless multi-armed bandit tasks (Daw et al., 2006; Guha et al., 2010), risky/safe bandit tasks (Tomov et al., 2020; Fan et al., 2022; Payzan et al., 2013), contextual multi-armed bandit tasks (Schulz et al., 2015; Schulz et al., 2015; Molinaro et al., 2023). However, these tasks either separate risk from ambiguity in uncertainty, or separate action from state (perception). In our work, we develop a contextual multi-armed bandit task to enable participants to actively reduce ambiguity, avoid risk, and maximize rewards using various policies (see Section 2.2) and Figure 4(a)). Our task makes it possible to study whether the brain represents these different types of uncertainty distinctly (Levy et al., 2010) and whether the brain represents both the value of reducing uncertainty and the degree of uncertainty. The active inference framework presents a theoretical approach to investigate these questions. Within this framework, uncertainties can be reduced to ambiguity and risk. Ambiguity is represented by the uncertainty about model parameters associated with choosing a particular action, while risk is signified by the variance of the environment's hidden states. The value of reducing ambiguity, the value of avoiding risk, and extrinsic value together constitute expected free energy (see Section 2.1).”

      Daw, N. D., O'doherty, J. P., Dayan, P., Seymour, B., & Dolan, R. J. (2006). Cortical substrates for exploratory decisions in humans. Nature, 441(7095), 876-879.

      Badre, D., Doll, B. B., Long, N. M., & Frank, M. J. (2012). Rostrolateral prefrontal cortex and individual differences in uncertainty-driven exploration. Neuron, 73(3), 595-607.

      Cavanagh, J. F., Figueroa, C. M., Cohen, M. X., & Frank, M. J. (2012). Frontal theta reflects uncertainty and unexpectedness during exploration and exploitation. Cerebral cortex, 22(11), 2575-2586.

      Guha, S., Munagala, K., & Shi, P. (2010). Approximation algorithms for restless bandit problems. Journal of the ACM (JACM), 58(1), 1-50.

      Tomov, M. S., Truong, V. Q., Hundia, R. A., & Gershman, S. J. (2020). Dissociable neural correlates of uncertainty underlie different exploration strategies. Nature communications, 11(1), 2371.

      Fan, H., Gershman, S. J., & Phelps, E. A. (2023). Trait somatic anxiety is associated with reduced directed exploration and underestimation of uncertainty. Nature Human Behaviour, 7(1), 102-113.

      Payzan-LeNestour, E., Dunne, S., Bossaerts, P., & O’Doherty, J. P. (2013). The neural representation of unexpected uncertainty during value-based decision making. Neuron, 79(1), 191-201.

      Schulz, E., Konstantinidis, E., & Speekenbrink, M. (2015, April). Exploration-exploitation in a contextual multi-armed bandit task. In International conference on cognitive modeling (pp. 118-123).

      Schulz, E., Konstantinidis, E., & Speekenbrink, M. (2015, November). Learning and decisions in contextual multi-armed bandit tasks. In CogSci.

      Molinaro, G., & Collins, A. G. (2023). Intrinsic rewards explain context-sensitive valuation in reinforcement learning. PLoS Biology, 21(7), e3002201.

      Levy, I., Snell, J., Nelson, A. J., Rustichini, A., & Glimcher, P. W. (2010). Neural representation of subjective value under risk and ambiguity. Journal of neurophysiology, 103(2), 1036-1047.

      Comment 2:

      The statistical reporting is inadequate. In most cases, only p-values are reported, not the relevant statistics, degrees of freedom, etc. It was also not clear if any corrections for multiple comparisons were applied. Many of the EEG results are described as "strong" or "robust" with significance levels of p<0.05; I am skeptical in the absence of more details, particularly given the fact that the corresponding plots do not seem particularly strong to me.

      Response 2: We deeply thank you for your comments about our statistical reporting. We have optimized the fitting model and rerun all the statistical analyses. As can be seen (Figure 6, 7, 8, S3, S4, S5), the new regression results are significantly improved compared to the previous ones. Due to the limitation of space, we place the other relevant statistical results, including t-values, std err, etc., on our GitHub (https://github.com/andlab-um/FreeEnergyEEG). Currently, we have not conducted multiple comparison corrections based on Reviewer 1’s comments (Comments 3) “Note that we did not attempt to correct for multiple comparisons; largely, because the correlations observed were sustained over considerable time periods, which would be almost impossible under the null hypothesis of no correlations”.

      Author response image 1.

      Comment 3:

      The authors compare their active inference model to a "model-free RL" model. This model is not described anywhere, as far as I can tell. Thus, I have no idea how it was fit, how many parameters it has, etc. The active inference model fitting is also not described anywhere. Moreover, you cannot compare models based on log-likelihood, unless you are talking about held-out data. You need to penalize for model complexity. Finally, even if active inference outperforms a model-free RL model (doubtful given the error bars in Fig. 4c), I don't see how this is strong evidence for active inference per se. I would want to see a much more extensive model comparison, including model-based RL algorithms which are not based on active inference, as well as model recovery analyses confirming that the models can actually be distinguished on the basis of the experimental data.

      Response 3: We deeply thank you for your comments about the model comparison details. We previously omitted some information about the comparison model, as classical reinforcement learning is not the focus of our work, so we put the specific details in the supplementary materials. Now we have placed relevant information in the main text (see the part we have highlighted in yellow). We have now added the relevant information regarding the model comparison in the Results section (Behavioral results, line 279-293):

      “To assess the evidence for active inference over reinforcement learning, we fit active inference (Eq.9), model-free reinforcement learning, and model-based reinforcement learning models to the behavioral data of each participant. This involved optimizing the free parameters of active inference and reinforcement learning models. The resulting likelihood was used to calculate the Bayesian Information Criterion (BIC) as the evidence for each model. The free parameters for the active inference model (AL, AI, EX, prior, and α) scaled the contribution of the three terms that constitute the expected free energy in Eq.9. These coefficients can be regarded as precisions that characterize each participant's prior beliefs about contingencies and rewards. For example, increasing α means participants would update their beliefs about reward contingencies more quickly, increasing AL means participants would like to reduce ambiguity more, and increasing AI means participants would like to learn the hidden state of the environment and avoid risk more. The free parameters for the model-free reinforcement learning model are the learning rate α and the temperature parameter γ and the free parameters for the model-based are the learning rate α, the temperature parameter γ and prior (the details for the model-free reinforcement learning model can be found in Eq.S1-11 and the details for the model-based reinforcement learning model can be found in Eq.S12-23 in the Supplementary Method). The parameter fitting for these three models was conducted using the `BayesianOptimization' package in Python, first randomly sampling 1000 times and then iterating for an additional 1000 times.”

      We have now incorporated model-based reinforcement learning into our comparison models and placed the descriptions of both model-free and model-based reinforcement learning algorithms in the supplementary materials. We have also changed the criterion for model comparison to Bayesian Information Criterion. As indicated by the results, the performance of the active inference model significantly outperforms both comparison models.

      Sorry, we didn't do model recovery before, but now we have placed the relevant results in the supplementary materials. From the result figures, we can see that each model fits its own generated simulated data well:

      “To demonstrate how reliable our models are (the active inference model, model-free reinforcement learning model, and model-based reinforcement learning model), we run some simulation experiments for model recovery. We use these three models, with their own fitting parameters, to generate some simulated data. Then we will fit all three sets of data using these three models.

      The model recovery results are shown in Fig.S6. This is the confusion matrix of models: the percentage of all subjects simulated based on a certain model that is fitted best by a certain model. The goodness-of-fit was compared using the Bayesian Information Criterion. We can see that the result of model recovery is very good, and the simulated data generated by a model can be best explained by this model.”

      Author response image 2.

      Comment 4:

      Another aspect of the behavioral modeling that's missing is a direct descriptive comparison between model and human behavior, beyond just plotting log-likelihoods (which are a very impoverished measure of what's going on).

      Response 4: We deeply thank you for your comments about the comparison between the model and human behavior. Due to the slight differences between our simulation experiments and real behavioral experiments (the "you can ask" stage), we cannot directly compare the model and participants' behaviors. However, we can observe that in the main text's simulation experiment (Figure 3), the active inference agent's behavior is highly consistent with humans (Figure 4), exhibiting an effective exploration strategy and a desire to reduce uncertainty. Moreover, we have included two additional simulation experiments in the supplementary materials, which demonstrate that active inference may potentially fit a wide range of participants' behavioral strategies.

      Author response image 3.

      (An active inference agent with AL=AI=EX=0. It can accomplish tasks efficiently like a human being, reducing the uncertainty of the environment and maximizing the reward.)

      Author response image 4.

      (An active inference agent with AL=AI=0, EX=10. It will only pursue immediate rewards (not choosing the "Cue" option due to additional costs), but it can also gradually optimize its strategy due to random effects.)

      Author response image 5.

      (An active inference agent with EX=0, AI=AL=10. It will only pursue environmental information to reduce the uncertainty of the environment. Even in "Context 2" where immediate rewards are scarce, it will continue to explore.) (a) shows the decision-making of active inference agents in the Stay-Cue choice. Blue corresponds to agents choosing the "Cue" option and acquiring "Context 1"; orange corresponds to agents choosing the "Cue" option and acquiring "Context 2"; purple corresponds to agents choosing the "Stay" option and not knowing the information about the hidden state of the environment. The shaded areas below correspond to the probability of the agents making the respective choices. (b) shows the decision-making of active inference agents in the Stay-Cue choice. The shaded areas below correspond to the probability of the agents making the respective choices. (c) shows the rewards obtained by active inference agents. (d) shows the reward prediction errors of active inference agents. (e) shows the reward predictions of active inference agents for the "Risky" path in "Context 1" and "Context 2".

      Comment 5:

      The EEG results are intriguing, but it wasn't clear that these provide strong evidence specifically for the active inference model. No alternative models of the EEG data are evaluated.

      Overall, the central claim in the Discussion ("we demonstrated that the active inference model framework effectively describes real-world decision-making") remains unvalidated in my opinion.

      Response 5: We deeply thank you for your comments. We applied the active inference model to analyze EEG results because it best fit the participants' behavioral data among our models, including the new added results. Further, our EEG results serve only to verify that the active inference model can be used to analyze the neural mechanisms of decision-making in uncertain environments (if possible, we could certainly design a more excellent reinforcement learning model with a similar exploration strategy). We aim to emphasize the consistency between active inference and human decision-making in uncertain environments, as we have discussed in the article. Active inference emphasizes both perception and action, which is also what we wish to highlight: during the decision-making process, participants not only passively receive information, but also actively adopt different strategies to reduce uncertainty and maximize rewards.

      Reviewer #3 (Public Review):

      Summary:

      This paper aims to investigate how the human brain represents different forms of value and uncertainty that participate in active inference within a free-energy framework, in a two-stage decision task involving contextual information sampling, and choices between safe and risky rewards, which promotes a shift from exploration to exploitation. They examine neural correlates by recording EEG and comparing activity in the first vs second half of trials and between trials in which subjects did and did not sample contextual information, and perform a regression with free-energy-related regressors against data "mapped to source space." Their results show effects in various regions, which they take to indicate that the brain does perform this task through the theorised active inference scheme.

      Strengths:

      This is an interesting two-stage paradigm that incorporates several interesting processes of learning, exploration/exploitation, and information sampling. Although scalp/brain regions showing sensitivity to the active-inference-related quantities do not necessarily suggest what role they play, it can be illuminating and useful to search for such effects as candidates for further investigation. The aims are ambitious, and methodologically it is impressive to include extensive free-energy theory, behavioural modelling, and EEG source-level analysis in one paper.

      Response: We would like to express our heartfelt thanks to you for carefully reviewing our work and offering insightful feedback. Your attention to detail and commitment to enhancing the overall quality of our work are deeply admirable. Your input has been extremely helpful in guiding us through the necessary revisions to enhance the work. We have implemented focused changes based on a majority of your comments. Nevertheless, owing to limitations such as time and resources, we have not included corresponding analyses for a few comments.

      Comment 1:

      Though I could surmise the above general aims, I could not follow the important details of what quantities were being distinguished and sought in the EEG and why. Some of this is down to theoretical complexity - the dizzying array of constructs and terms with complex interrelationships, which may simply be part and parcel of free-energy-based theories of active inference - but much of it is down to missing or ambiguous details.

      Response 1: We deeply thank you for your comments about our work’s readability. We have significantly revised the descriptions of active inference, models, research questions, etc. Focusing on active inference and the free energy principle, we have added relevant basic descriptions and unified the terminology. We have added information related to model comparison in the main text and supplementary materials. We presented our regression results in clearer language. Our research focused on the brain's representation of decision-making in uncertain environments, including expected free energy, the value of reducing ambiguity, the value of avoiding risk, extrinsic value, ambiguity, and risk.

      Comment 2:

      In general, an insufficient effort has been made to make the paper accessible to readers not steeped in the free energy principle and active inference. There are critical inconsistencies in key terminology; for example, the introduction states that aim 1 is to distinguish the EEG correlates of three different types of uncertainty: ambiguity, risk, and unexpected uncertainty. But the abstract instead highlights distinctions in EEG correlates between "uncertainty... and... risk" and between "expected free energy .. and ... uncertainty." There are also inconsistencies in mathematical labelling (e.g. in one place 'p(s|o)' and 'q(s)' swap their meanings from one sentence to the very next).

      Response 2: We deeply thank you for your comments about the problem of inconsistent terminology. First, we have unified the symbols and letters (P, Q, s, o, etc.) that appeared in the article and described their respective meanings more clearly. We have also revised the relevant expressions of "uncertainty" throughout the text. In our work, uncertainty refers to ambiguity and risk. Ambiguity can be reduced through continuous sampling and is referred to as uncertainty about model parameters in our work. Risk, on the other hand, is the inherent variance of the environment and cannot be reduced through sampling, which is referred to as uncertainty about hidden states in our work. In the analysis of the results, we focused on how the brain encodes the value of reducing ambiguity (Figure 8), the value of avoiding risk (Figure 6), and (the degree of) ambiguity (Figure S5) during action selection. We also analyzed how the brain encodes reducing ambiguity and avoiding risk during belief update (Figure 7).

      Comment 3:

      Some basic but important task information is missing, and makes a huge difference to how decision quantities can be decoded from EEG. For example:

      - How do the subjects press the left/right buttons - with different hands or different fingers on the same hand?

      Response 3: We deeply thank you for your comments about the missing task information. We have added the relevant content in the Methods section (Contextual two-armed bandit task and Data collection, line 251-253):

      “Each stage was separated by a jitter ranging from 0.6 to 1.0 seconds. The entire experiment consists of a single block with a total of 120 trials. The participants are required to use any two fingers of one hand to press the buttons (left arrow and right arrow on the keyboard).”

      Comment 4:

      - Was the presentation of the Stay/cue and safe/risky options on the left/right sides counterbalanced? If not, decisions can be formed well in advance especially once a policy is in place.

      Response 4: The presentation of the Stay/cue and safe/risky options on the left/right sides was not counterbalanced. It is true that participants may have made decisions ahead of time. However, to better study the state of participants during decision-making, our choice stages consist of two parts. In the first two seconds, we ask participants to consider which option they would choose, and after these two seconds, participants are allowed to make their choice (by pressing the button).

      We also updated the figure of the experiment procedure as below (We circled the time that the participants spent on making decisions).

      Author response image 6.

      Comment 5:

      - What were the actual reward distributions ("magnitude X with probability p, magnitude y with probability 1-p") in the risky option?

      Response 5: We deeply thank you for your comments about the missing task information. We have placed the relevant content in the Methods section (Contextual two-armed bandit task and Data collection, line 188-191):

      “The actual reward distribution of the risky path in "Context 1" was [+12 (55%), +9 (25%), +6 (10%), +3 (5%), +0 (5%)] and the actual reward distribution of the risky path in "Context 2" was [+12 (5%), +9 (5%), +6 (10%), +3 (25%), +0 (55%)].”

      Comment 6:

      The EEG analysis is not sufficiently detailed and motivated.

      For example,

      - why the high lower-filter cutoff of 1 Hz, and shouldn't it be acknowledged that this removes from the EEG any sustained, iteratively updated representation that evolves with learning across trials?

      Response 6: We deeply thank you for your comments about our EEG analysis. The 1Hz high-pass filter may indeed filter out some useful information. We chose a 1Hz high-pass filter to filter out most of the noise and prevent the noise from affecting our results analysis. Additionally, there are also many decision-related works that have applied 1Hz high-pass filtering in EEG data preprocessing (Yau et al., 2021; Cortes et al., 2021; Wischnewski et al., 2022; Schutte et al., 2017; Mennella et al., 2020; Giustiniani et al., 2020).

      Yau, Y., Hinault, T., Taylor, M., Cisek, P., Fellows, L. K., & Dagher, A. (2021). Evidence and urgency related EEG signals during dynamic decision-making in humans. Journal of Neuroscience, 41(26), 5711-5722.

      Cortes, P. M., García-Hernández, J. P., Iribe-Burgos, F. A., Hernández-González, M., Sotelo-Tapia, C., & Guevara, M. A. (2021). Temporal division of the decision-making process: An EEG study. Brain Research, 1769, 147592.

      Wischnewski, M., & Compen, B. (2022). Effects of theta transcranial alternating current stimulation (tACS) on exploration and exploitation during uncertain decision-making. Behavioural Brain Research, 426, 113840.

      Schutte, I., Kenemans, J. L., & Schutter, D. J. (2017). Resting-state theta/beta EEG ratio is associated with reward-and punishment-related reversal learning. Cognitive, Affective, & Behavioral Neuroscience, 17, 754-763.

      Mennella, R., Vilarem, E., & Grèzes, J. (2020). Rapid approach-avoidance responses to emotional displays reflect value-based decisions: Neural evidence from an EEG study. NeuroImage, 222, 117253.

      Giustiniani, J., Nicolier, M., Teti Mayer, J., Chabin, T., Masse, C., Galmès, N., ... & Gabriel, D. (2020). Behavioral and neural arguments of motivational influence on decision making during uncertainty. Frontiers in Neuroscience, 14, 583.

      Comment 7:

      - Since the EEG analysis was done using an array of free-energy-related variables in a regression, was multicollinearity checked between these variables?

      Response 7: We deeply thank you for your comments about our regression. Indeed, we didn't specify our regression formula in the main text. We conducted regression on one variable each time, so there was no need for a multicollinearity check. We have now added the relevant content in the Results section (“EEG results at source level” section, line 337-340):

      “The linear regression was run by the "mne.stats.linear regression" function in the MNE package (Activity ~ Regressor + Intercept). Activity is the activity amplitude of the EEG signal in the source space and regressor is one of the regressors that we mentioned (e.g., expected free energy, the value of reducing ambiguity, etc.).”

      Comment 8:

      - In the initial comparison of the first/second half, why just 5 clusters of electrodes, and why these particular clusters?

      Response 8: We deeply thank you for your comments about our sensor-level analysis. These five clusters are relatively common scalp EEG regions to analyze (left frontal, right frontal, central, left parietal, and right parietal), and we referred previous work analyzed these five clusters of electrodes (Laufs et al., 2006; Ray et al., 1985; Cole et al., 1985). In addition, our work pays more attention to the analysis in source space, exploring the corresponding functions of specific brain regions based on active inference models.

      Laufs, H., Holt, J. L., Elfont, R., Krams, M., Paul, J. S., Krakow, K., & Kleinschmidt, A. (2006). Where the BOLD signal goes when alpha EEG leaves. Neuroimage, 31(4), 1408-1418.

      Ray, W. J., & Cole, H. W. (1985). EEG activity during cognitive processing: influence of attentional factors. International Journal of Psychophysiology, 3(1), 43-48.

      Cole, H. W., & Ray, W. J. (1985). EEG correlates of emotional tasks related to attentional demands. International Journal of Psychophysiology, 3(1), 33-41.

      Comment 9:

      How many different variables are systematically different in the first vs second half, and how do you rule out less interesting time-on-task effects such as engagement or alertness? In what time windows are these amplitudes being measured?

      Response 9 (and the Response for Weaknesses 11): There were no systematic differences between the first half and the second half of the trials, with the only difference being the participants' experience. In the second half, participants had a better understanding of the reward distribution of the task (less ambiguity). The simulation results can well describe these.

      Author response image 7.

      As shown in Figure (a), agents can only learn about the hidden state of the environment ("Context 1" (green) or "Context 2" (orange)) by choosing the "Cue" option. If agents choose the "Stay" option, they will not be able to know the hidden state of the environment (purple). The risk of agents is only related to wh

      ether they choose the "Cue" option, not the number of rounds. Figure (b) shows the Safe-Risky choices of agents, and Figure (e) is the reward prediction of agents for the "Risky" path in "Context 1" and "Context 2". We can see that agents update the expected reward and reduce ambiguity by sampling the "Risky" path. The ambiguity of agents is not related to the "Cue" option, but to the number of times they sample the "Risky" path (rounds).

      In our choosing stages, participants were required to think about their choices for the first two seconds (during which they could not press buttons). Then, they were asked to make their choices (press buttons) within the next two seconds. This setup effectively kept participants' attention focused on the task. And the two second during the “Second choice” stage when participants decide which option to choose (they cannot press buttons) are measured for the analysis of the sensor-level results.

      Comment 10:

      In the comparison of asked and not-asked trials, what trial stage and time window is being measured?

      Response 10: We have added relevant descriptions in the main text. The two second during the “Second choice” stage when participants decide which option to choose (they cannot press buttons) are measured for the analysis of the sensor-level results.

      Author response image 8.

      Comment 11:

      Again, how many different variables, of the many estimated per trial in the active inference model, are different in the asked and not-asked trials, and how can you know which of these differences is the one reflected in the EEG effects?

      Response 11: The difference between asked trials and not-asked trials lies only in whether participants know the specific context of the risky path (the level of risk for the participants). A simple comparison indeed cannot tell us which of these differences is reflected in the EEG effects. Therefore, we subsequently conducted model-based regression analysis in the source space.

      Comment 12:

      The authors choose to interpret that on not-asked trials the subjects are more uncertain because the cue doesn't give them the context, but you could equally argue that they don't ask because they are more certain of the possible hidden states.

      Response 12: Our task design involves randomly varying the context of the risky path. Only by choosing to inquire can participants learn about the context. Participants can only become increasingly certain about the reward distribution of different contexts of the risky path, but cannot determine which specific context it is. Here are the instructions for the task that we will tell the participants (line 226-231).

      "You are on a quest for apples in a forest, beginning with 5 apples. You encounter two paths: 1) The left path offers a fixed yield of 6 apples per excursion. 2) The right path offers a probabilistic reward of 0/3/6/9/12 apples, and it has two distinct contexts, labeled "Context 1" and "Context 2," each with a different reward distribution. Note that the context associated with the right path will randomly change in each trial. Before selecting a path, a ranger will provide information about the context of the right path ("Context 1" or "Context 2") in exchange for an apple. The more apples you collect, the greater your monetary reward will be."

      Comment 13:

      - The EEG regressors are not fully explained. For example, an "active learning" regressor is listed as one of the 4 at the beginning of section 3.3, but it is the first mention of this term in the paper and the term does not arise once in the methods.

      Response 13: We have accordingly revised the relevant content in the main text (as in Eq.8). Our regressors now include expected free energy, the value of reducing ambiguity, the value of avoiding risk, extrinsic value, prediction error, (the degree of) ambiguity, reducing ambiguity, and avoiding risk.

      Comment 14:

      - In general, it is not clear how one can know that the EEG results reflect that the brain is purposefully encoding these very parameters while implementing this very mechanism, and not other, possibly simpler, factors that correlate with them since there is no engagement with such potential confounds or alternative models. For example, a model-free reinforcement learning model is fit to behaviour for comparison. Why not the EEG?

      Response 14: We deeply thank you for your comments. Due to factors such as time and effort, and because the active inference model best fits the behavioral data of the participants, we did not use other models to analyze the EEG data. At both the sensor and source level, we observed the EEG signal and brain regions that can encode different levels of uncertainties (risk and ambiguity). The brain's uncertainty driven exploration mechanism cannot be explained solely by a simple model-free reinforcement learning approach.

      Recommendations for the authors:

      Response: We have made point-to-point revisions according to the reviewer's recommendations, and as these revisions are relatively minor, we have only responded to the longer recommendations here.

      Reviewer #1 (Recommendations For The Authors)

      I enjoyed reading this sophisticated study of decision-making. I thought your implementation of active inference and the subsequent fitting to choice behaviour - and study of the neuronal (EEG) correlates - was impressive. As noted in my comments on strengths and weaknesses, some parts of your manuscript with difficult to read because of slight collapses in grammar and an inconsistent use of terms when referring to the mathematical quantities. In addition to the paragraphs I have suggested, I would recommend the following minor revisions to your text. In addition, you will have to fill in some of the details that were missing from the current version of the manuscript. For example:

      Recommendation 1:

      Which RL model did you use to fit the behavioural data? What were its free parameters?

      Response 1: We have now added information related to the comparison models in the behavioral results and supplementary materials. We applied both simple model-free reinforcement learning and model-based reinforcement learning. The free parameters for the model-free reinforcement learning model are the learning rate α and the temperature parameter γ, while the free parameters for the model-based approach are the learning rate α, the temperature parameter γ, and the prior.

      Recommendation 2:

      When you talk about neuronal activity in the final analyses (of time-dependent correlations) what was used to measure the neuronal activity? Was this global power over frequencies? Was it at a particular frequency band? Was it the maximum amplitude within some small window et cetera? In other words, you need to provide the details of your analysis that would enable somebody to reproduce your study at a certain level of detail.

      Response 2: In the final analyses, we used the activity amplitude at each point in the source space for our analysis. Previously, we had planned to make our data and models available on GitHub to facilitate easier replication of our work.

      Reviewer #3 (Recommendations For The Authors)

      Recommendation 1:

      It might help to explain the complex concepts up front, to use the concrete example of the task itself - presumably, it was designed so that the crucial elements of the active inference framework come to the fore. One could use hypothetical choice patterns in this task to exemplify different factors such as expected free energy and unexpected uncertainty at work. It would also be illuminating to explain why behaviour on this task is fit better by the active inference model than a model-free reinforcement learning model.

      Response 1: Thank you for your suggestions. We have given clearer explanations to the three terms in the active inference formula: the value of reducing ambiguity, the value of avoiding risk, and the extrinsic value (Eq.8), which makes it easier for readers to understand active inference.

      In addition, we can simply view active inference as a computational model similar to model-based reinforcement learning, where the expected free energy represents a subjective value, without needing to understand its underlying computational principles or neurobiological background. In our discussion, we have argued why the active inference model fits the participants' behavior better than our reinforcement learning model, as the active inference model has an inherent exploration mechanism that is consistent with humans, who instinctively want to reduce environmental uncertainty (line 435-442).

      “Active inference offers a superior exploration mechanism compared with basic model-free reinforcement learning  (Figure 4 (c)). Since traditional reinforcement learning models determine their policies solely on the state, this setting leads to difficulty in extracting temporal information (Laskin et al., 2020) and increases the likelihood of entrapment within local minima. In contrast, the policies in active inference are determined by both time and state. This dependence on time (Wang et al., 2016) enables policies to adapt efficiently, such as emphasizing exploration in the initial stages and exploitation later on. Moreover, this mechanism prompts more exploratory behavior in instances of state ambiguity. A further advantage of active inference lies in its adaptability to different task environments (Friston et al., 2017). It can configure different generative models to address distinct tasks, and compute varied forms of free energy and expected free energy.”

      Laskin, M., Lee, K., Stooke, A., Pinto, L., Abbeel, P., & Srinivas, A. (2020). Reinforcement learning with augmented data. Advances in neural information processing systems, 33, 19884-19895.

      Wang, J. X., Kurth-Nelson, Z., Tirumala, D., Soyer, H., Leibo, J. Z., Munos, R., ... & Botvinick, M. (2016). Learning to reinforcement learn. arXiv preprint arXiv:1611.05763.

      Friston, K., FitzGerald, T., Rigoli, F., Schwartenbeck, P., & Pezzulo, G. (2017). Active inference: a process theory. Neural computation, 29(1), 1-49.

      Recommendation 2:

      Figure 1A provides a key example of the lack of effort to help the reader understand. It suggests the possibility of a concrete example but falls short of providing one. From the caption and text, applied to the figure, I gather that by choosing either to run or to raise one's arms, one can control whether it is daytime or nighttime. This is clearly wrong but it is what I am led to think by the paper.

      Response 2: Thank you for your suggestion, which we had not considered before. In this figure, we aim to illustrate that "the agent receives observations and optimizes his cognitive model by minimizing variational free energy → the agent makes the optimal action by minimizing expected free energy → the action changes the environment → the environment generates new observations for the agent." We have now modified the image to be simpler to prevent any possible confusion for readers. Correspondingly, we removed the figure of a person raising their hand and the shadowed house in Figure a.

      Author response image 9.

      Recommendation 3:

      I recommend an overhaul in the labelling and methodological explanations for consistency and full reporting. For example, line 73 says sensory input is 's' and the cognitive model is 'q(s),' and the cause of the sensory input is 'p(s|o)' but on the very next line, the cognitive model is 'p(s|o)' and the causes of sensory input are 'q(s).' How this sensory input s relates to 'observations' or 'o' is unclear, and meanwhile, capital S is the set of environmental states. P seems to refer to the generative distribution, but it also means probability.

      Response 3: Thank you for your advice. Now we have revised the corresponding labeling and methodological explanations in our work to make them consistent. However, we are not sure how to make a good modification to P here. In many works, P can refer to a certain probability distribution or some specific probabilities.

      Recommendation 4:

      Even the conception of a "policy" is unclear (Figure 2B). They list 4 possible policies, which are simply the 4 possible sequences of steps, stay-safe, cue-risky, etc, but with no contingencies in them. Surely a complete policy that lists 'cue' as the first step would entail a specification of how they would choose the safe or risky option BASED on the information in that cue

      Response 4: Thank you for your suggestion. In active inference, a policy actually corresponds to a sequence of actions. The policy of "first choosing 'Cue' and then making the next decision based on specific information" differs from the meaning of policy in active inference.

      Recommendation 5:

      I assume that the heavy high pass filtering of the EEG (1 Hz) is to avoid having to baseline-correct the epochs (of which there is no mention), but the authors should directly acknowledge that this eradicates any component of decision formation that may evolve in any way gradually within or across the stages of the trial. To take an extreme example, as Figure 3E shows, the expected rewards for the risky path evolve slowly over the course of 60 trials. The filter would eliminate this.

      Response 5: Thank you for your suggestion. The heavy high pass filtering of the EEG (1 Hz) is to minimize the noise in the EEG data as much as possible.

      Recommendation 6:

      There is no mention of the regression itself in the Methods section - the section is incomplete.

      Response 6: Thank you for your suggestion. We have now added the relevant content in the Results section (EEG results at source level, line 337-340):

      “The linear regression was run by the "mne.stats.linear regression" function in the MNE package (Activity ∼ Regressor + Intercept, Activity is the activity amplitude of the EEG signal in the source space and regressor is one of the regressors that we mentioned).”

      Recommendation 7:

      On Lines 260-270 the same results are given twice.

      Response 7: Thank you for your suggestion. We have now deleted redundant content.

      Recommendation 8:

      Frequency bands are displayed in Figure 5 but there is no mention of those in the Methods. In Figure 5b Theta in the 2nd half is compared to Delta in the 1st half- is this an error?

      Response 8: Thank you for your suggestion. It indeed was an error (they should all be Theta) and now we have corrected it.

      Author response image 10.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1:

      Summary:

      In this study, Nishi et al. claim that the ratio of long-term hematopoietic stem cell (LT-HSC) versus short-term HSC (ST-HSC) determines the lineage output of HSCs and reduced ratio of ST-HSC in aged mice causes myeloid-biased hematopoiesis. The authors used Hoxb5 reporter mice to isolate LT-HSC and ST-HSC and performed molecular analyses and transplantation assays to support their arguments. How the hematopoietic system becomes myeloid-biased upon aging is an important question with many implications in the disease context as well. However, their study is descriptive with remaining questions.

      Weaknesses:

      Comment #1-1: The authors may need conceptual re-framing of their main argument because whether the ST-HSCs used in this study are functionally indeed short-term "HSCs" is questionable. The data presented in this study and their immunophenotypic definition of ST-HSCs (Lineage negative/Sca-1+/c-Kit+/Flk2-/CD34-/CD150+/Hoxb5-) suggest that authors may find hematopoietic stem cell-like lymphoid progenitors as previously shown for megakaryocyte lineage (Haas et al., Cell stem cell. 2015) or, as the authors briefly mentioned in the discussion, Hoxb5- HSCs could be lymphoid-biased HSCs.

      The authors disputed the idea that Hoxb5- HSCs as lymphoid-biased HSCs based on their previous 4 weeks post-transplantation data (Chen et al., 2016). However, they overlooked the possibility of myeloid reprogramming of lymphoid-biased population during regenerative conditions (Pietras et al., Cell stem cell., 2015). In other words, early post-transplant STHSCs (Hoxb5- HSCs) can be seen as lacking the phenotypic lymphoid-biased HSCs.

      Thinking of their ST-HSCs as hematopoietic stem cell-like lymphoid progenitors or lymphoidbiased HSCs makes more sense conceptually as well.

      Response #1-1: We appreciate this important suggestion and recognize the significance of the debate on whether Hoxb5- HSCs are ST-HSCs or lymphoid-biased HSCs.

      HSCs are defined by their ability to retain hematopoietic potential after a secondary transplantation1-2. If Hoxb5- HSCs were indeed lymphoid-biased HSCs, they would exhibit predominantly lymphoid hematopoiesis even after secondary transplantation. However, functional experiments demonstrate that these cells lose their hematopoietic output after secondary transplantation3 (see Fig. 2 in this paper). Based on the established definition of HSCs in this filed, it is appropriate to classify Hoxb5- HSCs as ST-HSCs rather than lymphoid-biased HSCs.

      Additionally, it has been reported that myeloid reprogramming may occur in the early posttransplant period, around 2-4 weeks after transplantation, even in lymphoid-biased populations within the MPP fraction, due to high inflammatory conditions4. However, when considering the post-transplant hematopoiesis of Hoxb5- HSC fractions as ST-HSCs, they exhibit almost the same myeloid hematopoietic potential as LT-HSCs not only during the early 4 weeks after transplantation but also at 8 weeks post-transplantation3, when the acute inflammatory response has largely subsided. Therefore, it is difficult to attribute the myeloid production by ST-HSCs post-transplant solely to myeloid reprogramming.

      References

      (1) Morrison, S. J. & Weissman, I. L. The long-term repopulating subset of hematopoietic stem cells is deterministic and isolatable by phenotype. Immunity 1, 661–673 (1994).

      (2) Challen, G. A., Boles, N., Lin, K. K. Y. & Goodell, M. A. Mouse hematopoietic stem cell identification and analysis. Cytom. Part A 75, 14–24 (2009).

      (3) Chen, J. Y. et al. Hoxb5 marks long-term haematopoietic stem cells and reveals a homogenous perivascular niche. Nature 530, 223–227 (2016).

      (4) Pietras, E. M. et al. Functionally Distinct Subsets of Lineage-Biased Multipotent Progenitors Control Blood Production in Normal and Regenerative Conditions. Cell Stem Cell 17, 35–46 (2015).

      Comment #1-2: ST-HSCs come from LT-HSCs and further differentiate into lineage-biased multipotent progenitor (MPP) populations including myeloid-biased MPP2 and MPP3. Based on the authors' claim, LT-HSCs (Hoxb5- HSCs) have no lineage bias even in aged mice. Then these LT-HSCs make ST-HSCs, which produce mostly memory T cells. These memory T cell-producing ST-HSCs then produce MPPs including myeloid-biased MPP2 and MPP3.

      This differentiation trajectory is hard to accept. If we think Hoxb5- HSCs (ST-HSCs by authors) as a sub-population of immunophenotypic HSCs with lymphoid lineage bias or hematopoietic stem cell-like lymphoid progenitors, the differentiation trajectory has no flaw.

      Response #1-2: Thank you for this comment, and we apologize for the misunderstanding regarding the predominance of memory T cells in ST-HSCs after transplantation. 

      Our data show that ST-HSCs are not biased HSCs that predominantly produce memory T cells, but rather, ST-HSCs are multipotent hematopoietic cells. ST-HSCs lose their ability to self-renew within a short period, resulting in the cessation of ST-HSC-derived hematopoiesis. As a result, myeloid lineage with a short half-life disappears from the peripheral blood, and memory lymphocytes with a long half-life remain (see Figure 5 in this paper). 

      Comment #1-3: Authors' experimental designs have some caveats to support their claims. Authors claimed that aged LT-HSCs have no myeloid-biased clone expansion using transplantation assays. In these experiments, authors used 10 HSCs and young mice as recipients. Given the huge expansion of old HSC by number and known heterogeneity in immunophenotypically defined HSC populations, it is questionable how 10 out of so many old HSCs can faithfully represent the old HSC population. The Hoxb5+ old HSC primary and secondary recipient mice data (Figure 2C and D) support this concern. In addition, they only used young recipients. Considering the importance of the inflammatory aged niche in the myeloid-biased lineage output, transplanting young vs old LT-HSCs into aged mice will complete the whole picture.

      Response #1-3: We appreciate the reviewer for the comments. We acknowledge that using ten HSCs may not capture the heterogeneity of aging HSCs.

      However, although most of our experiments have used a small number of transplanted cells (e.g., 10 cells), we have conducted functional experiments across Figures 2, 3, 5, 6, S3, and S6, totaling n = 126, equivalent to over 1260 cells. Previous studies have reported that myeloid-biased HSCs constitute more than 50% of the aged HSC population1-2. If myeloidbiased HSCs increase with age, they should be detectable in our experiments. Our functional experiments have consistently shown that Hoxb5+ HSCs exhibit unchanged lineage output throughout life. In contrast, the data presented in this paper indicate that changes in the ratio of LT-HSCs and ST-HSCs may contribute to myeloid-biased hematopoiesis.

      We believe that transplanting aged HSCs into aged recipient mice is crucial to analyzing not only the differentiation potential of aged HSCs but also the changes in their engraftment and self-renewal abilities. We aim to clarify further findings through these experiments in the future.

      References

      (1) Dykstra B, Olthof S, Schreuder J, Ritsema M, Haan G De. Clonal analysis reveals multiple functional defects of aged murine hematopoietic stem cells. J Exp Med. 2011 Dec 19;208(13):2691–703. 

      (2) Yamamoto R, Wilkinson AC, Ooehara J, Lan X, Lai CY, Nakauchi Y, et al. LargeScale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment. Cell Stem Cell [Internet]. 2018;22(4):600-607.e4. Available from: https://doi.org/10.1016/j.stem.2018.03.013

      Comment #1-4: The authors' molecular data analyses need more rigor with unbiased approaches. They claimed that neither aged LT-HSCs nor aged ST-HSCs exhibited myeloid or lymphoid gene set enrichment but aged bulk HSCs, which are just a sum of LT-HSCs and ST-HSCs by their gating scheme (Figure 4A), showed the "tendency" of enrichment of myeloid-related genes based on the selected gene set (Figure 4D). Although the proportion of ST-HSCs is reduced in bulk HSCs upon aging, since ST-HSCs do not exhibit lymphoid gene set enrichment based on their data, it is hard to understand how aged bulk HSCs have more myeloid gene set enrichment compared to young bulk HSCs. This bulk HSC data rather suggests that there could be a trend toward certain lineage bias (although not significant) in aged LT-HSCs or ST-HSCs. The authors need to verify the molecular lineage priming of LT-HSCs and ST-HSCs using another comprehensive dataset.

      Response #1-4: Thank you for pointing out that neither aged LT-HSCs nor aged ST-HSCs exhibited myeloid

      or lymphoid gene set enrichment, although aged bulk HSCs showed a tendency towards enrichment of myeloid-related genes.

      The actual GSEA result had an FDR > 0.05. Therefore, we cannot claim that bulk HSCs showed significant enrichment of myeloid-related genes with age. Consequently, we have revised the following sentences:

      [P11, L251] Neither aged LT-HSCs nor aged ST-HSCs exhibited myeloid/lymphoid gene set enrichment, while shared myeloid-related genes tended to be enriched in aged bulk-HSCs, although this enrichment was not statistically significant (Fig. 4, F and G).

      In addition to the above, we also found that the GSEA results differ among myeloid gene sets (Fig. 4, D-F; Fig. 4S, C-D). These findings suggest that discussing lineage bias in HSCs using GSEA is challenging. We believe that functional experimental data is crucial. From our functional experiments, when the ratio of LT-HSC to ST-HSC was reconstituted to match the ratio in young Bulk-HSCs (LT= 2:8) or aged bulk-HSCs (LT= 5:5), myeloid-biased hematopoiesis was observed with the aged bulk-HSC ratio. Based on this data, the authors concluded that age-related changes in the ratio between LT-HSCs and ST-HSCs in bulkHSCs cause myeloid-biased hematopoiesis rather than an increase in myeloid gene expression in the aged bulk-HSCs.

      Comment #1-5: Some data are too weak to fully support their claims. The authors claimed that age-associated extramedullary changes are the main driver of myeloid-biased hematopoiesis based on no major differences in progenitor populations upon transplantation of 10 young HSCs into young or old recipient mice (Figure 7F) and relatively low donor-derived cells in thymus and spleen in aged recipient mice (Figure 7G-J). However, they used selected mice to calculate the progenitor populations in recipient mice (8 out of 17 from young recipients denoted by * and 8 out of 10 from aged recipients denoted by * in Figure 7C). In addition, they calculated the progenitor populations as frequency in c-kit positive cells. Given that they transplanted 10 LT-HSCs into "sub-lethally" irradiated mice and 8.7 Gy irradiation can have different effects on bone marrow clearance in young vs old mice, it is not clear whether this data is reliable enough to support their claims. The same concern applies to the data Figure 7G-J. Authors need to provide alternative data to support their claims.

      Response #1-5: Thank you for useful comments. Our claim regarding Fig. 7 is that age-associated extramedullary changes are merely additional drivers for myeloid-biased hematopoiesis are not the main drivers. But we will address the issues pointed out.

      Regarding the reason for analyzing the asterisk mice

      We performed two independent experiments for Fig. 7. In the first experiment, we planned to analyze the BM of recipients 16 weeks after transplantation. However, as shown in Fig. 7B, many of the aged mice died before 16 weeks. Therefore, we decided to examine the BM of the recipient mice at 12 weeks in the second experiment. Below are the peripheral blood results 11-12 weeks after transplantation for the mice used in the second experiment.

      Author response image 1.

      For the second experiment, we analyzed the BM of all eight all eight aged recipients. Then, we selected the same number of young recipients for analysis to ensure that the donor myeloid output would be comparable to that of the entire young group. Indeed, the donor myeloid lineage output of the selected mice was 28.1 ± 22.9%, closely matching the 23.5 ± 23.3% (p = 0.68) observed in the entire young recipient population. 

      That being said, as the reviewer pointed out, it is considerable that the BM, thymus, and spleen of all mice were not analyzed. Hence, we have added the following sentences:

      [P14, L327] We performed BM analysis for the mice denoted by † in Figure 7C because many of the aged mice had died before the analysis.

      [P15, L338] The thymus and spleen analyses were also performed on the mice denoted by † in Figure 7C.

      Regarding the reason for 8.7 Gy.

      Thank you for your question about whether 8.7 Gy is myeloablative. In our previous report1, we demonstrated that none of the mice subjected to pre-treatment with 8.7 Gy could survive when non-LKS cells were transplanted, suggesting that 8.7 Gy is enough to be myeloablative with the radiation equipment at our facility.

      Author response image 2.

      Reference

      (1)  Nishi K, Sakamaki T, Sadaoka K, Fujii M, Takaori-Kondo A, Chen JY, et al. Identification of the minimum requirements for successful haematopoietic stem cell transplantation. Br J Haematol. 2022;196(3):711–23. 

      Regarding the normalization of c-Kit in Figure 7F.  

      Firstly, as shown in Supplemental Figures S1B and S1C, we analyze the upstream (HSC, MPP, Flk2+) and downstream (CLP, MEP, CMP, GMP) fractions in different panels. Therefore, normalization is required to assess the differentiation of HSCs from upstream to downstream. Additionally, the reason for normalizing by c-Kit+ is that the bone marrow analysis was performed after enrichment using the Anti-c-Kit antibody for both upstream and downstream fractions. Based on this, we calculated the progenitor populations as a frequency within the c-Kit positive cells.

      Next, the results of normalizing the whole bone marrow cells (live cells) are shown below. 

      Author response image 3.

      Similar to the results of normalizing c-Kit+ cells, myeloid progenitors remained unchanged, including a statistically significant decrease in CMP in aged mice. Additionally, there were no significant differences in CLP. In conclusion, we obtained similar results between the normalization with c-Kit and the normalization with whole bone marrow cells (live cells).

      However, as the reviewer pointed out, it is necessary to explain the reason for normalization with c-Kit. Therefore, we will add the following description.

      [P21, L502] For the combined analysis of the upstream (HSC, MPP, Flk2+) and downstream (CLP, MEP, CMP, GMP) fractions in Figures 1B and 7F, we normalized by c-Kit+ cells because we performed a c-Kit enrichment for the bone marrow analysis.

      Reviewer #2:

      Summary:  

      Nishi et al, investigate the well-known and previously described phenomenon of ageassociated myeloid-biased hematopoiesis. Using a previously established HoxB5mCherry mouse model, they used HoxB5+ and HoxB5- HSCs to discriminate cells with long-term (LTHSCs) and short-term (ST-HSCs) reconstitution potential and compared these populations to immunophenotypically defined 'bulk HSCs' that consists of a mixture of LT-HSC and STHSCs. They then isolated these HSC populations from young and aged mice to test their function and myeloid bias in non-competitive and competitive transplants into young and aged recipients. Based on quantification of hematopoietic cell frequencies in the bone marrow, peripheral blood, and in some experiments the spleen and thymus, the authors argue against the currently held belief that myeloid-biased HSCs expand with age. 

      Comment #2-1: While aspects of their work are fascinating and might have merit, several issues weaken the overall strength of the arguments and interpretation. Multiple experiments were done with a very low number of recipient mice, showed very large standard deviations, and had no statistically detectable difference between experimental groups. While the authors conclude that these experimental groups are not different, the displayed results seem too variable to conclude anything with certainty. The sensitivity of the performed experiments (e.g. Figure 3; Figure 6C, D) is too low to detect even reasonably strong differences between experimental groups and is thus inadequate to support the author's claims. This weakness of the study is not acknowledged in the text and is also not discussed. To support their conclusions the authors need to provide higher n-numbers and provide a detailed power analysis of the transplants in the methods section.

      Response #2-1: Thank you for your important remarks. The power analysis for this experiment shows that power = 0.319, suggesting that more number may be needed. On the other hand, our method for determining the sample size in Figure 3 is as follows:

      (1) First, we checked whether myeloid biased change is detected in the bulk-HSC fraction (Figure S3). The results showed that the difference in myeloid output at 16 weeks after transplantation was statistically significant (young vs. aged = 7.2 ± 8.9 vs. 42.1 ± 35.5%, p = 0.01), even though n = 10.

      (2) Next, myeloid biased HSCs have been reported to be a fraction with high self-renewal ability (2004, Blood). If myeloid biased HSCs increase with aging, the increase in myeloid biased HSCs in LT-HSC fraction would be detected with higher sensitivity than in the bulk-HSC fraction used in Figure S3.

      (3) However, there was no difference not only in p-values but also in the mean itself, young vs aged = 51.4±31.5% vs 47.4±39.0%, p = 0.82, even though n = 8 in Figure 3. Since there was no difference in the mean itself, it is highly likely that no difference will be detected even if n is further increased.

      Regarding Figure 6, we obtained a statistically significant difference and consider the sample size to be sufficient. 

      In addition, we have performed various functional experiments (Figures 2, 5, 6 and S6), and have obtained consistent results that expansion of myeloid biased HSCs does not occur with aging in Hoxb5+HSCs fraction. Based on the above, we conclude that the LT-HSC fraction does not differ in myeloid differentiation potential with aging.

      Comment #2-2: As the authors attempt to challenge the current model of the age-associated expansion of myeloid-biased HSCs (which has been observed and reproduced by many different groups), ideally additional strong evidence in the form of single-cell transplants is provided.

      Response #2-2: Thank you for the comments. As the reviewer pointed out, we hope we could reconfirm our results using single-cell level technology in the future.

      On the other hand, we have reported that the ratio of myeloid to lymphoid cells in the peripheral blood changes when the number of HSCs transplanted, or the number of supporting cells transplanted with HSCs, is varied1-2. Therefore, single-cell transplant data need to be interpreted very carefully to determine differentiation potential.

      From this viewpoint, future experiments will combine the Hoxb5 reporter system with a lineage tracing system that can track HSCs at the single-cell level over time. This approach will investigate changes in the self-renewal capacity of individual HSCs and their subsequent differentiation into progenitor cells and peripheral blood cells. We have reflected this comment by adding the following sentences in the manuscript.

      [P19, L451] In contrast, our findings should be considered in light of some limitations. In this report, we primarily performed ten to twenty cell transplantation assays. Therefore, the current theory should be revalidated using single-cell technology with lineage tracing system3-4. This approach will investigate changes in the self-renewal capacity of individual HSCs and their subsequent differentiation into progenitor cells and peripheral blood cells. 

      References

      (1) Nishi K, Sakamaki T, Sadaoka K, Fujii M, Takaori-Kondo A, Chen JY, et al. Identification of the minimum requirements for successful haematopoietic stem cell transplantation. Br J Haematol. 2022;196(3):711–23. 

      (2) Sakamaki T, Kao KS, Nishi K, Chen JY, Sadaoka K, Fujii M, et al. Hoxb5 defines the heterogeneity of self-renewal capacity in the hematopoietic stem cell compartment. Biochem Biophys Res Commun [Internet]. 2021;539:34–41. Available from: https://doi.org/10.1016/j.bbrc.2020.12.077

      (3) Yamamoto R, Wilkinson AC, Ooehara J, Lan X, Lai CY, Nakauchi Y, et al. LargeScale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment. Cell Stem Cell [Internet]. 2018;22(4):600-607.e4. Available from: https://doi.org/10.1016/j.stem.2018.03.013

      (4) Rodriguez-Fraticelli AE, Weinreb C, Wang SW, Migueles RP, Jankovic M, Usart M, et al. Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis. Nature [Internet]. 2020;583(7817):585–9. Available from: http://dx.doi.org/10.1038/s41586-020-2503-6

      Comment #2-3: It is also unclear why the authors believe that the observed reduction of ST-HSCs relative to LT-HSCs explains the myeloid-biased phenotype observed in the peripheral blood. This point seems counterintuitive and requires further explanation.

      Response #2-3: Thank you for your comment. We apologize for the insufficient explanation. Our data, as shown in Figures 3 and 4, demonstrate that the differentiation potential of LT-HSCs remains unchanged with age. Therefore, rather than suggesting that an increase in LT-HSCs with a consistent differentiation capacity leads to myeloid-biased hematopoiesis, it seems more accurate to highlight that the relative decrease in the proportion of ST-HSCs, which remain in peripheral blood as lymphocytes, leads to a relative increase in myeloid cells in peripheral blood and thus causes myeloid-biased hematopoiesis.

      However, if we focus on the increase in the ratio of LT-HSCs, it is also plausible to explain that “with aging, the proportion of LT-HSCs capable of long-term myeloid hematopoiesis increases. As a result, from 16 weeks after transplantation, the influence of LT-HSCs maintaining the long-term ability to produce myeloid cells becomes relatively more significant, leading to an increase in the ratio of myeloid cells in the peripheral blood and causing myeloid-biased hematopoiesis.”

      Comment #2-4: Based on my understanding of the presented data, the authors argue that myeloid-biased HSCs do not exist, as<br /> a) they detect no difference between young/aged HSCs after transplant (mind low n-numbers and large std!); b) myeloid progenitors downstream of HSCs only show minor or no changes in frequency and c) aged LT-HSCs do not outperform young LT-HSC in myeloid output LT-HScs in competitive transplants (mind low n-numbers and large std!).

      Response #2-4: We appreciate the comments. As mentioned above, we will correct the manuscript regarding the sample size.

      Regarding the interpreting of the lack of increase in the percentage of myeloid progenitor cells in the bone marrow with age, it is instead possible that various confounding factors, such as differentiation shortcuts or changes in the microenviroment, are involved.

      However, even when aged LT-HSCs and young LT-HSCs are transplanted into the same recipient mice, the timing of the appearance of different cell fractions in peripheral blood is similar (Figure 3 of this paper). Therefore, we have not obtained data suggesting that clear shortcuts exist in the differentiation process of aged HSCs into neutrophils or monocytes. Additionally, it is currently consensually accepted that myeloid cells, including neutrophils and monocytes, differentiate from GMPs1. Since there is no changes in the proportion of GMPs in the bone marrow with age, we concluded that the differentiation potential into myeloid cells remains consistent with aging.

      Reference

      (1) Akashi K and others, ‘A Clonogenic Common Myeloid Progenitor That Gives Rise to All Myeloid Lineages’, Nature, 404.6774 (2000), 193–97.

      Strengths: 

      The authors present an interesting observation and offer an alternative explanation of the origins of aged-associated myeloid-biased hematopoiesis. Their data regarding the role of the microenvironment in the spleen and thymus appears to be convincing. 

      Weaknesses: 

      Comment #2-5: "Then, we found that the myeloid lineage proportions from young and aged LT-HSCs were nearly comparable during the observation period after transplantation (Figure 3, B and C)."<br /> Given the large standard deviation and low n-numbers, the power of the analysis to detect differences between experimental groups is very low. Experimental groups with too large standard deviations (as displayed here) are difficult to interpret and might be inconclusive. The absence of clearly detectable differences between young and aged transplanted HSCs could thus simply be a false-negative result. The shown experimental results hence do not provide strong evidence for the author's interpretation of the data. The authors should add additional transplants and include a detailed power analysis to be able to detect differences between experimental groups with reasonable sensitivity.

      Response #2-5: Thank you for providing these insights. Regarding the sample size, we have addressed this in Response #2-1.

      Comment #2-6: Line 293: "Based on these findings, we concluded that myeloid-biased hematopoiesis observed following transplantation of aged HSCs was caused by a relative decrease in ST-HSC in the bulk-HSC compartment in aged mice rather than the selective expansion of myeloid-biased HSC clones."<br /> Couldn't that also be explained by an increase in myeloid-biased HSCs, as repeatedly reported and seen in the expansion of CD150+ HSCs? It is not intuitively clear why a reduction of ST-HSCs clones would lead to a myeloid bias. The author should try to explain more clearly where they believe the increased number of myeloid cells comes from. What is the source of myeloid cells if the authors believe they are not derived from the expanded population of myeloid-biased HSCs?

      Response #2-6: Thank you for pointing this out. We apologize for the insufficient explanation. We will explain using Figure 8 from the paper.

      First, our data show that LT-HSCs maintain their differentiation capacity with age, while ST-HSCs lose their self-renewal capacity earlier, so that only long-lived memory lymphocytes remain in the peripheral blood after the loss of self-renewal capacity in ST-HSCs (Figure 8, upper panel). In mouse bone marrow, the proportion of LT-HSCs increases with age, while the proportion of STHSCs relatively decreases (Figure 8, lower panel and Figure S5). 

      Our data show that merely reproducing the ratio of LT-HSCs to ST-HSCs observed in aged mice using young LT-HSCs and ST-HSCs can replicate myeloid-biased hematopoiesis. This suggests that the increase in LT-HSC and the relative decrease in ST-HSC within the HSC compartment with aging are likely to contribute to myeloid-biased hematopoiesis.

      As mentioned earlier, since the differentiation capacity of LT-HSCs remain unchaged with age, it seems more accurate to describe that the relative decrease in the proportion of STHSCs, which retain long-lived memory lymphocytes in peripheral blood, leads to a relative increase in myeloid cells in peripheral blood and thus causes myeloid-biased hematopoiesis.

      However, focusing on the increase in the proportion of LT-HSCs, it is also possible to explain that “with aging, the proportion of LT-HSCs capable of long-term myeloid hematopoiesis increases. As a result, from 16 weeks after transplantation, the influence of LT-HSCs maintaining the long-term ability to produce myeloid cells becomes relatively more significant, leading to an increase in the ratio of myeloid cells in the peripheral blood and causing myeloid-biased hematopoiesis.”

      Reviewer #3:

      Summary:

      In this manuscript, Nishi et al. propose a new model to explain the previously reported myeloid-biased hematopoiesis associated with aging. Traditionally, this phenotype has been explained by the expansion of myeloid-biased hematopoietic stem cell (HSC) clones during aging. Here, the authors question this idea and show how their Hoxb5 reporter model can discriminate long-term (LT) and short-term (ST) HSC and characterized their lineage output after transplant. From these analyses, the authors conclude that changes during aging in the LT/ST HSC proportion explain the myeloid bias observed. 

      Although the topic is appropriate and the new model provides a new way to think about lineage-biased output observed in multiple hematopoietic contexts, some of the experimental design choices, as well as some of the conclusions drawn from the results could be substantially improved. Also, they do not propose any potential mechanism to explain this process, which reduces the potential impact and novelty of the study. Specific concerns are outlined below. 

      Major 

      Comment #3-1: As a general comment, there are experimental details that are either missing or not clear. The main one is related to transplantation assays. What is the irradiation dose? The Methods sections indicates "recipient mice were lethally irradiated with single doses of 8.7 or 9.1 Gy". The only experimental schematic indicating the irradiation dose is Figure 7A, which uses 8.7 Gy. Also, although there is not a "standard", 11 Gy split in two doses is typically considered lethal irradiation, while 9.5 Gy is considered sublethal.

      Response #3-1: We agree with reviewer’s assessment about whether 8.7 Gy is myeloablative. To confirm this, it would typically be necessary to irradiate mice with different dose and observe if they do not survive. However, such an experiment is not ethically permissible at our facility. Instead, in our previous report1, we demonstrated that none of the mice subjected to pretreatment with 8.7 Gy could survive when non-LKS cells were transplanted, suggesting that

      8.7 Gy is enough to be myeloablative with the radiation equipment at our facility.

      Reference

      (1) Nishi K, Sakamaki T, Sadaoka K, Fujii M, Takaori-Kondo A, Chen JY, et al. Identification of the minimum requirements for successful haematopoietic stem cell transplantation. Br J Haematol. 2022;196(3):711–23. 

      Comment #3-2:  Is there any reason for these lower doses? Same question for giving a single dose and for performing irradiation a day before transplant. 

      Response #3-2: We appreciate the reviewer for these important comments. Although the 8.7 Gy dose used at our facility is lower than in other reports, we selected this dose to maintain consistency with our previous experiments. For the same reason, we used a single irradiation, not split.  Regarding the timing of irradiation, the method section specifies that irradiation timing is 12-24 hours prior to transplantation. In most experiments, irradiation is performed at 12 hours. However, due to experimental progress, there were occasional instances where nearly 24 hours elapsed between irradiation and transplantation. We provide this information to ensure accuracy.

      Comment #3-3: The manuscript would benefit from the inclusion of references to recent studies discussing hematopoietic biases and differentiation dynamics at a single-cell level (e.g., Yamamoto et. al 2018; Rodriguez-Fraticelli et al., 2020). Also, when discussing the discrepancy between studies claiming different biases within the HSC pool, the authors mentioned that Montecino-Rodriguez et al. 2019 showed preserved lymphoid potential with age. It would be good to acknowledge that this study used busulfan as the conditioning method instead of irradiation.

      Response #3-3: We agree with this comment and have incorporated this suggestion into the manuscript

      [P19, L451] In contrast, our findings should be considered in light of some limitations. In this report, we primarily performed ten to twenty cell transplantation assays. Therefore, the current theory should be revalidated using single-cell technology with lineage tracing system1-2. This approach will investigate changes in the self-renewal capacity of individual HSCs and their subsequent differentiation into progenitor cells and peripheral blood cells. Additionally, in this report we purified LT-HSCs by Hoxb5 reporter system. In contrast, various LT-HSC markers have been previously reported2-3.  Therefore, it is ideal to validate our findings using other LT-HSC makers.

      [P16, L368] Other studies suggest that blockage of lymphoid hematopoiesis in aged mice results in myeloid-skewed hematopoiesis through alternative mechanisms. However, this result should be interpreted carefully, since Busulfan was used for myeloablative treatment in this study4.   

      References

      (1) Yamamoto R, Wilkinson AC, Ooehara J, Lan X, Lai CY, Nakauchi Y, et al. LargeScale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment. Cell Stem Cell [Internet]. 2018;22(4):600-607.e4. Available from: https://doi.org/10.1016/j.stem.2018.03.013

      (2) Rodriguez-Fraticelli AE, Weinreb C, Wang SW, Migueles RP, Jankovic M, Usart M, et al. Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis. Nature [Internet]. 2020;583(7817):585–9. Available from: http://dx.doi.org/10.1038/s41586-020-2503-6

      (3) Sanjuan-Pla A, Macaulay IC, Jensen CT, Woll PS, Luis TC, Mead A, et al. Plateletbiased stem cells reside at the apex of the haematopoietic stem-cell hierarchy. Nature. 2013;502(7470):232–6. 

      (4) Montecino-Rodriguez E, Kong Y, Casero D, Rouault A, Dorshkind K, Pioli PD. Lymphoid-Biased Hematopoietic Stem Cells Are Maintained with Age and Efficiently Generate Lymphoid Progeny. Stem Cell Reports. 2019 Mar 5;12(3):584–96. 

      Comment #3-4: When representing the contribution to PB from transplanted cells, the authors show the % of each lineage within the donor-derived cells (Figures 3B-C, 5B, 6B-D, 7C-E, and S3 B-C). To have a better picture of total donor contribution, total PB and BM chimerism should be included for each transplantation assay. Also, for Figures 2C-D and Figures S2A-B, do the graphs represent 100% of the PB cells? Are there any radioresistant cells?

      Response #3-4: Thank you for highlighting this point. Indeed, donor contribution to total peripheral blood (PB) is important information. We have included the donor contribution data for each figure above mentioned.

      Author response image 4.

      In Figure 2C-D and Figure S2A-B, the percentage of donor chimerism in PB was defined as the percentage of CD45.1-CD45.2+ cells among total CD45.1-CD45.2+ and CD45.1+CD45.2+ cells as described in method section.

      Comment #3-5: For BM progenitor frequencies, the authors present the data as the frequency of cKit+ cells. This normalization might be misleading as changes in the proportion of cKit+ between the different experimental conditions could mask differences in these BM subpopulations. Representing this data as the frequency of BM single cells or as absolute numbers (e.g., per femur) would be valuable.

      Response #3-5: We appreciate the reviewer's comment on this point. 

      Firstly, as shown in Supplemental Figures S1B and S1C, we analyze the upstream (HSC, MPP, Flk2+) and downstream (CLP, MEP, CMP, GMP) fractions in different panels. Therefore, normalization is required to assess the differentiation of HSCs from upstream to downstream. Additionally, the reason for normalizing by c-Kit+ is that the bone marrow analysis was performed after enrichment using the Anti-c-Kit antibody for both upstream and downstream fractions. Based on this, we calculated the progenitor populations as a frequency within the c-Kit positive cells. Next, the results of normalizing the whole bone marrow cells (live cells) are shown in Author response image 2. 

      Similar to the results of normalizing c-Kit+ cells, myeloid progenitors remained unchanged, including a statistically significant decrease in CMP in aged mice. Additionally, there were no significant differences in CLP. In conclusion, similar results were obtained between the normalization with c-Kit and the normalization with whole bone marrow cells (live cells).

      However, as the reviewer pointed out, it is necessary to explain the reason for normalization with c-Kit. Therefore, we will add the following description.

      [P21, L502] For the combined analysis of the upstream (HSC, MPP, Flk2+) and downstream (CLP, MEP, CMP, GMP) fractions in Figures 1B and 7F, we normalized by c-Kit+ cells because we performed a c-Kit enrichment for the bone marrow analysis.

      Comment #3-6: Regarding Figure 1B, the authors argue that if myeloid-biased HSC clones increase with age, they should see increased frequency of all components of the myeloid differentiation pathway (CMP, GMP, MEP). This would imply that their results (no changes or reduction in these myeloid subpopulations) suggest the absence of myeloid-biased HSC clones expansion with age. This reviewer believes that differentiation dynamics within the hematopoietic hierarchy can be more complex than a cascade of sequential and compartmentalized events (e.g., accelerated differentiation at the CMP level could cause exhaustion of this compartment and explain its reduction with age and why GMP and MEP are unchanged) and these conclusions should be considered more carefully.

      Response #3-6: We wish to thank the reviewer for this comment. We agree with that the differentiation pathway may not be a cascade of sequential events but could be influenced by various factors such as extrinsic factors.

      In Figure 1B, we hypothesized that there may be other mechanisms causing myeloidbiased hematopoiesis besides the age-related increase in myeloid-biased HSCs, given that the percentage of myeloid progenitor cells in the bone marrow did not change with age. However, we do not discuss the presence or absence of myeloid-biased HSCs based on the data in Figure 1B. 

      Our newly proposed theories—that the differentiation capacity of LT-HSCs remains unchanged with age and that age-related myeloid-biased hematopoiesis is due to changes in the ratio of LT-HSCs to ST-HSCs—are based on functional experiment results. As the reviewer pointed out, to discuss the presence or absence of myeloid-biased HSCs based on the data in Figure 1B, it is necessary to apply a system that can track HSC differentiation at single-cell level. The technology would clarify changes in the self-renewal capacity of individual HSCs and their differentiation into progenitor cells and peripheral blood cells. The authors believe that those single-cell technologies will be beneficial in understanding the differentiation of HSCs. Based on the above, the following statement has been added to the text.

      [P19, L451] In contrast, our findings should be considered in light of some limitations. In this report, we primarily performed ten to twenty cell transplantation assays. Therefore, the current theory should be revalidated using single-cell technology with lineage tracing system1-2. This approach will investigate changes in the self-renewal capacity of individual HSCs and their subsequent differentiation into progenitor cells and peripheral blood cells. 

      References

      (1) Yamamoto R, Wilkinson AC, Ooehara J, Lan X, Lai CY, Nakauchi Y, et al. LargeScale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment. Cell Stem Cell [Internet]. 2018;22(4):600-607.e4. Available from: https://doi.org/10.1016/j.stem.2018.03.013

      (2) Rodriguez-Fraticelli AE, Weinreb C, Wang SW, Migueles RP, Jankovic M, Usart M, et al. Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis. Nature [Internet]. 2020;583(7817):585–9. Available from: http://dx.doi.org/10.1038/s41586-020-2503-6

      Comment #3-7: Within the few recipients showing good donor engraftment in Figure 2C, there is a big proportion of T cells that are "amplified" upon secondary transplantation (Figure 2D). Is this expected?

      Response #3-7: We wish to express our deep appreciation to the reviewer for insightful comment on this point. As the reviewers pointed out, in Figure 2D, a few recipients show a very high percentage of T cells. The authors had the same question and considered this phenomenon as follows:

      (1) One reason for the very high percentage of T cells is that we used 1 x 107 whole bone marrow cells in the secondary transplantation. Consequently, the donor cells in the secondary transplantation contained more T-cell progenitor cells, leading to a greater increase in T cells compared to the primary transplantation.

      (2) We also consider that this phenomenon may be influenced by the reduced selfrenewal capacity of aged LT-HSCs, resulting in decreased sustained production of myeloid cells in the secondary recipient mice. As a result, long-lived memory-type lymphocytes may preferentially remain in the peripheral blood, increasing the percentage of T cells in the secondary recipient mice.

      We have discussed our hypothesis regarding this interesting phenomenon. To further clarify the characteristics of the increased T-cell count in the secondary recipient mice, we will analyze TCR clonality and diversity in the future.

      Comment #3-8: Do the authors have any explanation for the high level of variability within the recipients of Hoxb5+ cells in Figure 2C?

      Response #3-8: We appreciate the reviewer's comment on this point. As noted in our previous report, transplantation of a sufficient number of HSCs results in stable donor chimerism, whereas a small number of HSCs leads to increased variability in donor chimerism1. Additionally, other studies have observed high variability when fewer than 10 HSCs are transplanted2-3. Based on this evidence, we consider that the transplantation of a small number of cells (10 cells) is the primary cause of the high level of variability observed.

      References

      (1) Nishi K, Sakamaki T, Sadaoka K, Fujii M, Takaori-Kondo A, Chen JY, et al. Identification of the minimum requirements for successful haematopoietic stem cell transplantation. Br J Haematol. 2022;196(3):711–23. 

      (2) Dykstra B, Olthof S, Schreuder J, Ritsema M, Haan G De. Clonal analysis reveals multiple functional defects of aged murine hematopoietic stem cells. J Exp Med. 2011 Dec 19;208(13):2691–703. 

      (3) Yamamoto R, Wilkinson AC, Ooehara J, Lan X, Lai CY, Nakauchi Y, et al. LargeScale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment. Cell Stem Cell [Internet]. 2018;22(4):600-607.e4. Available from: https://doi.org/10.1016/j.stem.2018.03.013

      Comment #3-9: Can the results from Figure 2E be interpreted as Hoxb5+ cells having a myeloid bias? (differences are more obvious/significant in neutrophils and monocytes).

      Response #3-9: Thank you for your insightful comments. Firstly, we have not obtained any data indicating that young LT-HSCs are myeloid biased HSCs so far. Therefore, we classify young LT-HSCs as balanced HSCs1. Secondly, our current data demonstrate no significant difference in differentiation capacity between young and aged LT-HSCs (see Figure 3 in this paper). Based on these findings, we interpret that aged LT-HSCs are balanced HSCs, similar to young LT-HSCs.

      Reference

      (1)  Chen JY, Miyanishi M, Wang SK, Yamazaki S, Sinha R, Kao KS, et al. Hoxb5 marks long-term haematopoietic stem cells and reveals a homogenous perivascular niche. Nature. 2016 Feb 10;530(7589):223–7. 

      Comment #3-10: Is Figure 2G considering all primary recipients or only the ones that were used for secondary transplants? The second option would be a fairer comparison.

      Response #3-10: We appreciate the reviewer's comment on this point. We considered all primary recipients in Figure 2G to ensure a fair comparison, given the influence of various factors such as the radiosensitivity of individual recipient mice1. Comparing only the primary recipients used in the secondary transplantation would result in n = 3 (primary recipient) vs. n = 12 (secondary recipient). Including all primary recipients yields n = 11 vs. n = 12, providing a more balanced comparison. Therefore, we analyzed all primary recipient mice to ensure the reliability of our results.

      Reference

      (1) Duran-Struuck R, Dysko RC. Principles of bone marrow transplantation (BMT): providing optimal veterinary and husbandry care to irradiated mice in BMT studies. J Am Assoc Lab Anim Sci. 2009; 48:11–22

      Comment #3-11: When discussing the transcriptional profile of young and aged HSCs, the authors claim that genes linked to myeloid differentiation remain unchanged in the LT-HSC fraction while there are significant changes in the ST-HSCs. However, 2 out of the 4 genes shown in Figure S4B show ratios higher than 1 in LT-HSCs.

      Response #3-11: Thank you for highlighting this important point. As the reviewer pointed out, when we analyze the expression of myeloid-related genes, some genes are elevated in aged LT-HSCs compared to young LT-HSCs. However, the GSEA analysis using myeloid-related gene sets, which include several hundred genes, shows no significant difference between young and aged LT-HSCs (see Figure S4C in this paper). Furthermore, functional experiments using the co-transplantation system show no difference in differentiation capacity between young and aged LT-HSCs (see Figure 3 in this paper). Based on these results, we conclude that LT-HSCs do not exhibit any change in differentiation capacity with aging.

      Comment #3-12: When determining the lymphoid bias in ST-HSCs, the authors focus on the T-cell subtype, not considering any other any other lymphoid population. Could the authors explain this?

      Response #3-12: We thank the reviewer for this comment. We conducted the experiments in Figure 5 to demonstrate that the hematopoiesis observed 16 weeks post-transplantation—when STHSCs are believed to lose their self-renewal capacity—is not due to de novo production of T cells from ST-HSCs. Instead, it is attributed to long-lived memory cells which can persistently remain in the peripheral blood.

      As noted by the reviewer, various memory cell types are present in peripheral blood. Our analysis focused on memory T cells due to the broad consensus on memory T cell markers1. 

      Our findings show that transplanted Hoxb5- HSCs do not continuously produce lymphoid cells, unlike lymphoid-biased HSCs. Rather, the loss of self-renewal capacity in Hoxb5- HSCs makes the presence of long-lived memory cells in the peripheral blood more apparent.

      Reference

      (1)  Yenyuwadee S, Sanchez-Trincado Lopez JL, Shah R, Rosato PC, Boussiotis VA. The evolving role of tissue-resident memory T cells in infections and cancer. Sci Adv. 2022;8(33). 

      Comment #3-13: Based on the reduced frequency of donor cells in the spleen and thymus, the authors conclude "the process of lymphoid lineage differentiation was impaired in the spleens and thymi of aged mice compared to young mice". An alternative explanation could be that differentiated cells do not successfully migrate from the bone marrow to these secondary lymphoid organs. Please consider this possibility when discussing the data.

      Response #3-13: We strongly appreciate the reviewer's comment on this point. In accordance with the reviewer's comment, we have incorporated this suggestion into our manuscript.

      [P15, L343] These results indicate that the process of lymphoid lineage differentiation is impaired in the spleens and thymi of aged mice compared to young mice, or that differentiating cells in the bone marrow do not successfully migrate into these secondary lymphoid organs. These factors contribute to the enhanced myeloid-biased hematopoiesis in peripheral blood due to a decrease in de novo lymphocyte production.

      Recommendations for the authors:

      Reviewer #2 (Recommendations For The Authors):

      Recommendation #2-1: To support their conclusions the authors need to provide higher n-numbers and provide a detailed power analysis of the transplants in the methods section.

      Response to Recommendation #2-1: Thank you for your important remarks. The power analysis for this experiment shows that power = 0.319, suggesting that more number may be needed. On the other hand, our method for determining the sample size in Figure 3 is as follows:

      (1) First, we checked whether myeloid biased change is detected in the bulk-HSC fraction (Figure S3). The results showed that the difference in myeloid output at 16 weeks after transplantation was statistically significant (young vs. aged = 7.2 ± 8.9 vs. 42.1 ± 35.5%, p = 0.01), even though n = 10.

      (2) Next, myeloid biased HSCs have been reported to be a fraction with high self-renewal ability (2004, Blood). If myeloid biased HSCs increase with aging, the increase in myeloid biased HSCs in LT-HSC fraction would be detected with higher sensitivity than in the bulk-HSC fraction used in Figure S3.

      (3) However, there was no difference not only in p-values but also in the mean itself, young vs aged = 51.4±31.5% vs 47.4±39.0%, p = 0.82, even though n = 8 in Figure 3. Since there was no difference in the mean itself, it is highly likely that no difference will be detected even if n is further increased.

      Regarding Figure S3, 5, 6, S6 and 7, we obtained a statistically significant difference and consider the sample size to be sufficient. 

      Recommendation #2-2: As the authors attempt to challenge the current model of the age-associated expansion of myeloid-biased HSCs (which has been observed and reproduced by many different groups), ideally additional strong evidence in the form of single-cell transplants is provided.

      Response to Recommendation #2-2: Thank you for the comments. As the reviewer pointed out, we hope we could reconfirm our results using single-cell level technology in the future.

      On the other hand, we have reported that the ratio of myeloid to lymphoid cells in the peripheral blood changes when the number of HSCs transplanted, or the number of supporting cells transplanted with HSCs, is varied1-2. Therefore, single-cell transplant data need to be interpreted very carefully to determine differentiation potential.

      From this viewpoint, future experiments will combine the Hoxb5 reporter system with a lineage tracing system that can track HSCs at the single-cell level over time. This approach will investigate changes in the self-renewal capacity of individual HSCs and their subsequent differentiation into progenitor cells and peripheral blood cells. We have reflected this comment by adding the following sentences in the manuscript.

      [P19, L451] In contrast, our findings should be considered in light of some limitations. In this report, we primarily performed ten to twenty transplantation assays. Therefore, the current theory should be revalidated using single-cell technology. This approach will investigate changes in the self-renewal capacity of individual HSCs and their subsequent differentiation into progenitor cells and peripheral blood cells.

      References

      (1) Nishi K, Sakamaki T, Sadaoka K, Fujii M, Takaori-Kondo A, Chen JY, et al. Identification of the minimum requirements for successful haematopoietic stem cell transplantation. Br J Haematol. 2022;196(3):711–23. 

      (2) Sakamaki T, Kao KS, Nishi K, Chen JY, Sadaoka K, Fujii M, et al. Hoxb5 defines the heterogeneity of self-renewal capacity in the hematopoietic stem cell compartment. Biochem Biophys Res Commun [Internet]. 2021;539:34–41. Available from: https://doi.org/10.1016/j.bbrc.2020.12.077

      Minor points:

      Recommendation #2-3: Figure 1: "Comprehensive analysis of hematopoietic alternations with age shows a discrepancy of age-associated changes between peripheral blood and bone marrow"

      [Comment to the authors]: For clarity, the nature of the discrepancy should be stated clearly.

      Response to Recommendation #2-3: Thank you for this important comment. Following the reviewer’s recommendation, we have revised the manuscript as follows

      [P7, L139] Our analysis of hematopoietic alternations with age revealed that age-associated transition patterns of immunophenotypically defined HSC and CMP in BM were not paralleled with myeloid cell in PB (Fig. 1 C).

      Recommendation #2-4: Figure 1B "(B) Average frequency of immunophenotypically defined HSC and progenitor cells in BM of 2-3-month mice (n = 6), 6-month mice (n = 6), 12-13-month mice (n = 6), {greater than or equal to} 23-month mice (n = 7).

      [Comment to the authors]: It should be stated in the figure and legend that the values are normalized to the 2-3-month-old mice.

      Response to Recommendation #2-4: Thank you for this comment. Figure 1B presents the actual measured values of each fraction in c-Kit positive cells in the bone marrow, without any normalization.

      Recommendation #2-5: "We 127 found that the frequency of immunophenotypically defined HSC in BM rapidly increased 128 up to the age of 12 months. After the age, they remained plateaued throughout the 129 observation period (Fig. 1 B)."

      [Comment to the authors]: The evidence for a 'plateau', where HSC numbers don't change after 12 months is weak. It appears that the numbers increase continuously (although less steep) after 12 months. I thus recommend adjusting the wording to better reflect the data.

      Response to Recommendation #2-5: We thank the reviewer for the comments above and have incorporated these suggestions in our revision as follows. 

      [P6, L126] We found that the frequency of immunophenotypically defined HSC in BM rapidly increased up to the age of 12 months. After the age, the rate of increase in their frequency appeared to slow down.

      Recommendation #2-6: Figure 2G: [Comment to the authors]: Please add the required statistics, please check carefully all figures for missing statistical tests.

      Response to Recommendation #2-6: Thank you for these important comments. In response, we have added the results of the significance tests for Figures 1A, 1C, 4C, and S5.

      Recommendation #2-7: "If bulk-HSCs isolated from aged mice are already enriched by myeloid-biased HSC clones, we should see more myeloid-biased phenotypes 16 weeks after primary and the secondary transplantation. However, we found that kinetics of the proportion of myeloid cells in PB were similar across primary and the secondary transplantation and that the proportion of myeloid cells gradually decreased over time (Fig. 2 G). These results suggest the following two possibilities: either myeloid-biased HSCs do not expand in the LT-HSC fraction, or the expansion of myeloid-biased clones in 2-year-old mice has already peaked."

      [Comment to the authors]: Other possible explanations include that the observed reduction in myeloid reconstitution over 16 weeks reflects the time required to return to homeostasis. In other words, it takes time until the blood system approaches a balanced output.

      Response to Recommendation #2-7: We agree with the reviewer's comment. As the reviewer pointed out, the gradual decrease in the proportion of myeloid cells over time is not related to our two hypotheses in this part of the manuscript but rather to the hematopoietic system's process of returning to a homeostatic state after transplantation. Therefore, the original sentence could be misleading, as it is part of the section discussing whether age-associated expansion of myeloid-biased HSCs is observed. Based on the above, we have revised the sentence as follows.

      [P8, L179] However, we found that kinetics of the proportion of myeloid cells in PB were similar across the primary and the secondary transplantation (Fig. 2 G). These results suggest the following two possibilities: either myeloid-biased HSCs do not expand in the LTHSC fraction, or the expansion of myeloid-biased clones in 2-year-old mice has already peaked.

      Recommendation #2-8: It is also important to consider that the transplant results are highly variable (see large standard deviation), therefore the sensitivity to detect smaller but relevant changes is low in the shown experiments. As the statistical analysis of these experiments is missing and the power seems low these results should be interpreted with caution. For instance, it appears that the secondary transplants on average produce more myeloid cells as expected and predicted by the classical clonal expansion model.

      Regarding "expansion of myeloid-biased clones in 2-year-old mice has already peaked". This is what the author suggested above. It might thus not be surprising that HSCs from 2-year-old mice show little to no increased myeloid expansion.

      Response to Recommendation #2-8: Thank you for providing these insights. The primary findings of our study are based on functional experiments presented in Figures 2, 3, 5, 6, and 7. In Figure 3, there was no significant difference between young and aged LT-HSCs, with mean values of 51.4±31.5% and 47.4±39.0%, respectively (p = 0.82). Given the lack of difference in the mean values, it is unlikely that increasing the sample size would reveal a significant change. For ethical reasons, to minimize the use of additional animals, we conclude that LT-HSCs exhibit no change in lineage output throughout life based on the data in Figure 3. Statistically significant differences observed in Figures 2, 5, 6, and 7 further support our conclusions.

      Additionally, because whole bone marrow cells were transplanted in the secondary transplantation, there may be various confounding factors beyond the differentiation potential of HSCs. Therefore, we consider that caution is necessary when evaluating the differentiation capacity of HSCs in the context of the second transplantation.

      Recommendation #2-9: Figure 7C: [Comment to the authors]: The star * indicates with analyzed BM. As stars are typically used as indicators of significance, this can be confusing for the reader. I thus suggest using another symbol.

      Response to Recommendation #2-9: We appreciate the reviewer for this comment and have incorporated the suggestion in the revised manuscript. We have decided to use † instead of the star*.

      Reviewer #3 (Recommendations For The Authors):

      Recommendation #3.1: In Figure 1A, the authors show the frequency of PB lineages (lymphoid vs myeloid) in mice of different ages. It would be great if they could show the same data for each subpopulation including these two main categories individually (granulocytes, monocytes, B cells, T cells...).

      Response to Recommendation #3-1: We thank for this suggestion. We provide the frequency of PB lineages (granulocytes, monocytes, B cells, T cells, and NK cells) in mice of different ages.

      Author response image 5.

      Average frequency of neutrophils, monocytes, B cells, T cells, and NK cells in PB analyzed in Figure 1A. Dots show all individual mice. *P < 0.05. **P < 0.01. Data and error bars represent means ± standard deviation. 

      Recommendation #3.2: It would be great if data from young mice could be shown in parallel to the graphs in Figure 2A.

      Response to Recommendation #3-2: We thank the reviewer for the comments above and have incorporated these suggestions in Figure 2A. 

      [P34, L916] (A) Hoxb5 reporter expression in bulk-HSC, MPP, Flk2+, and Lin-Sca1-c-Kit+ populations in the 2-year-old Hoxb5-tri-mCherry mice (Upper panel) and 3-month-old Hoxb5_tri-mCherry mice (Lower panel). Values indicate the percentage of mCherry+ cells ± standard deviation in each fraction (_n = 3). 

      Recommendation #3.3: Do the authors have any explanation for the high level of variability within the recipients of Hoxb5+ cells in Figure 2C?

      Response to Recommendation #3-3: Thank you for providing these insights. As noted in our previous report, transplantation of a sufficient number of HSCs results in stable donor chimerism, whereas a small number of HSCs leads to increased variability in donor chimerism1. Additionally, other studies have observed high variability when fewer than 10 HSCs are transplanted2-3. Based on this evidence, we consider that the transplantation of a small number of cells (10 cells) is the primary cause of the high level of variability observed.

      References

      (1) Nishi K, Sakamaki T, Sadaoka K, Fujii M, Takaori-Kondo A, Chen JY, et al. Identification of the minimum requirements for successful haematopoietic stem cell transplantation. Br J Haematol. 2022;196(3):711–23. 

      (2) Dykstra B, Olthof S, Schreuder J, Ritsema M, Haan G De. Clonal analysis reveals multiple functional defects of aged murine hematopoietic stem cells. J Exp Med. 2011 Dec 19;208(13):2691–703. 

      (3) Yamamoto R, Wilkinson AC, Ooehara J, Lan X, Lai CY, Nakauchi Y, et al. LargeScale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment. Cell Stem Cell [Internet]. 2018;22(4):600-607.e4. Available from: https://doi.org/10.1016/j.stem.2018.03.013

      Recommendation #3.4: Are the differences in Figure 3D statistically significant? If yes, please add statistics. Same for Figure 4C.

      Response to Recommendation #3-4: Thank you for providing these insights. For Figure 3D, we performed an ANOVA analysis for each fraction; however, the results were not statistically significant. In contrast, for Figure 4C, we have added the results of significance tests for comparisons between Young LT-HSC vs. Young Bulk-HSC.

      Recommendation #3.5: As a general comment, although the results in this study are interesting, the use of a Hoxb5 lineage tracing mouse model would be more valuable for this purpose than the Hoxb5 reporter used here. The lineage tracing model would allow for the assessment of lineage bias without the caveats introduced by the transplantation assays.

      Response to Recommendation #3-5: We appreciate the reviewer for the important comments. Following the reviewer’s recommendation, we have revised the manuscript as follows

      [P19, L451] In contrast, our findings should be considered in light of some limitations. In this report, we primarily performed ten to twenty transplantation assays. Therefore, the current theory should be revalidated using single-cell technology with lineage tracing system1-2. This approach will investigate changes in the self-renewal capacity of individual HSCs and their subsequent differentiation into progenitor cells and peripheral blood cells. 

      References

      (1) Yamamoto R, Wilkinson AC, Ooehara J, Lan X, Lai CY, Nakauchi Y, et al. LargeScale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment. Cell Stem Cell [Internet]. 2018;22(4):600-607.e4. Available from: https://doi.org/10.1016/j.stem.2018.03.013

      (2) Rodriguez-Fraticelli AE, Weinreb C, Wang SW, Migueles RP, Jankovic M, Usart M, et al. Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis. Nature [Internet]. 2020;583(7817):585–9. Available from: http://dx.doi.org/10.1038/s41586-020-2503-6

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer#1:

      Comment #1: It is unclear how the fraction of NK cell populations is quantified in the spatial-seq datasets. Figures display spatial data with expression scores, but the method for calculating the score and determining NK cell presence in tumor tissue is ambiguous. Clarification is needed on whether the identification relied solely on visual inspection or if quantitative analyses using other criteria were conducted.

      Thank you for your questions. We removed the background and made the accordingly modifications according to your demand. We used the AddModuleScore function in Seurat to quantify the main immune subpopulations in spatial-seq using the gene sets identified in single-cell-seq. Additionally, the tumor and non-tumor region was identified by immunohistochemistry as well as cell clusters in spatial-seq, it is rough that we can't quantify the NK cell presence in each region precisely. The consolation is that the differences of NK cell presence in tumor and non-tumor region is observable by visual inspection. The methodology has been supplemented in the revised manuscript (line 190-193).

      Comment #2: The authors do not provide a clear definition of "resting" NK cells. It remains unclear whether they refer to a senescent state or a non-matured NK cell population. Furthermore, the criteria used to define resting and activated cells based on the expression of KIR2DL4, GPR183, GRP171, CD69, IFNG, GZMK, TTC38, CD160, and PLEKNF1 in Figure 4 are not well-defined. The expression patterns of these genes in Figure 4D are not distinct, and it is unclear which combination of genes was used to classify the populations. Clarification is needed on whether the presence of GZMK alone defines resting NK cells, or if the presence of any of the described genes (GZMK, TTC38, or CD160) is sufficient. Additionally, the method used for this classification, whether visual or algorithm-based, should be described.

      Thank you for your question. The resting and activated NK cells was defined by the preferential expression of the described resting genes (AZU, BPI, CAMP, CD160,CD2, CDHR1, CEACAM8, DEFA4, ELANE, GFI1, GZMK, KLRC4, MGAM, MS4A3, NME8, PLEKHF1, TEP1, TRBC1, TTC38, ZNF135) and activated NK genes (APOBEC3G, APOL6, CCL4, CCND2, CD69, CDK6, CSF2, DPP4, FASLG, GPR171, GPR18, GRAP2, IFNG, KIR2DL4, KIR2DS4, LTA, LTB, NCR3, OSM, PTGER2, SOCS1, TNFSF14) in CIBERSORT. Actually, these marker genes were not specifically expressed in a single NK cells subset. On the other hand, combined with further flow cytometric analysis verification, the resting NK cell tend to be a decidual-like NK cells and tumor- infiltrated NK cells with higher expression of CD9, CD49a and PD-1.

      Comment #3: Criteria used to define high or low NK cell presence/infiltration in Figure 5 are not described in the main text or figure legend. Since, the claim that the presence of the resting or activated NK cells predicts cancer prognosis is based on this figure, this needs to be clearly described.

      Thank you for your questions. The activated and resting NK cell percentage in TCGA and GSE29623 was determined by CIBERSORT. Additionally, the infiltration of activated and resting NK cell was also determined by the AddModuleScore function using the gene sets of activated and resting NK cell identified in single-cell-seq, the differences of activated and resting NK cell presence in tumor and non-tumor region is also determined by visual inspection. We have amended in the main text and figure legend in the revised manuscript.

      Comment #4: The absence of FMO controls for KIR2DL4 or GZMK and the lack of increase in GZMK expression during co-culture with tumour lines raises concerns since GZMK was used as a defining feature of resting NK cells.

      Thank you for your questions. We did a new batch of flow experiments and FMO controls of all the markers used in the experiments were set up to define the precise positive gate locations.

      Author response image 1.

      The positive gate locations of CD56, GZMK, KIR2DL4, CD9, CD49a, PD-1 defined according to the FMO control.

      Comment #5: All the co-cultures were performed with tumour cell line only and no healthy cells, such as human foreskin fibroblasts, were used as control. In the absence of a non-tumour cell line, it is very difficult to draw any conclusions. Furthermore, to claim that resting or activated NK cells are responsible for tumour migration or proliferation, it is important to at least isolate resting and activated NK cells ex vivo and culture with tumour lines, instead of NK cell lines.

      Thank you for your questions. According to your suggestion, NK cells were co-cultured with human foreskin fibroblasts, the phenotype was identified by Flow cytometry. When co-cultured with HFF in direct contact (CN group), NK cells were also tending towards tissue infiltration state (high expression of CD9). However, the domestication effect is significantly reduced compared to co-culturing with tumor cells. Additionally, unlike supernatant of CNS group (NK and HCT were in contact) from NK and HCT co-culture system could significantly increase the migration of fresh HCT, fresh HCT underwent a limited increase (no statistical significance was found) in migration when cultured in the supernatant from the co-culture system in which NK and HFF were in contact (CNS group), but not when co-cultures were performed in the cell supernatant (SNS group) and fresh medium (MNS group). Finally, we tried to isolate resting and activated NK cells from fresh colon cancer surgical specimen. Unfortunately, the NK cells were too few to perform further functional experiments such as migration and proliferation.

      Author response image 2.

      Phenotype switch of NK cells in different co-cultured system and the corresponding NK cell-mediated effect on cell migration of fresh colon cancer cell (HCT-116). A-B: NK cells underwent phenotype switch (high expression of CD9) when cocultured with HCT and HFF, the phenotype switch was more obvious when co-cultured with HCT. CN: NK cells cocultured with HCT/HFF; SN: NK cells cocultured with supernatant of HCT/HFF; MN: NK cells cocultured in fresh medium. C-E: Transwell assay showed the only tumor co-cultured NK mediated the inductive effect on cell migration of colon cancer cell (HCT-116). CNS: Colon cancer cells were cultured in the supernatant from co-culture system that NK and HCT/HFF were cultured in direct contact; SNS: Colon cancer cells were cultured in the supernatant from co-culture system that NK cocultured with supernatant of HCT/HFF; MNS: Colon cancer cells were cultured in the fresh medium.

      Comment #6: It seems that flow cytometric analyses and GZMK and KIR2DL4 staining were performed without cell permeabilization. Could authors confirm if this is accurate, or if they performed intracellular staining instead?

      Thank you for your questions. For GZMK, which known as the secretory protein, flow cytometric analyses were performed both with (Fig.3) and without cell fixation and permeabilization, no significant differences were found among each group. The difference is that GZMK was nearly all negative without fixation and permeabilization while it is all positive with fixation and permeabilization. Conditions of flow cytometry analyses for GZMK may need further optimization or GZMK may not be a suitable flow cytometric marker for resting NK cells. On the other hand, for membrane protein such as CD56, CD9, CD49a, KIR2DL4, PD-1, staining was performed without cell permeabilization.

      Author response image 3.

      Phenotype switch (CD56+, GZMK+) of NK cells was analyzed by FACS after fixation and permeabilization in different co-cultured groups. CN: NK cells cocultured with colon cancer cells; SN: NK cells cocultured with supernatant of cancer cells; MN: NK cells cocultured in fresh medium.

      Comment #7: The identity of the published datasets used for analysis is not provided, and references are not cited in the results section.

      Thank you for your questions. We are sorry for the neglect of our previous work. We have added the information in the revised manuscript (section of Materials and Methods) (Line 123-128).

      Comment #8: References are difficult to locate, as the main text follows APA style while the reference section is organized numerically with no clear order.

      Thank you for your questions. We have modified the format of the references in the revised manuscript.

      Comment #9: Figure 3 shows volcano plots showing DEG genes between tumor and healthy tissue NK cells are not described clearly, and authors did not discuss the significance of these genes, highlighted in the plot.

      Thank you for your questions. Volcano plots of Figure 3 showed the DEGs between colon cancer with metastasis and without metastasis in TCGA database. We focused on the genes which were enriched in the pathway of “Natural killer cell mediated cytotoxicity” and found nearly all the genes enriched in the pathway were down-regulated in the colon cancer with metastasis. We have modified the description in the result section and added the description of importance of these genes in the discussion section in the revise manuscript (Line 322-326).

      Comment #10: The meaning of "M0" and "M1" in Figures 5A and 5B is unclear and should be defined in the text.

      Thank you for your questions. "M0" and "M1" in Figure 5A and 5B means “colon cancer without metastasis” and “colon cancer with metastasis”, respectively. We have modified in the revise manuscript (Line 350-354).

      Comment #11: Terms such as "dynamic remodelling of NK cells" and "landscape of NK cells" are used without explanation, necessitating clarification of their meaning.

      Thank you for your questions. We have modified in the revise manuscript (Line 331-334).

      Comment #12: In vitro assays are described vaguely, making it difficult for readers to understand. More clarity is needed in describing these assays.

      Thank you for your questions. We have added clarification in the revise manuscript (Line 205-211).

      Reviewer #2:

      Comment #1: This manuscript investigates the role of the abundant NK cells that are observed in colon cancer liver metastasis using sequencing and spatial approaches in an effort to clarify the pro and anti-tumorigenic properties of NK cells. This descriptive study characterises different categories of NK cells in tumor and tumor-adjacent tissues and some correlations. An attempt has been made using pseudotime trajectory analysis but no models around how these NK cells might be regulated are provided.

      Thank you for your questions. The single-cell sequencing data enrolled in this study are CD45 positive immune cells and do not involve tumor cells, cellular communication analysis between NK cells and tumor cells cannot be conducted. The change process of NK can only be predicted through pseudotime trajectory analysis. Our hypothesis is that tumor cells domesticate NK cells into a tumor- infiltrated NK cells through direct contact, and flow cytometry experiments have also confirmed that tumor cells can only have such domestication through direct contact with NK cells (with prominent high expression of CD9). However, the detailed mechanism remained unclear.

      Comment #2: A small number of patients are analyzed in this study. The descriptive gene markers, while interesting, need to be further validated to understand how strong this analysis might be and its potential application.

      Thank you for your questions. The sample size included in this study is indeed a bit small, which is also a limitation of our study. However, this is the only large sample single-cell sequencing dataset could be found that includes primary colon cancer tissues, paired paratumor normal colon tissues, paired liver metastatic cancer tissue, and paired paratumor normal liver tissues. We will expand the sample size to further verify the current conclusion in subsequent experiments. In addition, the marker genes of different NK groups used in this study refer to the CIBERSORT's classification of activated NK cells and resting NK cells, which is a widely recognized indicator. We will verify the expression and clinical application value of the screened genes in tissues in subsequent studies.

      Comment #3: Figure 1C and other figures throughout the paper. It is not clear how marker genes were selected.

      Thank you for your questions. The marker genes displayed in the Figure.3C were the highly variable genes of each cell group as well as the marker genes of each immune cells, such as T cells (CD3D, CD3E), NK cells (NKG7, KLRD1), monocytes (LYZ, S100A8, S100A9), B cells (CD79A), plasma cells (JCHAIN, IGHA1, IGHA2), Neutrophils (CXCL8, FCGR3B).

      Comment #4: Figure 1E. P and T have not been defined. Lines should not connect the datasets as they are independent assessments.

      Thank you for your questions. P and T means paratumor normal tissues and tumor tissues, respectively. Which have been added in the caption of Figure 1E. Additionally, the single cell sequencing samples included in the study were paired, with primary colon cancer tissues, paired normal tissues adjacent to colon cancer, paired liver metastatic cancer tissue, and paired normal liver tissues from 20 colon cancer patients with liver metastasis, paired test analysis was thus performed.

      Comment #5: Figure 2C. It is unclear what ST-P1 means. This is not a particularly informative figure.

      Thank you for your questions. We are sorry that it was our annotation error. Actually, it is the spatial transcriptome of the primary colon cancer tissue and liver metastasis tissue of four patients. We have made the modifications in the revised manuscript.

      Comment #6: Multiple figures - abbreviations are used but not provided in the legend. They occur in the text but are not directly related to the figures where they are used to label axes or groups.

      Thank you for your questions. We have rechecked and made corresponding modifications in the revised manuscript.

      Comment #6: Patients: it is not clear what other drugs patients have been exposed to or basic data (sex, age, underlying conditions etc)

      Thank you for your questions. The baseline data of the patient of SC dataset and ST dataset were showed in the Table.1 and Table.2 followed, respectively. They were not presented before as no patients characteristics related analysis was performed in the current study.

      Author response table 1.

      The baseline data of patient from single cell sequencing database.

      Author response table 2.

      The baseline data of patient from spatial transcriptome database.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1

      (1) In the "Introduction" section, an important aspect that requires attention pertains to the discussion surrounding the heterodimerization of CXCR4 and CCR5. Notably, the manuscript overlooks a recent study (https://doi.org/10.1038/s41467-023-42082-z) elucidating the mechanism underlying the formation of functional dimers within these G protein-coupled receptors (GPCRs)…The inclusion of this study within the manuscript would significantly enrich the contextual framework of the work, offering readers a comprehensive understanding of the current knowledge surrounding the structural dynamics and functional implications of CXCR4 and CCR5 heterodimerization.

      We thank the reviewer for his/her recommendation to enrich the contextual framework of our study. The Nature Communications paper by Di Marino et al. was published after we sent the first version of our manuscript to eLife, and therefore was not included in the discussion. As the reviewer rightly indicates, this paper elucidates the mechanism underlying the formation of functional dimers within CCR5 and CXCR4. Using metadynamics approaches, the authors emphasize the importance of distinct transmembrane regions for dimerization of the two receptors. In particular, CXCR4 shows two low energy dimer structures and the TMVI-TMVII helices are the preferred interfaces involved in the protomer interactions in both cases. Although the study uses in silico techniques, it also includes the molecular binding mechanism of CCR5 and CXCR4 in the membrane environment, as the authors generate a model in which the receptors are immersed in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) phospholipid bilayer with 10% cholesterol. This is an important point in this study, as membrane lipids also interact with membrane proteins, and the lipid composition affects CXCR4 oligomerization (Gardeta S.R. et al. Front. Immunol. 2023). In particular, Di Marino et al. find a cholesterol molecule placed in-between the two CXCR4 protomers where it engages a series of hydrophobic interactions with residues including Leu132, Val214, Leu216 and Phe249. Then, the polar head of cholesterol forms an H-bond with Tyr135 that further stabilizes protomer binding. In our hands, the F249L mutation in CXCR4 reverted the antagonism of AGR1.137, suggesting that the compound binds, among others, this residue. We should, nonetheless, indicate that we analyzed receptor oligomerization and not CXCR4 dimerization, which was the main object of the Di Marino et al. study. It is therefore also plausible that other residues than those described as essential for CXCR4 dimerization might participate in receptor oligomerization. We can speculate that AGR1.137 might affect cholesterol binding to CXCR4 and, therefore, alter dimerization/oligomerization. Additionally, the CXCR4 x-ray structure with PDB code 3ODU (Wu B. et al. Science, 2010) experimentally shows the presence of two fatty acid molecules in contact with both TMV and TMVI. These molecules closely interact with hydrophobic residues in the protein, thereby stabilizing it in a hydrophobic environment. Although more experiments will be needed to clarify the mechanism involved, our results suggest that cholesterol and/or other lipids also play an important role in CXCR4 oligomerization and function, as seen for other GPCRs (Jakubik J. & ElFakahani E.E. Int J Mol Sci. 2021). However, we should also consider that other factors not included in the analysis by Di Marino et al. can also affect CXCR4 oligomerization; for instance, the co-expression of other chemokine receptors and/or other GPCRs that heterodimerize with CXCR4 might affect CXCR4 dynamics at the cell membrane, similar to other membrane proteins such as CD4, which also forms complexes with CXCR4 (Martinez-Muñoz L. et al. Mol. Cell 2018).

      The revised discussion contains references to the study by Di Marino et al. to enrich the contextual framework of our data.

      (2) In "various sections" of the manuscript, there appears to be confusion surrounding the terminology used to refer to antagonists. It is recommended to provide a clearer distinction between allosteric and orthosteric antagonists to enhance reader comprehension. An orthosteric antagonist typically binds to the same site as the endogenous ligand, directly blocking its interaction with the receptor. On the other hand, an allosteric antagonist binds to a site distinct from the orthosteric site, inducing a conformational change in the receptor that inhibits the binding of the endogenous ligand. By explicitly defining the terms "allosteric antagonist" and "orthosteric antagonist" within the manuscript, readers will be better equipped to discern the specific mechanisms discussed in the context of the study.

      The behavior of the compounds described in our manuscript (AGR1.35 and AGR1.137) fits with the definition of allosteric antagonists, as they bind on a site distinct from the orthosteric site, although they only block some ligand-mediated functions and not others. This would mean that they are not formally antagonists and should be not considered as allosteric compounds, as their binding on CXCR4 does not alter CXCL12 binding, although they might affect its affinity. In this sense, our compounds respond much better to the concept of negative allosteric modulators (Gao Z.-G. & Jacobson K.A. Drug Discov. Today Technol. 2013). They act by binding on a site distinct from the orthosteric site and selectively block some downstream signaling pathways but not others induced by the same endogenous agonist.

      To avoid confusion and to clarify the role of the compounds described in this study, we now refer to them as negative allosteric modulators along the manuscript.

      (3) In the Results section, the computational approach employed for "screening small compounds targeting CXCR4, particularly focusing on the inhibition of CXCL12-induced CXCR4 nanoclustering", requires clarification due to several points of incomprehension. The following recommendations aim to address these concerns and enhance the overall clarity of the section:

      (1) Computational Approach and Binding Mode Description: 

      -Explicitly describe the methodology for identifying the pocket/clef area in angstroms (Å) on the CXCR4 protein structure. Include details on how the volume of the cleft enclosed by TMV and TMVI was determined, as this information is not readily apparent in the provided reference (https://doi.org/10.1073/pnas.1601278113).

      The identification of the cleft was based on the observations by Wu et al. (Wu B. et al. Science 2010) who described the presence of bound lipids in the area formed by TMV and VI, and those of Wescott et al. (Wescott M.P. et al. Proc. Natl. Acad. Sci. 2016) on the importance of TMVI in the transmission of conformational changes promoted by CXCL12 on CXCR4 towards the cytoplasmic surface of the receptor to link the binding site with signaling activation. Collectively, these results, and our previous data on the critical role of the N-terminus region of TMVI for CXCR4 oligomerization (Martinez-Muñoz L. et al. Mol. Cell 2018), focused our in silico screening to this region. Once we detected that several compounds bound CXCR4 in this region, the cleavage properties were calculated by subtracting the compound structure. The resulting PDB was analyzed using the PDBsum server (Laskowski R.A. et. al. Protein Sci. 2018). Volume calculations were obtained using the server analyzing surface clefts by SURFNET (Laskowski R. A. J. Mol. Graph. 1995). The theoretical interaction surface between the selected compounds and CXCR4 and the atomic distances between the protein residues and the compounds was calculated using the PISA server (Krissinel E. & Henrick K. J. Mol. Biol. 2007) (Fig. I, only for review purposes). The analysis of the cleft occupied by AGR1.135 showed two independent cavities of 434 Å3 and 1,381 Å3 that were not connected to the orthosteric site. In the case of AGR1.137, the data revealed two distinct clefts of 790 Å3 and 580 Å3 (Fig. I, only for review purposes). These details have been included in the revised manuscript (New Fig. 1A, Supplementary Fig 8A, B).

      (4) Clarify the statement regarding the cleft being "surface exposed for interactions with the plasma membrane," particularly in the context of its embedding within the membrane.

      For GPCRs, transmembrane domains represent binding sites for bioactive lipids that play important functional and physiological roles (Huwiler A. & Zangemeister-Wittke U. Pharmacol. Ther. 2018). The channel between TMV and TMVI connects the orthosteric chemokine binding pocket to the lipid bilayer and is occupied by an oleic acid molecule, according to the CXCR4 structure published in 2010 (Wu B. et al. Science 2010). In addition, the target region contains residues involved in cholesterol (and perhaps other lipids) engagement (Di Marino et al. Nat. Commun. 2023). Taken together, these data support our statement that the cleft supports interactions between CXCR4 molecules and the plasma membrane. 

      Moreover, the data of Di Marino et al. also support that CCR5 and CXCR4 have a symmetric and an asymmetric binding mode. Therefore, either dimeric structure has the possibility to form trimers, tetramers, and even oligomers by using the free binding interface to complex with another protomer. This hypothesis suggests that the interaction of dimers to form oligomers should involve residues distinct from those included in the dimeric conformation.

      The sentence has been modified in the revised manuscript to clarify comprehension.

      (5) Discuss the rationale behind targeting the allosteric binding pocket instead of the orthosteric pocket, outlining potential advantages and disadvantages.

      The advantages and disadvantages of using negative allosteric modulators vs orthosteric antagonists have been now included in the revised discussion. 

      The majority of GPCR-targeted drugs function by binding to the orthosteric site of the receptor, and are agonists, partial agonists, antagonists or inverse agonists. These orthosteric compounds can have off-target effects and poor selectivity due to highly homologous receptor orthosteric sites and to abrogation of spatial and/or temporal endogenous signaling patterns. 

      The alternative is to use allosteric modulators, which can tune the functions associated with the receptors without affecting the orthosteric site. They can be positive, negative or neutral modulators, depending on their effect on the functionality of the receptor (Foster D.J. & Conn P.J. Neuron 2017). For example, the use of a negative allosteric modulator of a chemokine receptor to dampen pathological signaling events, while retaining full signaling for non-pathological activities might limit adverse effects (Kohout T.A.et al. J. Biol. Chem. 2004). In this case, the negative allosteric modulator 873140 blocks CCL3 binding on CCR5 but does not alter CCL5 binding (Watson C. et al. Mol. Pharmacol. 2005). In other cases, allosteric modulators can stabilize a particular receptor conformation and block others. The mechanism of action of the anti-HIV-1, FDAapproved, CCR5 allosteric modulator, maraviroc (Jin J. et al. Sci. Signal. 2018) is attributed to its ability to modulate CCR5 dimer populations and their subsequent subcellular trafficking and localization to the cell membrane (Jin J .et al. Sci. Signal. 2018). Two CCR5 dimeric conformations that are imperative for membrane localization were present in the absence of maraviroc; however, an additional CCR5 dimer conformation was discovered after the addition of maraviroc, and all homodimeric conformations were further stabilized. This finding is consistent with the observation that CCR5 dimers and oligomers inhibit HIV host-cell entry, likely by preventing the HIV-1 co-receptor formation.

      It is well known that GPCRs activate G proteins, but they also recruit additional proteins (e.g., β-arrestins) that induce signaling cascades which, in turn, can direct specific subsets of cellular responses independent of G protein activation (Eichel K. et al. Nature 2018) and are responsible for either therapeutic or adverse effects. Allosteric modulators can thus be used to block these adverse effects without influencing the therapeutic benefits. This was the case in the design of G protein-biased agonists for the kappa opioid receptor, which maintain the desirable antinociceptive and antipruritic effects and eliminate the sedative and dissociative effects in rodent models (Brust T.F. et al. Sci. Signal 2016).

      (6) Provide the PDB ID of the CXCR4 structure used as a template for modeling with SwissModel. Explain the decision to model the structure from the amino acid sequence and suggest an alternative approach, such as utilizing AlphaFold structures and performing classical molecular dynamics with subsequent clustering for the best representative structure.

      The PDB used as a template for modeling CXCR4 was 3ODU. This information was already included in the material and methods section. At the time we performed these analyses, there were several crystallographic structures of CXCR4 in complex with different molecules and peptides deposited at the PDB. None of them included a full construct containing the complete receptor sequence to provide a suitable sample for Xray structure resolution, as the N- and C-terminal ends of CXCR4 are very flexible loops. In addition, the CXCR4 constructs contained T4 lysozyme inserted between helices TMV and TMVI to increase the stability of the protein––a common strategy used to facilitate crystallogenesis of GPCRs (Zou Y. et al. PLoS One 2012). Therefore, we generated a CXCR4 homology model using the SWISS-MODEL server (Waterhouse A. et al. Nucleic Acids Res. 2018). This program reconstructed the loop between TMV and TMVI, a domain particularly important in this study that was not present in any of the crystal structure available in PDB. The model structure was, nonetheless, still incomplete, as it began at P27 and ended at S319 because the terminal ends were not resolved in the crystal structure used as a template. Nevertheless, we considered that these terminal ends were not involved in CXCR4 oligomerization. 

      As Alphafold was not available at the time we initiated this project, we didn’t use it. However, we have now updated our workflow to current methods and predicted the structure of the target using AlphaFold (Jumper J. et al. Nature 2021) and the sequence available under UniProt entry P61073. We prepared the ligands using OpenBabel (O’Boyle N.M. et al., J. Cheminformatics 2011), with a gasteiger charge assignment, and generated 10 conformers for each input ligand using the OpenBabel genetic algorithm. We then prepared the target structure with Openmm, removing all waters and possible heteroatoms, and adding all missing atoms. We next predicted the target binding pockets with fPocket (Le Guilloux V. et al. BMC Bioinformatics 2009), p2rank (Krivak R. & Hoksza, J. Cheminformatics 2018), and AutoDock autosite (Ravindranath P.A. & Sanner M.F. Bioinformatics 2016). We chose only those pockets between TMV and TMVI (see answer to point 3). We merged the results of the three programs into so-called consensus pockets, as two pockets are said to be sufficiently similar if at least 75% of their surfaces are shared (del Hoyo D. et al. J. Chem. Inform. Model. 2023). From the consensus pockets, there was one pocket that was significantly larger than the others and was therefore selected. We then docked the ligand conformers in this pocket using AutoDock GPU (Santos-Martins D. et al. J. Chem. Theory Comput. 2021), LeDock (Liu N & Xu Z., IOP Conf. Ser. Earth Environ. Sci. 2019), and Vina (Eberhardt J. et al. J. Chem. Inf. Model. 2021). The number of dockings varied from 210 to 287 poses. We scored each pose with the Vina score using ODDT (Wójcikowski M. et al. J. Cheminform. 2015). Then, we clustered the different solutions into groups whose maximum RMSD was 1Å. This resulted in 40 clusters, the representative of each cluster was the one with maximum Vina score and confirmed that the selected compounds bound this pocket (Author response image 1). When required, we calculated the binding affinity using Schrodinger’s MM-GBSA procedure (Greenidge P.A. et al. J. Chem. Inf. Model. 2013), in two ways: first, assuming that the ligand and target are fixed; second, with an energy minimization of all the atoms within a distance of 3Å from the ligand. This information has now been included in the revised version of the manuscript.

      Author response image 1.

      AGR1.135 docking in CXCR4 using the updated protocol for ligand docking. Cartoon representation colored in gray with TMV and TMVI shown in blue and pink, respectively. AGR1.135 is shown in stick representation with carbons in yellow, oxygens in red and nitrogens in blue.

      (7) Specify the meaning of "minimal interaction energy" and where (if present) the interaction scores are reported in the text.

      We refer to minimal interaction energy, the best docking score, that is, the best score obtained in our docking studies. These data were not included in the previous manuscript due to space restrictions but are now included in the reviewed manuscript.

      (8) You performed docking studies using GLIDE to identify potential binding sites for the small compounds on the CXCR4 protein. The top-scoring binders were then subjected to further refinement using PELE simulations. However, I realize that a detailed description of the specific binding modes of these compounds was not provided in the text. Please make the description of binding poses more detailed

      Firstly, to assess the reliability of this method, a PELE study was carried out for the control molecule IT1t, which is a small drug-like isothiourea derivative that has been crystallized in complex with CXCR4 (PDB code: 3ODU). IT1t is a CXCR4 antagonist that binds to the CXCL12 binding cavity and inhibits HIV-1 infection (Das D. Antimicrob. Agents Chemother. 2015; Dekkers S. et al. J. Med. Chem. 2023). From the best five trajectories, two of them had clearly better binding energies, and corresponded to almost the same predicted pose of the molecule. Although the predicted binding mode was not exactly the same as the one in the crystal structure, the approximation was very good, giving validation to the approach. Although PELE is a suitable technique to find potential binding sites, the predicted poses must be subsequently refined using docking programs.

      Analyzing the best trajectories for the remaining ligands, at least one of the best-scored poses was always located at the orthosteric binding site of CXCR4. Even though these poses showed good binding energies, they were discarded as the in vitro biological experiments indicated that the compounds were unable to block CXCL12 binding or CXCL12-mediated inhibition of cAMP release or CXCR4 internalization. Collectively, these data indicated that the selected compounds did not behave as orthosteric inhibitors of CXCR4. The CXCL12 binding pocket is the biggest cavity in CXCR4, and so PELE may tend to place the molecules near it. However, all the compounds presented other feasible binding sites with a comparable binding energy.

      AGR1.135 and AGR1.137 showed interesting poses between TMV and TMVI with very good binding energy (-51.4 and -37.2 kcal/mol, respectively). This was precisely the region we had previously selected for the in silico screening, as previously described (see response to point 3).

      AGR1.131 showed two poses with low binding energy that were placed between helices TMI and TMVII (-43.6 kcal/mol) and between helices TMV and TMVI (-39.8 kcal/mol). This compound was unable to affect CXCL12-mediated chemotaxis and was therefore used as an internal negative control as it was selected in the in silico screening with the same criteria as the other compounds but failed to alter any CXCL12-mediated functions. PELE studies nonetheless provided different binding sites for each molecule, which had to be further studied using docking to obtain a more accurate binding mode. In agreement with the previous commentary, we repeated the analysis using AlphaFold and the rest of the procedure described (see our response to point 6) and calculated the binding energies for all the compounds using Schrodinger’s MM-GBSA procedure (Greenidge P.A. et al. J. Chem. Inf. Model. 2013). Calculations were performed in two ways: first, assuming that the ligand and target are fixed; second, with an energy minimization of all the atoms within a distance of 3Å from the ligand. The results using the first method indicated that AGR1.135 and AGR1.137 showed poses between TMV and TMVI with - 56.4 and -62.4 kcal/mol, respectively and AGR1.131 had a pose between TMI and TMVII with -61.6kcal/mol.  In the second method AGR1.135 and AGR1.137 showed poses between TMV and TMVI with -57.9, and -67.6 kcal/mol, respectively, and AGR1.131 of -62.2 kcal/mol between TMI and TMVII.

      This information is now included in the text.

      (9) (2) Experimental Design:-Justify the choice of treating Jurkat cells with a concentration of 50 μM of the selected compound. Consider exploring different concentrations and provide a rationale for the selected dosage. Additionally, clearly identify the type of small compound used in the initial experiment.

      The revised version contains a new panel in Fig. 1B to show a more detailed kinetic analysis with different concentrations (1-100 µM) of the compounds in the Jurkat migration experiments. In all cases, 100 µM nearly completely abrogated cell migration, but in order to reduce the amount of DMSO added to the cells we selected 50 µM for further experiments, as it was the concentration that inhibits 50-75% of ligand-induced cell migration. Regarding the type of small compounds used in the initial experiments, they were compounds included in the library described in reference #24 (Sebastian-Pérez V. et al Med. Biol. Chem. 2017), which contains heterocyclic compounds. We would note that we do not consider AGR1.137 a final compound. We think that there is scope to develop AGR1.137-based second-generation compounds with greater solubility in water, greater specificity or affinity for CXCR4, and to evaluate delivery methods to hopefully increase activity.  

      (10) Avoid reporting details in rounded parentheses within the text; consider relocating such information to the Materials and Methods section or figure captions for improved readability.

      Most of the rounded parentheses within the text have been eliminated in the revised version of the manuscript to improve readability.

      (11) Elaborate on the virtual screening approach using GLIDE software, specifying the targeted site and methodology employed.

      For the virtual screening, we used the Glide module (SP and XP function scoring) included in the Schrödinger software package, utilizing the corresponding 3D target structure and our MBC library (Sebastián-Pérez V et al. J. Chem. Inf. Model. 2017).  The center of the catalytic pocket was selected as the centroid of the grid. In the grid generation, a scaling factor of 1.0 in van der Waals radius scaling and a partial charge cutoff of 0.25 were used. A rescoring of the SP poses of each compound was then performed with the XP scoring function of the Glide. The XP mode in Glide was used in the virtual screening, the ligand sampling was flexible, epik state penalties were added and an energy window of 2.5 kcal/mol was used for ring sampling. In the energy minimization step, the distance-dependent dielectric constant was 4.0 with a maximum number of minimization steps of 100,000. In the clustering, poses were considered as duplicates and discarded if both RMS deviation is less than 0.5 Å and maximum atomic displacement is less than 1.3 Å.

      (12) Provide clarity on the statement that AGR1.131 "theoretically" binds the same motif, explaining the docking procedure used for this determination.

      In the in silico screening, AGR1.131 was one of the 40 selected compounds that showed, according to the PELE analysis (see answer to point 8), a pose with low binding energy (-39.8 kcal/mol) between TMV and TMVI helices, which is the selected area for the screening. It, nonetheless, also showed a best pose placed between helices TM1 and TM7 (-43.7 kcal/mol) using the initial workflow. In conclusion, although AGR1.131 also faced to the TMV-TMVI, the most favorable pose was in the area between TMI and TMVII. In addition, the compound was included in the biological screening, where it did not affect CXCL12-mediated chemotaxis. We thus decided to use it as an internal negative control, as it has a skeleton very similar to AGR1.135 and AGR1.137 and can interact with the TM domains of CXCR4 without promoting biological effects. This statement has been clarified in the revised text.

      (13) Toxicity Testing:

      -Enhance the explanation of the approach to testing the toxicity of the compound in Jurkat cells. Consider incorporating positive controls to strengthen the assessment and clarify the experimental design.

      All the selected compounds in the in silico screening were initially tested for propidium iodide incorporation in treated cells in a toxicity assay, and some of them were discarded for further experiments (e.g., AGR1.103 and VSP3.1).

      Further evaluation of Jurkat cell viability was determined by cell cycle analysis using propidium iodide.  Supplementary Fig. 1B included the percentage of each cell cycle phase, and data indicated no significant differences between the treatments tested. Nevertheless, at the suggestion of the reviewer, and to clarify this issue, positive controls inducing Jurkat cell death (staurosporine and hydrogen peroxide) have also been included in the new Supplementary Fig. 2. The new figure also includes a table showing the percentage of cells in each cell-cycle phase.  

      (14) In the Results section concerning "AGR1.135 and AGR1.137 blocking CXCL12-mediated CXCR4 nanoclustering and dynamics", several points can be improved to enhance clarity and coherence: 1. Specificity of Low Molecular Weight Compounds:  

      -Clearly articulate how AGR1.135 and AGR1.137 specifically target homodimeric CXCR4 and provide an explanation for their lack of impact on heterodimeric CXCR4-CCR5 in that region.

      First of all, we should clarify that when we talk about receptor nanoclustering, oligomers refer to complexes including 3 or more receptors and, therefore, the residues involved in these interactions can differ from those involved in receptor dimerization. Moreover, our FRET experiments did not indicate that the compounds alter receptor dimerization (see new Supplementary Fig. 7). Of note, mutant receptors unable to oligomerize can still form dimers (Martínez-Muñoz L. et al. Mol. Cell 2018; García-Cuesta E.M .et al. Proc. Natl. Acad. Sci. USA 2022). Additionally, we believe that these oligomers can also include other chemokine receptors/proteins expressed at the cell membrane, which we are currently studying using different models and techniques.

      We have results supporting the existence of CCR5/CXCR4 heterodimers (Martínez-Muñoz L et al. Proc. Natl. Acad. Sci. USA 2014), in line with the data published by Di Marino et al. However, in the current study we have not evaluated the impact of the selected compounds on other CXCR4 complexes distinct from CXCR4 oligomers. Our Jurkat cells do not express CCR5 and, therefore, we cannot discuss whether AGR1.137 affects CCR5/CXCR4 heterodimers. The chemokine field is very complex and most receptors can form dimers (homo- and heterodimers) as well as oligomers (Martinez-Muñoz L., et al Pharmacol & Therap. 2011) when co-expressed. To evaluate different receptor combinations in the same experiment is a complex task, as the number of potential combinations between distinct expressed receptors makes the analysis very difficult. We started with CXCR4 as a model, to continue later with other possible CXCR4 complexes. In addition, for the analysis of CCR5/CXCR4 dynamics, it is much better to use dual-TIRF techniques, which allow the simultaneous detection of two distinct molecules coupled to different fluorochromes.

      Regarding the data of Di Marino et al., it is possible that the compounds might also affect heterodimeric conformations of CXCR4. This aspect has also been broached in the revised discussion. We would again note that we evaluated CXCR4 oligomers and not monomers or dimers; this is especially relevant when we compare the residues involved in these processes as they might differ depending on the receptor conformation considered. This issue was also hypothesized by Di Marino et al. (see our response to point 4).

      (15) When referring to "unstimulated" cells, provide a more detailed explanation to elucidate the experimental conditions and cellular state under consideration.

      Unstimulated cells refer to the cells in basal conditions, that is, cells in the absence of CXCL12. For TIRF-M experiments, transiently-transfected Jurkat cells were plated on glass-bottomed microwell dishes coated with fibronectin; these are the unstimulated cells. To observe the effect of the ligand, dishes were coated as above plus CXCL12 (stimulated cells). We have clarified this point in the material and methods section of the revised version.

      (16) 2. Paragraph Organization

      -Reorganize the second paragraph to eliminate redundancy and improve overall flow. A more concise and fluid presentation will facilitate reader comprehension and engagement.

      The second paragraph has been reorganized to improve overall flow.

      (17) Ensure that each paragraph contributes distinct information, avoiding repetition and redundancy.

      We have carefully revised each paragraph of the manuscript to avoid redundancy.

      (18) 3. Claim of Allosteric Antagonism:

      -Exercise caution when asserting that "AGR1.135 and AGR1.137 behave as allosteric antagonists of CXCR4" based on the presented results. Consider rephrasing to reflect that the observed effects suggest the potential allosteric nature of these compounds, acknowledging the need for further investigations and evidence.

      To avoid misinterpretations on the effect of the compounds on CXCR4, as we have commented in our response to point 2, we have substituted the term allosteric inhibitors with negative allosteric modulators, which refer to molecules that act by binding a site distinct from the orthosteric site, and selectively block some downstream signaling pathways, whereas others induced by the same endogenous or orthosteric agonist are unaffected (Gao Z.-G. & Jacobson K.A. Drug Discov. Today Technol. 2013). Our data indicate that the selected small compounds do not block ligand binding or G protein activation or receptor internalization, but inhibit receptor oligomerization and ligand-mediated directed cell migration.

      (19) In the Results section discussing the "incomplete abolition of CXCR4-mediated responses in Jurkat cells by AGR1.135 and AGR1.137", several points can be refined for better clarity and completeness:  1. Inclusion of Positive Controls: 

      -Consider incorporating positive controls in relevant experiments to provide a comparative benchmark for assessing the impact of AGR1.135 and AGR1.137. This addition will strengthen the interpretation of results and enhance the experimental rigor. 

      The in vivo experiments (Fig. 7E,F) used AMD3100, an orthosteric antagonist of CXCR4, as a positive control. We also included AMD3100, as a positive control of inhibition when evaluating the effect of the compounds on CXCL12 binding (Fig. 3, new Supplementary Fig. 3). The revised version of the manuscript also includes the effect of this inhibitor on other relevant CXCL12-mediated responses such as cell migration (Fig. 1B), receptor internalization (Fig. 3A), cAMP production (Fig. 3C), ERK1/2 and AKT phosphorylation (Supplementary Fig. 4), actin polymerization (Fig. 4A), cell polarization (Fig. 4B, C) and cell adhesion (Fig. 4D), to facilitate the interpretation of the results and improve the experimental rigor.

      (20) 2. Clarification of Terminology: 

      -Clarify the term "CXCR4 internalizes" by providing context, perhaps explaining the process of receptor internalization and its relevance to the study.

      We refer to CXCR4 internalization as a CXCL12-mediated endocytosis process that results in reduction of CXCR4 levels on the cell surface. We use CXCR4 internalization in this study with two purposes: First, for CXCR4 and other chemokine receptors, internalization processes are mediated by ligand-induced clathrin vesicles (Venkatesan et al 2003) a process that triggers CXCR4 aggregation in these vesicles. We have previously determined that the oligomers of receptors detected by TIRF-M remain unaltered in cells treated with inhibitors of clathrin vesicle formation and of internalization processes (Martinez-Muñoz L. et al. Mol. Cell 2018). Moreover, we have described a mutant CXCR4 that cannot form oligomers but internalizes normally in response to CXCL12 (Martinez-Muñoz L. et al. Mol. Cell 2018). The observation in this manuscript of normal CXCL12-mediated endocytosis in the presence of the negative allosteric inhibitors of CXCR4 that abrogate receptor oligomerization reinforces the idea that the oligomers detected by TIRF are not related to receptor aggregates involved in endocytosis; Second, receptor internalization is not affected by the allosteric compounds, indicating that they downregulate some CXCL12-mediated signaling events but not others (new Fig. 3).

      All these data have been included in the revised discussion of the manuscript.

      (21) Elaborate on the meaning of "CXCL12 triggers normal CXCR4mut internalization" to enhance reader understanding.

      We have previously described a triple-mutant CXCR4 (K239L/V242A/L246A; CXCR4mut). The mutant residues are located in the N-terminal region of TMVI, close to the cytoplasmic region, thus limiting the CXCR4 pocket described in this study (see our response to point 3). This mutant receptor dimerizes but neither oligomerizes in response to CXCL12 nor supports CXCL12-induced directed cell migration, although it can still trigger some Ca2+ flux and is internalized after ligand activation (Martinez-Muñoz L. et al. Mol. Cell 2018).  We use the behavior of this mutant (CXCR4mut) to show that the CXCR4 oligomers and the complexes involved in internalization processes are not the same and to explain why we evaluated CXCR4 endocytosis in the presence of the negative allosteric modulators.

      As we indicated in a previous answer to the reviewer, these issues have been re-elaborated in the revised version.

      (22) 3. Discrepancy in CXCL12 Concentration:

      -Address the apparent discrepancy between the text stating, "...were stimulated with CXCL12 (50 nM, 37{degree sign}C)," and the figure caption (Fig. 3A) reporting a concentration of 12.5 nM. Rectify this inconsistency and provide an accurate and clear explanation.

      We apologize for this error, which is now corrected in the revised manuscript. With the exception of the cell migration assays in Transwells, where the optimal concentration was established at 12.5 nM, in the remaining experiments the optimal concentration of CXCL12 employed was 50 nM. These concentrations were optimized in previous works of our laboratory using the same type of experiment. We should also remark that in the experiments using lipid bilayers or TIRF-M experiments, CXCL12 is used to coat the plates and therefore it is difficult to determine the real concentration of the ligand that is retained in the surface of the plates after the washing steps performed prior to adding the cells. In addition, we use 100 nM CXCL12 to create the gradient in the chambers used to perform the directed-cell migration experiments.

      (23) 4. Speculation on CXCL12 Binding:

      -Refrain from making speculative statements, such as "These data suggest that none of the antagonists alters CXCL12 binding to CXCR4," unless there is concrete evidence presented up to that point. Clearly outline the results that support this conclusion.

      Figure 3B and Supplementary Figure 3 show CXCL12-ATTO700 binding by flow cytometry in cells pretreated with the negative allosteric modulators. We have also included AMD3100, the orthosteric antagonist, as a control for inhibition. While these experiments showed no major effect of the compounds on CXCL12 binding, we cannot discard small changes in the affinity of the interaction between CXCL12 and CXCR4. In consequence we have re-written these statements.

      (24) 5. Corroboration of Data:

      -Specify where the corroborating data from immunostaining and confocal analysis are reported, ensuring readers can access the relevant information to support the conclusions drawn in this section.

      In agreement with the suggestion of the reviewer, the revised manuscript includes data from immunostaining and confocal analysis to complement Fig. 4B (new Fig. 4C). The revised version also includes some representative videos for the TIRF experiments showed in Figure 2 to clarify readability.

      (25) In the Results section concerning "AGR1.135 and AGR1.137 antagonists and their direct binding to CXCR4", several aspects need clarification and refinement for a more comprehensive and understandable presentation: 1. Workflow Clarification:

      -Clearly articulate the workflow used for assessing the binding of AGR1.135 and AGR1.137 to CXCR4. Address the apparent contradiction between the inability to detect a direct interaction and the utilization of Glide for docking in the TMV-TMVI cleft.

      To address the direct interaction of the compounds with CXCR4, we intentionally avoided the modification of the small compounds with different labels, which could affect their properties. We therefore attempted a fluorescence a spectroscopy strategy to formally prove the ability of the small compounds to bind CXCR4, but this failed because the AGR1.135 is yellow in color, which interfered with the determinations. We also tried a FRET strategy (see new Supplementary Fig. 7) and detected a significant increase in FRET efficiency of CXCR4 homodimers when AGR1.135 was evaluated, but again the yellow color interfered with FRET determinations. Moreover, AGR1.137 did not modify FRET efficiency of CXCR4 dimers. Therefore, we were unable to detect the interaction of the compounds with CXCR4.

      We elected to develop an indirect strategy; in silico, we evaluated the binding-site using docking and molecular dynamics to predict the most promising CXCR4 binding residues involved in the interaction with the selected compounds. Next, we generated point mutant receptors of the predicted residues and re-evaluated the behavior of the allosteric antagonists in a CXCL12-induced cell migration experiment. Obviously, we first discarded those CXCR4 mutants that were not expressed on the cell membrane as well as those that were not functional when activated with CXCL12. Using this strategy, we eliminated the interference due to the physical properties of the compounds and demonstrated that if the antagonism of a compound is reversed in a particular CXCR4 mutant it is because the mutated residue participates or interferes with the interaction between CXCR4 and the compound, thus assuming (albeit indirectly) that the compound binds CXCR4. 

      To select the specific mutations included in the analysis, our strategy was to generate point mutations in residues present in the TMV-TMVI pocket of CXCR4 that were not directly proposed as critical residues involved in chemokine engagement, signal initiation, signal propagation, or G protein-binding, based on the extensive mutational study published by Wescott MP et. al. (Wescott M.P. et. al. Proc. Natl. Acad. Sci. U S A. 2016).

      (26) Provide a cohesive explanation of the transition from docking evaluation to MD analysis, ensuring a transparent representation of the methodology.

      Based on the aim of this work, the workflow shown in Author response image 2, was proposed to predict the binding mode of the selected molecules. Firstly, a CXCR4 model was generated to reconstruct some unresolved parts of the protein structure; then a binding site search using PELE software was performed to identify the most promising binding sites; subsequently, docking studies were performed to refine the binding mode of the molecules; and finally, molecular dynamics simulations were run to determine the most stable poses and predict the residues that we should mutate to test that the compounds interact with CXCR4. 

      Author response image 2.

      Workflow followed to determine the binding mode of the  studied compounds.

      (27) 2. Choice of Software and Techniques:

      -Justify the use of "AMBER14" and the PELE approach, considering  their potential obsolescence.

      These experiments were performed five years ago when the project was initiated. As the reviewer indicates, AMBER14 and PELE approaches might perhaps be considered obsolescent. Thus, we have predicted the structure of the target using AlphaFold (Jumper J. et al, Nature 2021) and the sequence available under UniProt entry P61073. The complete analysis performed (see our response to point 4) confirmed that the compounds bound the selected pocket, as we had originally determined using PELE. These new analyses have been incorporated into the revised manuscript.

      (28)-Discuss the role of the membrane in the receptor-ligand interac7on. Elaborate on how the lipidic double layer may influence the binding of small compounds to GPCRs embedded in the membrane.

      Biological membranes are vital components of living organisms, providing a diffusion barrier that separates cells from the extracellular environment, and compartmentalizing specialized organelles within the cell. In order to maintain the diffusion barrier and to keep it electrochemically sealed, a close interaction of membrane proteins with the lipid bilayer is necessary. It is well known that this is important, as many membrane proteins undergo conformational changes that affect their transmembrane regions and that may regulate their activity, as seen with GPCRs (Daemen F.J. & Bonting S.L., Biophys. Struct. Mech. 1977; Gether U. et al. EMBO J. 1997). The lateral and rotational mobility of membrane lipids supports the sealing function while allowing for the structural rearrangement of membrane proteins, as they can adhere to the surface of integral membrane proteins and flexibly adjust to a changing microenvironment. In the case of the first atomistic structure of CXCR4 (Wu B. et al. Science 2010), it was indicated that for dimers, monomers interact only at the extracellular side of helices V and VI, leaving at least a 4-Å gap between the intracellular regions, which is presumably filled by lipids. In particular, they indicated that the channel between TMV and TMVI that connects the orthosteric chemokine binding pocket to the lipid bilayer is occupied by an oleic acid molecule. Recently, Di Marino et al., analyzing the dimeric structure of CXCR4, found a cholesterol molecule placed in between the two protomers, where it engages a series of hydrophobic interactions with residues located in the area between TMI and TMVI (Leu132, Val214, Leu216, Leu246, and Phe249). The polar head of cholesterol forms an H-bond with Tyr135 that further stabilizes its binding mode. This finding confirms that cholesterol might play an important role in mediating and stabilizing receptor dimerization, as seen in other GPCRs (Pluhackova, K., et al. PLoS Comput. Biol. 2016). In addition, we have previously observed that, independently of the structural changes on CXCR4 triggered by lipids, the local lipid environment also regulates CXCR4 organization, dynamics and function at the cell membrane and modulates chemokine-triggered directed cell migration. Prolonged treatment of T cells with bacterial sphingomyelinase promoted the complete and sustained breakdown of sphingomyelins and the accumulation of the corresponding ceramides, which altered both membrane fluidity and CXCR4 nanoclustering and dynamics. Under these conditions, CXCR4 retained some CXCL12-mediated signaling activity but failed to promote efficient directed cell migration (Gardeta S.R. et al. Front. Immunol. 2022). Collectively, these data demonstrate the key role that lipids play in the stabilization of CXCR4 conformations and in regulating its lateral mobility, influencing their associated functions. These considerations have been included in the revised version of the manuscript. 

      (29) 3. Stable Trajectories and Binding Mode Superimposi7on -Specify the criteria for defining "stable trajectories" to enhance reader understanding

      There could be several ways to describe the stability of a MD simulation, based on the convergence of energies, distances or ligand-target interactions, among others. In this work, we use the expression “stable trajectories” to refer to simulations in which the ligand trajectory converges and the ligand RMSD does not fluctuate more than 0.25Å. This definition is now included in the revised text.

      (30)  Clarify the meaning behind superimposing the two small compounds and ensure that the statement in the figure caption aligns with the information presented in the main text.

      We apologize for the error in the previous Fig. 5A and in its legend. The figure was created by superimposing the protein component of the poses for the two compounds, AGR1.135 and AGR1.137, rather than the compounds themselves. As panel 5A was confusing, we have modified all Fig. 5 in the revised manuscript to improve clarity.

      (31) 4. Volume Analysis and Distances:

      -Provide details on how the volume analysis was computed and how distances were accounted for. Consider adding a figure to illustrate these analyses, aiding reader comprehension.

      The cleft search and analysis were performed using the default settings of SURFNET (Laskowski R.A. J. Mol. Graph. 1995) included in the PDBsum server (Laskowski R.A. et. al. Trends Biochem. Sci. 1997). The first run of the input model for CXCR4 3ODU identified a promising cleft of 870 Å3 in the lower half of the region flanked by TMV and TMVI, highlighting this area as a possible small molecule binding site (Fig. I, only for review purposes). Analysis of the cleft occupied by AGR1.135 showed two independent cavities of 434 Å3 and 1381 Å3 that were not connected to the orthosteric site. The same procedure for AGR1.137 revealed two distinct clefts of 790 Å3 and 580 Å3, respectively (Fig. I, only for review purposes). Analysis of the atomic distances between the protein residues and the compounds was performed using the PISA server. Krissinel E. & Henrick K. J. Mol. Biol. 2007). (Please see our response to point 3 and the corresponding figure).

      (32) 5. Mutant Selection and Relevance:

      -Clarify the rationale behind selecting the CXCR4 mutants used in the study. Consider justifying the choice and exploring the possibility of performing an alanine (ALA) scan for a more comprehensive mutational analysis.  

      The selection of the residues to be mutated along the cleft was first based on their presence in the proposed cleft and the direct interaction of the compounds with them, either by hydrogen bonding or by hydrophobic interactions. Secondly, all mutated residues did not belong to any of the critical residues involved in transmitting the signal generated by the interaction of CXCL12 with the receptor. In any case, mutants producing a non-functional CXCR4 at the cell membrane were discarded after FACS analysis and chemotaxis experiments. Finally, the length and nature of the resulting mutations were designed mainly to occlude the cleft in case of the introduction of long residues such as lysines (I204K, L208K) or to alter hydrophobic interactions by changing the carbon side chain composition of the residues in the cleft. Indeed, we agree that the alanine scan mutation analysis would have been an alternative strategy to evaluate the residues involved in the interactions of the compounds. 

      (33) Reevaluate the statement regarding the relevance of the Y256F muta7on for the binding of AGR1.137. If there is a significant impact on migra7on in the mutant (Fig. 6B), elaborate on the significance in the context of AGR1.137 binding.

      In the revised discussion we provide more detail on the relevance of Y256F mutation for the binding of AGR1.137 as well as for the partial effect of G207I and R235L mutations. The predicted interactions for each compound are depicted in new Fig. 6 C, D after LigPlot+ analysis (Laskowski R.A. & Swindells M.B. J. Chem. Inf. Model. 2011), showing that AGR1.135 interacted directly with the receptor through a hydrogen bond with Y256. When this residue was mutated to F, one of the anchor points for the compound was lost, weakening the potential interaction in the region of the upper anchor point.

      It is not clear how the Y256F mutation will affect the binding of AGR1.137, but other potential contacts cannot be ruled out since that portion of the compound is identical in both AGR1.135 and AGR1.137. This is especially true for its neighboring residues in the alpha helix, F249, L208, as shown in 3ODU structure (Fig. 6D), which are shown to be directly implicated in the interaction of both compounds. Alternatively, we cannot discard that Y256 interacts with other TMs or lipids stabilizing the overall structure, which could reverse the effect of the mutant at a later stage (Author response image 3).

      Author response image 3.

      Cartoon representation of Y256 and its intramolecular interactions in the CXCR4 Xray solved structure 3ODU. TMV helix is colored in blue and TMVI in pink.

      (34) Address the apparent discrepancy in residue involvement between AGR1.135 and AGR1.137, particularly if they share the same binding mode in the same clef.

      AGR1.135 and AGR1.137 exhibit comparable yet distinct binding modes, engaging with CXCR4 within a molecular cavity formed by TMV and TMVI. AGR1.135 binds to CXCR4 through three hydrogen bonds, two on the apical side of the compound that interact with residues TMV-G207 and TMVI-Y256 and one on the basal side that interacts with TMVI-R235 (Fig. 5A). This results in a more extended and rigid conformation when sharing hydrogen bonds, with both TMs occupying a surface area of 400 Å2 and a length of 20 Å in the cleft between TMV and TMVI (Supplementary Fig. 8A). AGR1.137 exhibits a distinct binding profile, interacting with a more internal region of the receptor. This interaction involves the formation of a hydrogen bond with TMIIIV124, which induces a conformational shift in the TMVI helix towards an active conformation (Fig. 5B; Supplementary Fig. 13). Moreover, AGR1.137 may utilize the carboxyl group of V124 in TMIII and overlap with AGR1.135 binding in the cavity, interacting with the other 19 residues dispersed between TMV and VI to create an interaction surface of 370 Å2 along 20 Å (Supplementary Fig. 8B). This is illustrated in the new Fig. 5B. AGR1.137 lacks the phenyl ring present in AGR1.135, resulting in a shorter compound with greater difficulty in reaching the lower part of TMVI where R235 sits. 

      Author response image 4.

      AGR1.135 and AGR1.137 interaction with TMV and TMVI.  The model shows the location of the compounds within the TMV-VI cleft, illustrated by a ribbon and stick representation. The CXCR4 segments of TMV and TMVI are represented in blue and pink ribbons respectively, and side chains for some of the residues defining the cavity are shown in sticks. AGR1.135 and AGR1.137 are shown in stick representation with carbon in yellow, nitrogen in blue, oxygen in red, and fluorine in green. Hydrogen bonds are indicated by dashed black lines, while hydrophobic interactions are shown in green. The figure reproduces the panels A, B of Fig. 5 in the revised manuscript.

      (35) In the Results sec7on regarding "AGR1.137 treatment in a zebrafish xenograf model", the following points can be refined for clarity and completeness: 1. Cell Line Choice for Zebrafish Xenograft Model:

      -Explain the rationale behind the choice of HeLa cells for the zebrafish xenograft model when the previous experiments primarily focused on Jurkat cells. Address any specific biological or experimental considerations that influenced this decision.

      As far as we know, there are no available models of tumors in zebrafish using Jurkat cells. We looked for a tumoral cell system that expresses CXCR4 and could be transplanted into zebrafish. HeLa cells are derived from a human cervical tumor, express a functional CXCR4, and have been previously used for tumorigenesis analyses in zebrafish (Brown H.K. et al. Expert Opin. Drug Discover. 2017; You Y. et al Front. Pharmacol. 2020). These cells grow in the fish and disseminate through the ventral area and can be used to determine primary tumor growth and metastasis. Nonetheless, we first analyzed in vitro the expression of a functional CXCR4 in these cells (Supplementary Fig. 10A), whether AGR1.137 treatment specifically abrogated CXCL12-mediated direct cell migration (Fig. 7A, B), as whether it affected cell proliferation (Supplementary Fig. 10B). As HeLa cells reproduce the in vitro effects detected for the compounds in Jurkat cells, we used this model in zebrafish. These issues were already discussed in the first version of our manuscript. 

      (36) 2. Toxicity Assessment in Zebrafish Embryos: 

      -Clarify the basis for stating that AGR1.137 is not toxic to zebrafish embryos. Consider referencing the Zebrafish Embryo Acute Toxicity Test (ZFET) and provide relevant data on lethal concentration (LC50) and non-lethal toxic phenotypes such as pericardial edema, head and tail necrosis, malformation, brain hemorrhage, or yolk sac edema.

      Tumor growth and metastasis kinetics within the zebrafish model have been extensively evaluated in many publications (White R. et al. Nat. Rev. Cancer. 2013; Astell K.R. and Sieger D. Cold Spring Harb. Perspect. Med. 2020; Chen X. et al. Front. Cell Dev. Biol. 2021; Weiss JM. Et al. eLife 2022; Lindhal G. et al NPJ Precis. Oncol. 2024). Our previous experience using this model shows that tumors start having a more pronounced proliferation and lower degree of apoptosis from day 4 onwards, but we cannot keep the tumor-baring larvae for that long due to ethical reasons and also because we don’t see much scientific benefit of unnecessarily extending the experiments. Anti-proliferative or pro-apoptotic effects of drugs can still be observed within the three days, even if this is then commonly seen as larger reduction (instead of a smaller growth as it is commonly seen in for example mouse tumor models) compared to controls. Initially we characterized the evolution of implanted tumors in our system and how much they metastasize over time in the absence of treatment before to test the compounds (Author response image 5).

      The in vivo experiments were planned to validate efficacious concentrations of the investigated drugs rather than to derive in vivo IC50 or other values, which require testing of multiple doses. We have, however, included an additional concentration to show concentration-dependence and therefore on-target specificity of the drugs in the revised version of the manuscript (data also being elaborated in ongoing experiments). At this stage, we believe that adding the LC50 does not provide interesting new knowledge, and it is standard to only show results from the experimental endpoint (in our case 3 days post implantation). We agree that showing these new data points strengthens the manuscript and facilitates independent evaluation and conclusions to be drawn from the presented data. We have created new graphs where datapoints for each compound dose are shown.  

      Author response image 5.

      Evolution of the tumors and metastasis along the time in the absence of any treatment. HeLa cells were labeled with 8 µg/mL Fast-DiI™ oil and then implanted in the dorsal perivitelline space of 2-days old zebrafish embryos. Tumors were imaged within 2 hours of implantation and re-imaged each 24 h for three days. Changes in tumor size was evaluated as tumor area at day 1, 2 and 3 divided by tumor area at day 0, and metastasis was evaluated as the number of cells disseminated to the caudal hematopoietic plexus at day 1, 2 and 3 divided by the number of cells at day  3.

      Regarding the statement that AGR1.137 was not toxic, this was based on visual inspection of the zebrafish larvae at the end of the experiment, which also revealed a lack of drug-related mortality in these experiments. There are a number of differences in how our experiment was run compared with the standardized ZFET. ZFET evaluates toxicity from 0 hours post-fertilization to 1 or 2 days post-fertilization, whereas here we exposed zebrafish from 2 days post-fertilization to 5 days post-fertilization. The ZFET furthermore requires that the embryos are raised at 26ºC whereas kept the temperature as close as possible to a physiologically relevant temperature for the tumor cells (36ºC). In the ZFET, embryos are incubated in 96-well plates whereas for our studies we required larger wells to be able to manipulate the larvae and avoid well edge-related imaging artefacts, and we therefore used 24-well plates. As such, the ZFET was for various reasons not applicable to our experimental settings. As we were not interested in rigorously determining the LD50 or other toxicity-related measurements, as our focus was instead on efficacy and we found that the targeted dose was tolerated, we did not evaluate multiple doses, including lethal doses of the drug, and are therefore not able to determine an LD50/LC50. We also did not find drug-induced non-lethal toxic phenotypes in this study, and so we cannot elaborate further on such phenotypes other than to simply state that the drug is well tolerated at the given doses. Therefore, the reference to ZFET in the manuscript was eliminated.

      (37) If supplementary information is available, consider providing it for a comprehensive understanding of toxicity assessments. 

      The effective concentration used in the zebrafish study was derived from the in vitro experiments. That being said, and as elaborated in our response to comment 36, we have added data for one additional dose to show the dose-dependent regulation of tumor growth and metastasis. 

      (38) 3. Optimization and Development of AGR1.137: 

      -Justify the need for further optimization and development of AGR1.137 if it has a comparable effect to AMD3100. Explain the specific advantages or improvements that AGR1.137 may offer over AMD3100. 

      AGR1.137 is highly hydrophobic and is very difficult to handle, particularly in in vivo assays; thus, for the negative allosteric modulators to be used clinically, it would be very important to increase their solubility in water. Contrastingly, AMD3100 is a water-soluble compound. Before using the zebrafish model, we performed several experiments in mice using AGR1.137, but the inhibitory results were highly variable, probably due to its hydrophobicity. We also believe that it would be important to increase the affinity of AGR1.137 for CXCR4, as the use of lower concentrations of the negative allosteric modulator would limit potential in vivo side effects of the drug. On the other hand, we are also evaluating distinct administration alternatives, including encapsulation of the compounds in different vehicles. These alternatives may also require modifications of the compounds. 

      AMD3100 is an orthosteric inhibitor and therefore blocks all the signaling cascades triggered by CXCL12. For instance, we observed that AMD3100 treatment blocked CXCL12 binding, cAMP inhibition, calcium flux, cell adhesion and cell migration (Fig. 3, Fig. 4), whereas the effects of AGR1.137 were restricted to CXCL12-mediated directed cell migration. Although AMD3100 was well tolerated by healthy volunteers in a singledose study, it also promoted some mild and reversible events, including white blood cells count elevations and variations of urine calcium just beyond the reported normal range (Hendrix C.W. et al. Antimicrob. Agents Chemother. 2000). To treat viral infections, continuous daily dosing requirements of AMD3100 were impractical due to severe side effects including cardiac arrhythmias (De Clercq E. Front Immunol. 2015). For AMD3100 to be used clinically, it would be critical to control the timing of administration. In addition, side effects after long-term administration have potential problems. Shorter-term usage and lower doses would be fundamental keys to its success in clinical use (Liu T.Y. et al. Exp. Hematol. Oncol. 2016). The use of a negative allosteric modulator that block cell migration but do not affect other signaling pathways triggered by CXCL12 would be, at least in theory, more specific and produce less side effects. These ideas have been incorporated into the revised discussion to reflect potential advantages or improvements that AGR1.137 may offer over AMD3100.

      (39) 4. Discrepancy in AGR1.137 and AMD3100 Effects:

      -Discuss the observed discrepancy where AGR1.137 exhibits similar effects to AMD3100 but only after 48 hours. Provide insights into the temporal dynamics of their actions and potential implications for the experimental design.

      Images and data shown in Fig. 7E, F correspond to days 0 and 3 after HeLa cell implantation (tumorigenesis) and only to day 3 in the case of metastasis data. The revised version contains the effect of two distinct doses of the compounds (10 and 50 µM, for AGR1.135 and AGR1.137 and 1 and 10 µM for AMD3100). 

      (40) In the "Discussion" section, there are several points that require clarifica7on and refinement to enhance the overall coherence and depth of the analysis:  1. Reduction of Side-Effects: 

      -Provide a more detailed explanation of how the identified compounds, specifically AGR1.135 and AGR1.137, contribute to the reduction of side effects. Consider discussing specific mechanisms or characteristics that differentiate these compounds from existing antagonists.

      The sentence indicating that AGR1.135 and AGR1.137 contribute to reduce side effects is entirely speculative, as we have no experimental evidence to support it. We have therefore corrected this in the revised version. The origin of the sentence was that orthosteric antagonists typically bind to the same site as the endogenous ligand, thus blocking its interaction with the receptor. Therefore, orthosteric inhibitors (i.e. AMD3100) block all signaling cascades triggered by the ligand and therefore their functional consequences. However, the compounds described in this project are essentially negative allosteric modulators, that is, they bind to a site distinct from the orthosteric site, inducing a conformational change in the receptor that does not alter the binding of the endogenous ligand, and therefore block some specific receptor-associated functions without altering others. We observed that AGR1.137 blocked receptor oligomerization and directed cell migration whereas CXCL12 still bound CXCR4, triggered calcium mobilization, did not inhibit cAMP release or promoted receptor internalization. This is why we speculated on the limitation of side effects. The statements have been nonetheless revised in the new version of the manuscript.

      (41) 2. Binding Site Clarification:

      -Address the apparent discrepancy between docking the small compounds in a narrow cleft formed by TMV and TMVI helices and the statement that AGR1.131 binds elsewhere. Clarify the rationale behind this assertion

      After the in silico screening, a total of 40 compounds were selected.  These compounds showed distinct degrees of interaction with the cleft formed by TMV and TMVI and even with other potential interaction sites on CXCR4, with the exception of the ligand binding site according to the data described by Wescott et al. (PNAS 2016 113:9928-9933), as this possibility was discarded in the initial approach of the in silico screening. According to PELE analysis, AGR1.131 was one of the 40 selected compounds that showed a pose with low binding energy, -39.8 kcal/mol, between TMV and TMVI helices, that is, it might interact with CXCR4 through the selected area for the screening. It nonetheless also showed a best pose placed between helices TMI and TMVII, -43.7 kcal/mol. In any case, the compound was included in the biological screening, where it was unable to impact CXCL12-mediated chemotaxis (Fig. 1B). We then focused on AGR1.135 and AGR1.137, as showed a higher inhibitory effect on CXCL12-mediated migration, and on AGR1.131 as an internal negative control. AGR1.131 has a skeleton very similar to the other compounds (Fig. 1C) and can interact with the TM domains of CXCR4 without promoting effects. None of the three compounds affected CXCL12 binding, or CXCL12mediated inhibition of cAMP release, or receptor internalization. However, whereas AGR1.135 and AGR1.137, blocked CXCL12-mediated CXCR4 oligomerization and directed cell migration towards CXCL12 gradients, AGR1.131 had no effect in these experiments (Fig. 3, Fig.  4). 

      Next, we performed additional theoretical calculations (PELE, docking, MD) to inspect in detail the potential binding modes of active and inactive molecules. Based on these additional calculations, we identified that whereas AGR1.135 and AGR1.137 showed preferent binding on the molecular pocket between TMV and TMVI, the best pose for AGR1.131 was located between TMI and TMVII, as the initial experiments indicated.  These observations and data have been clarified in the revised discussion. 

      (42) 3. Impact of Chemical Modifications:

      -Discuss the consequences of the distinct chemical groups in AGR1.135, AGR1.137, and AGR1.131, specifically addressing how variations in amine length and chemical nature may influence binding affinity and biological activity. Provide insights into the potential effects of these modifications on cellular responses and the observed outcomes in zebrafish. 

      The main difference between AGR1.131 and the other two compounds is the higher flexibility of AGR1.131 due to the additional CH2 linker, together with the lack of a piperazine ring. The additional CH2 linking the phenyl ring increases the flexibility of AGR1.131 when compared with AGR1.135 and AGR1.137, and the absence of the piperazine ring might be responsible for its lack of activity, as it makes this compound able to bind to CXCR4 (Fig. 1C).

      AGR1.137 was chosen in a second round. The additional presence of the tertiary amine (in the piperazine ring) allows the formation of quaternary ammonium salts in the aqueous medium and its substituents to increase its solubility (Fig 1C). This characteristic might be related to the absence of toxic effects of the compound in the zebrafish model.

      (43) 4. Existence of Distinct CXCR4 Conformational States: 

      -Provide more detailed support for the statement suggesting the "existence of distinct CXCR4 conformational states" responsible for activating different signaling pathways. Consider referencing relevant studies or experiments that support this claim.

      Classical models of GPCR allostery and activation, which describe an equilibrium between a single inactive and a single signaling-competent active conformation, cannot account for the complex pharmacology of these receptors. The emerging view is that GPCRs are highly dynamic proteins, and ligands with varying pharmacological properties differentially modulate the balance between multiple conformations.

      Just as a single photograph from one angle cannot capture all aspects of an object in movement, no one biophysical method can visualize all aspects of GPCR activation. In general, there is a tradeoff between high-resolution information on the entire protein versus dynamic information on limited regions. In the former category, crystal and cryo-electron microscopy (cryoEM) structures have provided comprehensive, atomic-resolution snapshots of scores of GPCRs both in inactive and active conformations, revealing conserved conformational changes associated with activation. However, different GPCRs vary considerably in the magnitude and nature of the conformational changes in the orthosteric ligand-binding site following agonist binding (Venkatakrishnan A.J.V. et al. Nature 2016). Spectroscopic and computational approaches provide complementary information, highlighting the role of conformational dynamics in GPCR activation (Latorraca N.R.V. et al. Chem. Rev 2017). In the absence of agonists, the receptor population is typically dominated by conformations closely related to those observed in inactive-state crystal structures (Manglik A. et al. Cell 2015). While agonist binding drives the receptor population towards conformations similar to those in activestate structures, a mixture of inactive and active conformations remains, reflecting “loose” or incomplete allosteric coupling between the orthosteric and transducer pockets (Dror R.O. et al. Proc. Natl. Acad. Sci. USA 2011). Surprisingly, for some GPCRs, and under some experimental conditions, a substantial fraction of unliganded receptors already reside in an active-like conformation, which may be related to their level of basal or constitutive signaling (Staus D.P. et al. J. Biol. Chem. 2019);  Ye L. et al. Nature 2016).  In our case, the negative allosteric modulators, (Staus DP, et al. J. Biol. Chem 2019); Ye L. et al. Nature 2016) did not alter ligand binding and had only minor effects on specific CXCL12-mediated functions such as inhibition of cAMP release or receptor internalization, among others, but failed to regulate CXCL12-mediated actin dynamics and receptor oligomerization. Collectively, these data suggest that the described compounds alter the active conformation of CXCR4 and therefore support the presence of distinct receptor conformations that explain a partial activation of the signaling cascade.

      All these observations are now included in the revised discussion of the manuscript.

      (44) 5. Equilibrium Shift and Allosteric Ligands: 

      -Clarify the statement about "allosteric ligands shifting the equilibrium to favor a particular receptor conformation". Support this suggestion with references or experimental evidence

      In a previous answer (see our response to point 2), we explain why we define the compounds as negative allosteric modulators. These compounds do not bind the orthosteric binding site or a site distinct from the orthosteric site that alters the ligand-binding site. Their effect should be due to changes in the active conformation of CXCR4, which allow some signaling events whereas others are blocked. Our functional data thus support that through the same receptor the compounds separate distinct receptor-mediated signaling cascades, that is, our data suggest that CXCR4 has a conformational heterogeneity. It is known that GPCRs exhibit more than one “inactive” and “active” conformation, and the endogenous agonists stabilize a mixture of multiple conformations. Biased ligands or allosteric modulators can achieve their distinctive signaling profiles by modulating this distribution of receptor conformations. (Wingler L.M. & Lefkowitz R.J. Trends Cell Biol. 2020). For instance, some analogs of angiotensin II do not appreciably activate Gq signaling (e.g., increases in IP3 and Ca2+) but still induce receptor phosphorylation, internalization, and mitogen-activated protein kinase (MAPK) signaling (Wei H, et al. Proc. Natl. Acad. Sci. USA 2003). Some of these ligands activate Gi and G12 in bioluminescence resonance energy transfer (BRET) experiments (Namkung Y. et al. Sci. Signal. 2018). A similar observation was described in the case of CCR5, where some chemokine analogs promoted G protein subtype-specific signaling bias (Lorenzen E. et al. Sci. Signal 2018). Structural analysis of distinct GPCRs in the presence of different ligands vary considerably in the magnitude and nature of the conformational changes in the orthosteric ligand-binding site following agonist binding (Venkatakrishnan A.J.V. et al. Nature 2016). Yet, these changes modify conserved motifs in the interior of the receptor core and induce common conformational changes in the intracellular site involved in signal transduction. That is, these modifications might be considered distinct receptor conformations. 

      The revised discussion contains some of these interpretations to support our statement about the stabilization of a particular receptor conformation triggered by the negative allosteric modulators. 

      (45) 6. Refinement of Binding Mode: 

      -Clarify the workflow for obtaining the binding mode, particularly the role of GLIDE and PELE. Clearly explain how these software tools were used in tandem to refine the binding mode. 

      The computational sequential workflow applied in this project included, i) Protein model construction, ii) Virtual screening (Glide), iii) PELE, iv) Docking (AutoDock and Glide) and v) Molecular Dynamics (AMBER).

      Glide was applied for the structure-based virtual screening to explore which compounds could fit and interact with the previously selected binding site.

      After the identification of theoretically active compounds (modulators of CXCR4), additional calculations were done to identify a potential binding site. PELE was used in this sense, to study how the compounds could bind in the whole surface of the target (TMV-TMVI). By applying PELE, we avoided biasing the calculation, and we found that the trajectories with better interaction energies identified the cleft between TMV and TMVI as the binding site for AGR1.135 and AGR1.137, and not for AGR1.131. AGR1.131 showed a pose with low binding energy, -39.8 kcal/mol, between TMV and TMVI helices, that is, it might interact with CXCR4 in the selected area for the screening. But it also showed a better pose placed between helices TMI and TMVII, - 43.7 kcal/mol (see our response to point 41). These data have been now confirmed using Schrodinger’s MM-GBSA procedure (see our response to points 6 and 8). In any case, the compound was included in the biological screening, where it was unable to affect CXCL12-mediated chemotaxis (Fig. 1B). Docking and MD simulations were then performed to study and refine the specific binding mode in this cavity. These data were important to choose the mutations on CXCR4 required, to test whether the compounds reversed its behavior. In these experiments we also confirmed that AGR1.131 had a better pose on the TMI-TMVII region. 

      (46) 7. Impact of Compound Differences on CXCR4-F249L mutant: 

      -Provide visual aids, such as figures, and additional experiments to support the statement about differences in the behavior of AGR1.135 and AGR1.137 on cells expressing CXCR4-F249L mutant. Elaborate on the closer interaction suggested between the triazole group of AGR1.137 and the F249 residue

      At the reviewer’s suggestion, Fig. 5 has been modified to incorporate a closer view of the interactions identified and new panels in new Fig. 6 have been added to show in detail the effect of the mutations selected on the structure of the cleft between TMV and TMVI. The main difference between AGR1.135 and AGR1.137 is how the triazole group interacts with F249 and L216 (Author response image 6). In AGR1.137, the three groups are aligned in a parallel organization, which appears to be more effective: This might be due to a better adaptation of this compound to the cleft since there is only one hydrogen bond with V124. In AGR1.135, the compound interacts with the phenyl ring of F249 and has a stronger interaction at the apical edge to stabilize its position in the cleft. However, there is still an additional interaction present. When changing F249

      Author response image 6.

      Cartoon representation of the interaction of CXCR4 F249L mutant with AGR1.135 (A) and AGR1.137 (B). The two most probable conformations of Leucine rotamers are represented in cyan A and B conformations. Van der Waals interactions are depicted in blue cyan dashed lines, hydrogen bonds in black dashed lines. CXCR4 segments of TMV and TMVI are colored in blue and pink, respectively

      to L (Fig. VIIA, B, only for review purposes) and showing the two most likely rotamers resulting from the mutation, it is observed that rotamer B is in close proximity to the compound, which may cause the binding to either displace or adopt an alternative conformation that is easier to bind into the cleft. As previously mentioned, it is likely that AGR1.135 can displace the mutant rotamer and bind into the cleft more easily due to its higher affinity.

      (47) In the "Materials and Methods" section, the computational approach for the "discovery of CXCR4 modulators" requires significant revision and clarification. The following suggestions aim to address the identified issues: 1. Structural Modeling: 

      -Reconsider the use of SWISS-MODEL if there is an available PDB code for the entire CXCR4 structure. Clearly articulate the rationale for choosing one method over the other and explain any limitations associated with the selected approach. 

      The SWISS-model server allows for automated comparative modeling of 3D protein structures that was pioneered in the fields of automated modeling. At the time we started this project. it was the most accurate method to generate reliable 3D protein structure models.

      As explained above, we have now predicted the structure of the target using AlphaFold (Jumper J. et al, Nature 2021) and performed several additional experiments that confirm that the small compounds bind the selected pocket as the original strategy indicated (see our response to point 6). (Fig. II, only for review purposes).

      (48) 2. Parametriza7on of Small Compounds: 

      -Provide a detailed description of the parametrization process for the small compounds used in the study. Specify the force field and parameters employed, considering the obsolescence of AMBER14 and ff14SB. Consider adopting more contemporary force fields and parameterization strategies. 

      When we performed these experiments, some years ago, the force fields applied (ff14SB, AMBER14 used in MD or OPLS2004 in docking with Glide) were well accepted and were gold standards. It is, however, true that the force fields have evolved in the past few years, Moreover, in the case of the MD simulations, to consider the parameters of the ligands that are not contained within the force field, we performed an additional parameterization as a standard methodology. We then generated an Ab initio optimization of the ligand geometry, defining as basis sets B3LYP 6-311+g(d), using Gaussian 09, Revision A.02, and then a single point energy calculation of ESP charges, with HF 6311+g(d) on the optimized structure. As the last step of the parametrization, the antechamber module was used to adapt these charges and additional parameters for MD simulations.

      (49) 3. Treatment of Lipids and Membrane: 

      -Elaborate on how lipids were treated in the system. Clearly describe whether a membrane was included in the simulations and provide details on its composition and structure. Address the role of the membrane in the study and its relevance to the interactions between CXCR4 and small compounds 

      To stabilize CXCR4 and more accurately reproduce the real environment in the MD simulation, the system was embedded in a lipid bilayer using the Membrane Builder tool (Sunhwan J. et al. Biophys. J. 2009) from the CHARMM-GUI server. The membrane was composed of 175 molecules of the fatty acid 1-palmitoyl-2-oleoyl-sn-glycero-3phosphocholine (POPC) in each leaflet. The protein-membrane complex was solvated with TIP3 water molecules. Chloride ions were added up to a concentration of 0.15 M in water, and sodium ions were added to neutralize the system. This information was previously described in detail.

      (50) 4. Molecular Dynamics Protocol: 

      -Provide a more detailed and coherent explanation of the molecular dynamics protocol. Clarify the specific steps, parameters, and conditions used in the simulations. Ensure that the protocol aligns with established best practices in the field.

      Simulations were calculated on an Asus 1151 h170 LVX-GTX-980Ti workstation, with an Intel Core i7-6500 K Processor (12 M Cache, 3.40 GHz) and 16 GB DDR4 2133 MHz RAM, equipped with a Nvidia GeForce GTX 980Ti available for GPU (Graphics Processing Unit) computations. MD simulations were performed using AMBER14 (Case D.A. et al. AMBERT 14, Univ. of California, San Francisco, USA, 2014) with ff14SB (Maier J.A. et al. J. Chem. Theory Comput. 2015) and lipid14 (Dickson C. J. et al. J. Chem. Theory Comput. 2014) force fields in the NPT thermodynamic ensemble (constant pressure and temperature). Minimization was performed using 3500 Steepest Descent steps and 4500 Conjugate Gradient steps three times, firstly considering only hydrogens, next considering only water molecules and ions, and finally minimizing all atoms. Equilibration raises system temperature from 0 to 300 K at a constant volume fixing everything but ions and water molecules. After thermalization, several density equilibration phases were performed. In the production phase, 50 ns MD simulations without position restraints were calculated using a time step of 2 fs. Trajectories of the most interesting poses were extended to 150 ns. All bonds involving hydrogen atoms were constrained with the SHAKE algorithm (Lippert R.A. et al. J. Chem. Phys. 2007). A cutoff of 8 Å was used for the Lennard-Jones interaction and the short-range electrostatic interactions. Berendsen barostat (Berendsen H.J. et al. J. Chem. Phys.  1984) and Langevin thermostat were used to regulate the system pression and temperature, respectively. All trajectories were processed using CPPTRAJ (Roe D.R. & Cheatham III T.E. J. Chem. Theory Comput. 2013) and visualized with VMD (Visual Molecular Dynamics) (Humphrey W. et al. J. Mol. Graphics. 1996). To reduce the complexity of the data, Principal Component Analysis (PCA) was performed on the trajectories using CPPTRAJ.

      (51) Consider updating the molecular dynamics protocol to incorporate more contemporary methodologies, considering advancements in simulation techniques and software.

      In our answer to points 6 and 47, we describe why we use the technology based on Swiss-model and PELE analysis and how we have now used Alphafold and other more contemporary methodologies to confirm that the small compounds bind the selected pocket.

      (52) Figure 1A: 

      •  Consider switching to a cavity representation for CXCL12 to enhance clarity and emphasize the cleft.

      Fig. 1A has been modified to emphasize the cleft.

      (53) Explicitly show the TMV-TMVI cleft in the figure for a more comprehensive visualization. 

      In Fig. 1A we have added an insert to facilitate TMV-TMVI visualization.

      (54) Figure 1B: 

      •  Clearly explain the meaning of the second DMSO barplot to avoid confusion. 

      To clarify this panel, we have modified the figure and the figure legend. Panel B now includes a complete titration of the three compounds analyzed in the manuscript.  The first bar shows cell migration in the absence of both treatment with AMD3100 and stimulation with CXCL12.  The second bar shows migration in response to CXCL12 in the absence of AMD3100. The third bar shows the effect of AMD3100 on CXCL12-induced migration, as a known control of inhibition of migration.  We hope that this new representation of the data results is clearer.

      (55) Figure 1C: 

      •  Provide a clear legend explaining the significance of the green shading on the small compounds. 

      The legend for Fig. 1C has been modified accordingly to the reviewer’s suggestion.

      (56) Figure 2: 

      •  Elaborate on the role of fibronectin in the experiment and explain the specific contribution of CD86-AcGFP.

      The ideal situation for TIRF-M determinations is to employ cells on a physiological substrate complemented with or without chemokines. Fibronectin is a substrate widely used in different studies that allows cell adhesion, mimicking a physiological situation. Jurkat cells express alpha4beta1 and alpha5beta1 integrins that mediate adhesion to fibronectin (Seminario M.C. et al. J. Leuk. Biol. 1999).

      Regarding the use of CD86-AcGFP in TIRF-M experiments. We currently determine the number of receptors in individual trajectories of CXCR4 using, as a reference, the MSI value of CD86-AcGFP that strictly showed a single photobleaching step (Dorsch S. et al. Nat Methods 2009).

      We preferred to use CD86-AcGFP in cells instead of AcGFP on glass, to exclude any potential effect on the different photodynamics exhibited by AcGFP when bound directly to glass. In any case, this issue has been clarified in the revised version.

      (57) Figure 3D: 

      •  Include a plot for the respective band intensity to enhance data presentation 

      The plot showing the band intensity analysis of the experiments shown in Fig. 3D was already included in the original version (see old Supplementary Fig. 3). However, in the revised version, we include these plots in the same figure as panels 3E and 3F.  As a control of inhibition of CXCL12 stimulation, we have also included a new figure (Supplementary Fig. 4) showing the effect of AMD3100 on CXCL12-induced activation of Akt and ERK as analyzed by western blot.

      (58) Consider adding AMD3100 as a control for comparison. 

      In agreement with the reviewer’s suggestion, we have added the effect of AMD3100 in most of the functional experiments performed.

      (59) Figure 4: 

      •  Address the lack of positive controls in Figure 4 and consider their inclusion for a more comprehensive analysis. 

      DMSO bars correspond to the control of the experiment, as they represent the effect of CXCL12 in the absence of any allosteric modulator. As previously described in this point-by-point reply, DMSO bars correspond to the control performed with the solvent with which the small compounds, at maximum concentration, are diluted.  Therefore, they show the effect of the solvent on CXCL12 responses. In any case, and in order to facilitate the comprehension of the figure we have also added the controls in the absence of DMSO to demonstrate that the solvent does not affect CXCL12-mediated functions, together with the effect of the orthosteric inhibitor AMD3100. In addition, we have also included representative images of the effect of the different compounds on CXCL12-induced polarization (Fig. 4C).

      (60) In Figure 4A, carefully assess overlapping error bars and ensure accurate interpreta7on. If necessary, consider alternative representation. 

      We have tried alternative representations of data in Fig. 4A, but in all cases the figure was unclear. We believe that the way we represent the data in the original manuscript is the most clear and appropriate.  Nevertheless, we have now included significance values as a table annexed to the figure, as well as the effect of AMD3100, as a control of inhibition

      (61) Supplementary Figure 1A: 

      •  Improve the clarity of bar plots for better understanding. Consider reordering them from the most significant to the least. 

      This was a good idea, and therefore Supplementary Fig. 1A has been reorganized to improve clarity.

      (62) Supplementary Figure 1C: 

      •  Clarify the rationale behind choosing the 12.5 nM concentration and explain if different concentrations of CXCL12 were tested. 

      In old Supplementary Fig. 1C, we used untreated cells, that is, CXCL12 was not present in the assay.  These experiments were performed to test the potential toxicity of DMSO (solvent) or the negative allosteric modulators on Jurkat cells. The 12.5 nM concentration of CXCL12 mentioned in the figure legend applied only to panels A and B, as indicated in the figure legend. We previously optimized this concentration for Jurkat cells using different concentrations of CXCL12 between 5 and 100 nM.  Nevertheless, we have reorganized old supplementary fig. 1 and clarified the figure legend to avoid misinterpretations (see Supplementary Fig 1A, B and Supplementary Fig. 2A, B).

      (63) Explain the observed reduction in fluorescence intensity for AGR1.135. 

      The cell cycle analysis has been moved from Supplementary Fig. 1C to a new Supplementary Fig. 2.  It now includes the flow cytometry panels to show fluorescence intensity as a function of the number of cells analyzed (Panel 1A) as well as a table (panel B) with the percentage of cells in each phase of the cell cycle. We believe that the apparent reduction in fluorescence that the reviewer observes is mainly due to the number of events analyzed. However, we have changed the flow cytometry panels for others that are more representative and included a table with the mean of the different results. When we determined the percentage of cells in each cell cycle phase, we observed that it looks very similar in all the experimental conditions. That is, none of the compounds affected any of the cell cycle phases. We have also included the effect of H2O2 and staurosporine as control compounds inducing cell death and cell cycle alteration of Jurkat cells.

      (64) Supplementary Table 1: 

      •  Include a column specifying the scoring for each compound to provide a clear reference for readers. 

      To facilitate references to readers, we have now included the inhibitory effect of each compound on Jurkat cell migration in the revised version of this table. 

      (65) Minor Points 

      Page 2 - Abstract: Rephrase the first sentence of the abstract to enhance fluidity. 

      Although the entire manuscript was revised by a professional English editor, we appreciate the valuable comments of this reviewer and we have corrected these issues accordingly.

      (66) Page 2 - Abstract: Explicitly define "CXCR4" as "C-X-C chemokine receptor type 4" the first time it appears.

      We have not used C-X-C chemokine receptor type 4 the first time it appears in the abstract. CXCR4 is an acronym normally accepted to identify this chemokine receptor, and it is used as CXCR4 in many articles published in eLife. However, we introduce the complete name the first time it appears in the introduction.

      (67) Page 2 - Abstract: Explicitly define "CXCL12" as "C-X-C motif chemokine 12" the first time it is mentioned. 

      As we have discussed in the previous response, we have not used C-X-C motif chemokine 12 the first time CXCL12 appears in the abstract, as it is a general acronym normally accepted to identify this specific chemokine, even in eLife papers. However, we introduce the complete name the first time it appears in the introduction section.

      (68) Page 2 - Abstract: Explicitly define "TMV and TMVI" upon its first mention.

      The acronym TM has been defined as “Transmembrane” in the revised version

      (69) Page 2 - Abstract: Review the use of "in silico" in the sentence for accuracy and consider revising if necessary.

      With the term “in silico” we want to refer to those experiments performed on a computer or via computer simulation software. We have carefully reviewed its use in the new version of the manuscript.

      (70) Page 2 - Abstract: Add a comma after "compound" in the sentence, "We identified AGR1.137, a small compound that abolishes...".

      A comma after “compound” has been added in the revised sentence.

      (71) Page 2 - Significance Statement: Rephrase the first sentence of the "Significance Statement" to avoid duplication with the abstract.

      The first sentence of the Significance Statement has been revised to avoid duplication with the abstract. 

      (72) Page 2 - Significance Statement: Break down the lengthy sentence, "Here, we performed in silico analyses..." for better readability. 

      The sentence starting by “Here, we performed in silico analyses…” has been broken down in the revised manuscript.

      (73) Page 2 - Introduction: Replace "Murine studies" with a more specific term for clarity.

      The term “murine studies” is normally used to refer to experimental studies developed in mice. We have nonetheless rephrased the sentence.

      (74) Page 3 - Introduction: Rephrase the sentence for clarity: "Finally, using a zebrafish model, ..."

      The sentence has been now rephrased for clarity.

      (75) Results-AGR1.135 and AGR1.137 block CXCL12-mediated CXCR4 nanoclustering and dynamics: 

      Rephrase the sentence for clarity: "Retreatment with AGR1.135 and AGR1.137, but not with AGR1.131, substantially impaired CXCL12-mediated receptor nanoclustering.”

      The sentence has been rephrased for clarity.

      (76) Results - AGR1.135 and AGR1.137 incompletely abolish CXCR4-mediated responses in Jurkat cells: Clarify the sentence: "In contrast to the effect promoted by AMD3100, a binding-site antagonist of CXCR4..."

      The sentence has been modified for clarity.

      (77) Consider using "orthosteric" instead of "binding-site" antagonist.

      The term orthosteric is now used throughout to refer to a binding site antagonist.

      (78) Discussion: Use the term "in silico" only when necessary.

      We have carefully reviewed the use of “in silico” in the manuscript.

      (79) Discussion: Clarify the sentence: "...not affect neither CXCR2-mediated cell migration...". Confirm if "CXCL12" is intended.

      The sentence refers to the chemokine receptor CXCR2, which binds the chemokine CXCL2. To test the specificity of the compounds for the CXCL12/CXCR4 axis, we evaluated CXCL2-mediated cell migration.  The results indicated that CXCL2/CXCR2 axis was not affected by the negative allosteric modulators, whereas CXCL12-mediated cell migration was blocked.  The sentence has been clarified in the new version of the manuscript.

      (80) Figure 4B: Bold the "B" in the figure label for consistency.

      The “B” in Fig. 4B has been bolded.

      Reviewer #2

      (1) Fig 2. The SPT data is sub-optimal in its presentation as well as analysis. Example images should be shown. The analysis and visualization of the data should be reconsidered for improvements. Graphs with several hundreds, in some conditions over 1000 tracks, per condition are very hard to compare. The same (randomly selected representative set) number of data points should be shown for better visualization. Also, more thorough analyses like MSD or autocorrelation functions are lacking - they would allow enhanced overall representation of the data.

      In agreement with the reviewer’s commentary, we have modified the representation of Fig. 2. We have carefully read the paper published by Lord S.J. and col. (Lord S. J. et al., J. Cell Biol. 2020) and we apply their recommendations for these type of data. We have also included as supplementary material representative videos for the TIRF-M experiments performed to allow readers to visualize the original images. Regarding the MSD analyses, they were developed to determine all D1-4 values. According to the data published by Manzo & García-Parajo (Manzo C. & García-Parajo M.F. Rep.Prog. Phys. 2015) due to the finite trajectory length the MSD curve at large tlag has poor statistics and deviates from linearity. However, the estimation of the Diffusion Coefficient (D1-4) can be obtained by fitting of the short tlag region of the MSD plot giving a more accurate idea of the behavior of particles. In agreement we show D1-4 values and not MSD data. 

      Due to the space restrictions, it is very difficult to include all the figures generated, but, only for review purposes, we included in this point-by-point reply some representative plots of the MSD values as a function of the time from individual trajectories showing different types of motion obtained in our experiments (Author response image 7).

      Author response image 7.

      Representative MSD plots from individual trajectories of CXCR4-AcGFP showing different types of motion: A) confined, B) Brownian/Free, C) direct transport of CXCR4-AcGFP particles diffusing at the cell membrane detected by SPT-TIRF in resting JKCD4 cells.

      Further analysis, such as the classification based on particle motion, has not been included in this article. This classification uses the moment scaling spectrum (MSS), described by Ewers H. et al. 2005 PNAS, and requires particles with longer trajectories (>50 frames). Only for review purposes, we include a figure showing the percentage of the MSS-based particle motion classification for each condition. As expected, most of long particles are confined, with a slight increase in the percentage upon CXCL12 stimulation in all conditions, except in cell treated with AGR1.137 (Author response image 8).

      Author response image 8.

      Effects of the negative allosteric modulators on the Types of Motion of CXCR4. Percentage of single trajectories with different types of motion, classified by MSS (DMSO: 58 particles in 59 cells on FN; 314 in 63 cells on FN+CXCL12; AGR1.131: 102 particles in 71 cells on FN; 258in 69 cells on FN+CXCL12; AGR1.135: 86 particles in 70 cells on FN; 120 in 77 cells on FN+CXCL12; AGR1.137: 47 particles in 66 cells on FN; 74 in 64 cells on FN+CXCL12) n = 3.

      (2) Fig 3. The figure legends have inadequate information on concentrations and incubation times used, both for the compounds and other treatments like CXCL12 and forskolin. For the Western blot data, also the quantification should be added to the main figure. The compounds, particularly AGR1.137 seem to lead to augmented stimulation of pAKT and pERK. This should be discussed

      The Fig. 3 legend has been corrected in the revised manuscript. Fig. 3D now contains representative western blots and the densitometry evaluation of these experiments. As the reviewer indicates, we also detected in the western blot included, augmented stimulation of pAKT and pERK in cells treated with AGR1.137. However, as shown in the densitometry analysis, no significant differences were noted between the data obtained with each compound. As a control of inhibition of CXCL12 stimulation we have included a new Supplementary Fig. 4 showing the effect of AMD3100 on CXCL12-induced activation of Akt and ERK as analyzed by western blot.

      (3) Fig. 4 immunofluorescence data on polarization as well as the flow chamber data lack the representative images of the data. The information on the source of the T cells is missing. Not clear if this experiment was done on bilayers or on static surfaces.

      Representative images for the data shown in Figure 4B have been added in the revised figure (Fig. 4C). The experiments in Fig. 4B were performed on static surfaces. As indicated in the material and methods section, primary T cell blasts were added to fibronectin-coated glass slides and then were stimulated or not with CXCL12 (5 min at 37ºC) prior to fix permeabilize and stain them with Phalloidin. Primary T cell blasts were generated from PBMCs isolated from buffy coats that were activated in vitro with IL-2 and PHA as indicated in the material and methods section.

      (4) The data largely lacks titration of different concentrations of the compounds. How were the effective concentration and treatment times determined? What happens at higher concentrations? It is important to show, for instance, if the CXCR12 binding gets inhibited at higher concentrations. most experiments were performed with 50 uM, but HeLa cell data with 100 uM. Why and how was this determined? 

      The revised version contains a new panel in Fig. 1B to show a more detailed kinetic analysis with different concentrations (1-100 µM) of the compounds in the migration experiments using Jurkat cells. We choose 50 µM for further studies as it was the concentration that inhibits 50-75% of the ligand induced cell migration. 

      We have also included the effect of two doses of the compounds (10 and 50 µM) in the zebrafish model as well as AMD3100 (1 and 10 µM) as control (new Fig. 7D, E).  Tumors were imaged within 2 hours of implantation and tumor-baring embryos were treated with either vehicle (DMSO) alone, AGR1.131 or AGR1.137 at 10 and 50 µM or AMD3100 at 1 and 10 µM for three days, followed by re-imaging.

      Regarding the amount of CXCL12 used in these experiments, with the exception of cell migration assays in Transwells, where the optimal concentration was established at 12.5 nM, in all the other experiments the optimal concentration of CXCL12 employed was 50 nM. In the case of the directional cell migration assays, we use 100 nM to create the chemokine gradient in the device. These concentrations have been optimized in previous works of our laboratory using these types of experiments. It should also be noted that in the experiments using lipid bilayers or TIRF-M experiments, CXCL12 is used to coat the plates and therefore it is difficult to determine the real concentration that is retained in the surface after the washing steps performed prior adding the cells.

      (5) The authors state that they could not detect direct binding of the compounds and the CXCR14. It should be reported what approaches were tried and discussed why this was not possible. 

      We attempted a fluorescence spectroscopy strategy to formally prove the ability of AGR1.135 to bind CXCR4, but this strategy failed because the compound has a yellow color that interfered with the determinations. We also tried a FRET strategy (see supplementary Fig. 7) and detected a significant increase in FRET efficiency of CXCR4 homodimers in cells treated with AGR1.135; this effect was due to the yellow color of this compound that interferes with FRET determinations. In the same assays, AGR1.137 did not modify FRET efficiency for CXCR4 homodimers and therefore we cannot assume that AGR1.137 binds on CXCR4. All these data have been considered in the revised discussion.

      (6) The proliferation data in Supplementary Figure 1 lacks controls that affect proliferation and indication of different cell cycle stages. What is the conclusion of this data? More information on the effects of the drug to cell viability would be important.

      Toxicity in Jurkat cells was first determined by propidium iodide incorporation. Some compounds (i.e., AGR1.103 and VSP3.1) were discarded from further analysis as they were toxic for cells. In a deeper analysis of cell toxicity, even if these compounds did not kill the cells, we checked whether they could alter the cell cycle of the cells. New Supplementary Fig. 2 includes a table (panel B) with the percentage of cells in each cell cycle phase, and no differences between any of the treatments tested were detected. 

      Nevertheless, to clarify this issue the revised version of the figure also includes H2O2 and staurosporine stimuli to induce cell death and cell cycle alterations as controls of these assays.

      (7) The flow data in Supplementary Figure 2 should be statistically analysed. 

      Bar graphs corresponding to the old Supplementary Fig. 2 (new Supplementary Fig. 3) are shown in Fig. 3B. We have also incorporated the corresponding statistical analysis to this figure. 

      (8) In general, the authors should revise the figure legends to ensure that critical details are added. 

      We have carefully revised all the figure legends in the new version of the manuscript.

      (9) Bar plots are very poor in showing the heterogeneity of the data. Individual data points should be shown whenever feasible. Superplot-type of representation is strongly advised (https://doi.org/10.1083/jcb.202001064).

      We have carefully read the paper published by Lord S.J. and col. (Lord S. J. et al., J. Cell Biol. 2020) and we apply their recommendations for our TIRF-M data (see revised Fig.  2).

    1. Author response:

      Reviewer #1 (Public Review):

      Summary: 

      BMP signaling is, arguably, best known for its role in the dorsoventral patterning, but not in nematodes, where it regulates body size. In their paper, Vora et al. analyze ChIP-Seq and RNA-Seq data to identify direct transcriptional targets of SMA-3 (Smad) and SMA-9 (Schnurri) and understand the respective roles of SMA-3 and SMA-9 in the nematode model Caenorhabditis elegans. The authors use publicly available SMA-3 and SMA-9 ChIP-Seq data, own RNA-Seq data from SMA-3 and SMA-9 mutants, and bioinformatic analyses to identify the genes directly controlled by these two transcription factors (TFs) and find approximately 350 such targets for each. They show that all SMA-3-controlled targets are positively controlled by SMA-3 binding, while SMA-9-controlled targets can be either up or downregulated by SMA-9. 129 direct targets were shared by SMA-3 and SMA-9, and, curiously, the expression of 15 of them was activated by SMA-3 but repressed by SMA-9. Since genes responsible for cuticle collagen production were eminent among the SMA-3 targets, the authors focused on trying to understand the body size defect known to be elicited by the modulation of BMP signaling. Vora et al. provide compelling evidence that this defect is likely to be due to problems with the BMP signaling-dependent collagen secretion necessary for cuticle formation. 

      We thank the reviewer for this supportive summary. We would like to clarify the status of the publicly available ChIP-seq data. We generated the GFP tagged SMA-3 and SMA‑9 strains and submitted them to be entered into the queue for ChIP-seq processing by the modENCODE (later modERN) consortium. Due to the nature of the consortium’s funding, the data were required to be released publicly upon completion. Nevertheless, we have provided the first comprehensive analysis of these datasets.

      Strengths: 

      Vora et al. provide a valuable analysis of ChIP-Seq and RNA-Seq datasets, which will be very useful for the community. They also shed light on the mechanism of the BMP-dependent body size control by identifying SMA-3 target genes regulating cuticle collagen synthesis and by showing that downregulation of these genes affects body size in C. elegans. 

      Weaknesses: 

      (1) Although the analysis of the SMA-3 and SMA-9 ChIP-Seq and RNA-Seq data is extremely useful, the goal "to untangle the roles of Smad and Schnurri transcription factors in the developing C. elegans larva", has not been reached. While the role of SMA-3 as a transcriptional activator appears to be quite straightforward, the function of SMA-9 in the BMP signaling remains obscure. The authors write that in SMA-9 mutants, body size is affected, but they do not show any data on the mechanism of this effect. 

      We thank the reviewer for directing our attention to the lack of clarity about SMA-9’s function. We will revise the text to highlight what this study and others demonstrate about SMA-9’s role in body size. We also plan to analyze additional target genes to deepen our model for how SMA-3 and SMA-9 interact functionally to produce a given transcriptional response.

      (2) The authors clearly show that both TFs can bind independently of each other, however, by using distances between SMA-3 and SMA-9 ChIP peaks, they claim that when the peaks are close these two TFs act as complexes. In the absence of proof that SMA-3 and SMA-9 physically interact (e.g. that they co-immunoprecipitate - as they do in Drosophila), this is an unfounded claim, which should either be experimentally substantiated or toned down. 

      A physical interaction between Smads and Schnurri has been amply demonstrated in other systems. The limitation in the previous work is that only a small number of target genes was analyzed. Our goal in this study was to determine how widespread this interaction is on a genomic scale.  Our analyses demonstrate for the first time that a Schnurri transcription factor has significant numbers of both Smad-dependent and Smad-independent target genes. We will revise the text to clarify this point.

      (3) The second part of the paper (the collagen story) is very loosely connected to the first part. dpy-11 encodes an enzyme important for cuticle development, and it is a differentially expressed direct target of SMA-3. dpy-11 can be bound by SMA-9, but it is not affected by this binding according to RNA-Seq. Thus, technically, this part of the paper does not require any information about SMA-9. However, this can likely be improved by addressing the function of the 15 genes, with the opposing mode of regulation by SMA-3 and SMA-9. 

      We appreciate this suggestion and will clarify how SMA-9 and its target genes contribute to collagen organization and body size regulation.

      (4) The Discussion does not add much to the paper - it simply repeats the results in a more streamlined fashion. 

      We thank the reviewer for this suggestion. We will add more context to the Discussion.

      Reviewer #2 (Public Review): 

      In the present study, Vora et al. elucidated the transcription factors downstream of the BMP pathway components Smad and Schnurri in C. elegans and their effects on body size. Using a combination of a broad range of techniques, they compiled a comprehensive list of genome-wide downstream targets of the Smads SMA-3 and SMA-9. They found that both proteins have an overlapping spectrum of transcriptional target sites they control, but also unique ones. Thereby, they also identified genes involved in one-carbon metabolism or the endoplasmic reticulum (ER) secretory pathway. In an elaborate effort, the authors set out to characterize the effects of numerous of these targets on the regulation of body size in vivo as the BMP pathway is involved in this process. Using the reporter ROL-6::wrmScarlet, they further revealed that not only collagen production, as previously shown, but also collagen secretion into the cuticle is controlled by SMA-3 and SMA-9. The data presented by Vora et al. provide in-depth insight into the means by which the BMP pathway regulates body size, thus offering a whole new set of downstream mechanisms that are potentially interesting to a broad field of researchers. 

      The paper is mostly well-researched, and the conclusions are comprehensive and supported by the data presented. However, certain aspects need clarification and potentially extended data. 

      (1) The BMP pathway is active during development and growth. Thus, it is logical that the data shown in the study by Vora et al. is based on L2 worms. However, it raises the question of if and how the pattern of transcriptional targets of SMA-3 and SMA-9 changes with age or in the male tail, where the BMP pathway also has been shown to play a role. Is there any data to shed light on this matter or are there any speculations or hypotheses? 

      We agree that these are intriguing questions and we are interested in the roles of transcriptional targets at other developmental stages and in other physiological functions, but these analyses are beyond the scope of the current study.

      (2) As it was shown that SMA-3 and SMA-9 potentially act in a complex to regulate the transcription of several genes, it would be interesting to know whether the two interact with each other or if the cooperation is more indirect. 

      A physical interaction between Smads and Schnurri has been amply demonstrated in other systems. Our goal in this study was not to validate this physical interaction, but to analyze functional interactions on a genome-wide scale.

      (3) It would help the understanding of the data even more if the authors could specifically state if there were collagens among the genes regulated by SMA-3 and SMA-9 and which. 

      We thank the reviewer for this suggestion and will add the requested information in the text.

      (4) The data on the role of SMA-3 and SMA-9 in the regulation of the secretion of collagens from the hypodermis is highly intriguing. The authors use ROL-6 as a reporter for the secretion of collagens. Is ROL-6 a target of SMA-9 or SMA-3? Even if this is not the case, the data would gain even more strength if a comparable quantification of the cuticular levels of ROL-6 were shown in Figure 6, and potentially a ratio of cuticular versus hypodermal levels. By that, the levels of secretion versus production can be better appreciated. 

      rol-6 has been identified as a transcriptional target of this pathway. The level of ROL-6 protein, however, is not changed in sma-3 and sma-9 mutants, indicating that there is post-transcriptional compensation. We will include these data in the revised manuscript.

      (5) It is known that the BMP pathway controls several processes besides body size. The discussion would benefit from a broader overview of how the identified genes could contribute to body size. The focus of the study is on collagen production and secretion, but it would be interesting to have some insights into whether and how other identified proteins could play a role or whether they are likely to not be involved here (such as the ones normally associated with lipid metabolism, etc.). 

      We will add this information to the Discussion.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Work by Brosseau et. al. combines NMR, biochemical assays, and MD simulations to characterize the influence of the C-terminal tail of EmrE, a model multi-drug efflux pump, on proton leak. The authors compare the WT pump to a C-terminal tail deletion, delta_107, finding that the mutant has increased proton leak in proteoliposome assays, shifted pH dependence with a new titratable residue, faster-alternating access at high pH values, and reduced growth, consistent with proton leak of the PMF.

      Strengths:

      The work combines thorough experimental analysis of structural, dynamic, and electrochemical properties of the mutant relative to WT proteins. The computational work is well aligned in vision and analysis. Although all questions are not answered, the authors lay out a logical exploration of the possible explanations.

      Weaknesses:

      There are a few analyses that are missing and important data left out. For example, the relative rate of drug efflux of the mutant should be reported to justify the focus on proton leak. Additionally, the correlation between structural interactions should be directly analyzed and the mutant PMF also analyzed to justify the claims based on hydration alone. Some aspects of the increased dynamics at high pH due to a potential salt bridge are not clear.

      Reviewer #2 (Public review):

      Summary:

      This manuscript explores the role of the C-terminal tail of EmrE in controlling uncoupled proton flux. Leakage occurs in the wild-type transporter under certain conditions but is amplified in the C-terminal truncation mutant D107. The authors use an impressive combination of growth assays, transport assays, NMR on WT and mutants with and without key substrates, classical MD, and reactive MD to address this problem. Overall, I think that the claims are well supported by the data, but I am most concerned about the reproducibility of the MD data, initial structures used for simulations, and the stochasticity of the water wire formation. These can all be addressed in a revision with more simulations as I point out below. I want to point out that the discussion was very nicely written, and I enjoyed reading the summary of the data and the connection to other studies very much.

      Strengths:

      The Henzler-Wildman lab is at the forefront of using quantitative experiments to probe the peculiarities in transporter biophysics, and the MD work from the Voth lab complements the experiments quite well. The sheer number of different types of experimental and computational approaches performed here is impressive.

      Weaknesses:

      The primary weaknesses are related to the reproducibility of the MD results with regard to the formation of water wires in the WT and truncation mutant. This could be resolved with simulations starting from structures built using very different loops and C-terminal tails.

      The water wire gates identified in the MD should be tested experimentally with site-directed mutagenesis to determine if those residues do impact leak.

      We appreciate the reviewers thoughtful consideration of our manuscript, and their recognition of the variety of experimental and computational approaches we have brought to bear in probing the very challenging question of uncoupled proton leak through EmrE.

      We did record SSME measurements with MeTPP+, a small molecule substrate at two different protein:lipid ratios. These experiments report the rate of net flux when both proton-coupled substrate antiport and substrate-gated proton leak are possible. We will add this data to the revision, including data acquired with different lipid:protein ratio that confirms we are detecting transport rather than binding. In brief, this data shows that the net flux is highly dependent on both proton concentration (pH) and drug-substrate concentration, as predicted by our mechanistic model. This demonstrates that both types of transport contribute to net flux when small molecule substrates are present.

      In the absence of drug-substrate, proton leak is the only possible transport pathway. The pyranine assay directly assesses proton leak under these conditions and unambiguously shows faster proton entry into proteoliposomes through the ∆107-EmrE mutant than through WT EmrE, with the rate of proton entry into ∆107-EmrE proteoliposomes matching the rate of proton entry achieved by the protonophore CCCP. We have revised the text to more clearly emphasize how this directly measures proton leak independently of any other type of transport activity. The SSME experiments with a proton gradient only (no small molecule substrate present) provide additional data on shorter timescales that is consistent with the pyranine data. The consistency of the data across multiple LPRs and comparison of transport to proton leak in the SSME assays further strengthens the importance of the C-terminal tail in determining the rate of flux.

      None of the current structural models have good resolution (crystallography, EM) or sufficient restraints (NMR) to define the loop and tail conformations sufficiently for comparison with this work. We are in the process of refining an experimental structure of EmrE with better resolution of the loop and tail regions implicated in proton-entry and leak. Direct assessment of structural interactions via mutagenesis is complicated because of the antiparallel homodimer structure of EmrE. Any point mutation necessarily affects both subunits of the dimer, and mutations designed to probe the hydrophobic gate on the more open face of the transporter also have the potential to disrupt closure on the opposite face, particularly in the absence of sufficient resolution in the available structures. Thus, mutagenesis to test specific predicted structural features is deferred until our structure is complete so that we can appropriately interpret the results.

      In our simulation setup, the MD results can be considered representative and meaningful for two reasons. First, the C-terminal tail, not present in the prior structure and thus modeled by us, is only 4 residues long. We will show in the revision and detailed response that the system will lose memory of its previous conformation very quickly, such that velocity initialization alone is enough for a diverse starting point. Second, our simulation is more like simulated annealing, starting from a high free energy state to show that, given such random initialization, the tail conformation we get in the end is consistent with what we reported. It is also difficult to sample back-and-forth tail motion within a realistic MD timescale. Therefore, it can be unconclusive to causally infer the allosteric motions with unbiased MD of the wildtype alone. The best viable way is to look at the equilibrium statistics of the most stable states between WT- and ∆107-EmrE and compare the differences.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The work is well done and well presented. In my opinion, the authors must address the following questions.

      (1) It is unclear to a non-SSME-expert, why the net charge translocated in delta_107 is larger than in WT. For such small pH gradients (0.5-1pH unit), it seems that only a few protons would leave the liposome before the internal pH is adjusted to be the same as the external. This number can be estimated given the size of the liposomes. What is it? Once the pH gradient is dissipated, no more net proton transport should be observed. So, why would more protons flow out of the mutant relative to WT?

      We appreciate the complexity of both the system and assay and have made revisions to both the main text and SI to address these points more clearly. While we can estimate liposomes size, we cannot easily quantify the number of liposomes on the sensor surface so cannot calculate the amount of charge movement as suggested by the reviewer. We have revised Fig. 3.2 and added additional data at low and high pH with different lipid to protein ratios to distinguish pre-steady state (proton release from the protein) and steady state processes (transport). An extended Fig. 3.2 caption and revised discussion in the main text clarify these points.

      We have also revised SI figure 3.2 to include an example of transport driven by an infinite drug gradient. Drug-proton antiport results in net charge build-up in the liposome since two protons will be driven out for every +1 drug transported in. This also creates a pH gradient is created (higher proton concentration outside). The negative inside potential inhibits further antiport of drug. However, both the negative-inside potential and proton gradient will drives protons back into the liposome if there is a leak pathway available. This is clearly visible with a reversal of current negative (antiport) to positive (proton backflow), and the magnitude of this back flow is larger for ∆107-EmrE which lacks the regulatory elements provided by the C-terminal tail. We have amended the main text and SI to include this discussion.

      (2) Given the estimated rate of transport, size of liposomes, and pH gradient, how quickly would the SSME liposomes reach pH balance?

      Since SSME measurements are due to capacitive coupling and will represent the net charge movement, including pre-steady state contributions, the current values will be incredibly sensitive to individual rates of alternating access, proton and drug on- and off-rates. Time to pH balance would, therefore, differ based on the construct, LPR, absolute pH or drug concentrations as well as the magnitude of the given gradients. For this reason, we necessarily use integrated currents (transported charge over time) when comparing mutants as it reflects kinetic differences inherent to the mutant without over-processing the data, for example, by normalizing to peak currents which would over emphasize certain properties that will differ across mutants. This process allows for qualitative comparisons by subjecting mutants to the same pH and substrate gradients when the same density of transporter construct is present, and care is given to not overstate the importance of the actual quantities of charges that are moving as they will be highly context dependent. This is clearly seen in Fig 3.2 where the current is not zero and the net transported charge is still changing at the end of 1 second. We have amended SI figure 3.2 and the main text to include this discussion.

      (3) Given that H110 and E14 would deprotonate when the external pH is elevated above 7 and that these protons would be released to external bulk, the external bulk pH would decrease twice as much for WT compared to delta107. This would decrease the pH gradient for WT relative to the mutant. Can these effects be quantified and accounted for? Would this ostensibly decrease the amount of charge that transfers into the liposomes for WT? How would this impact the current interpretation that the two systems are driven by the same gradient?

      The reviewer is correct that there will be differences in deprotonation of WT and ∆107 and the amount of proton release will also change with pH. We have amended Figure 3.2 to clarify this difference and its significance. For the proton gradient only conditions in Figure 3, each set of liposomes were equilibrated to the starting pH by repeated washings and incubation before measurement occurred. For example, for the pH 6.5 inside, pH 7 outside condition, both the inside and outside pH were equilibrated at 6.5, and both E14 residues will be predominantly protonated in WT and ∆107, and H110 will be predominantly protonated in WT-EmrE. Upon application of the external pH 7 solution, protons will be released from the E14 of either construct, with additional proton being released from H110 for WT-EmrE causing a large pre-steady state negative contribution to the signal (Fig. 3.2A). Under this pH condition, we the peak current correlates with the LPR, as this release of protons will depend on density of the transporter. However, we also see that the longer-time decay of the signal correlates with the construct (WT or ∆107) and is relatively independent of LPR, consistent with a transport process rather than a rapid pre-steady state release of protons. Therefore, when we look at the actual transported charge over time, despite the higher contribution of proton release to the WT-EmrE signal, the significant increase in uncoupled proton transport for the C-terminal deletion mutant dominates the signal.

      As a contrast, we apply this same analysis to the pH 8 inside, pH 8.5 outside condition where both sets of transports will be deprotonated from the start (Fig. 3.2B). Now the peak currents, decay rates, and transported charge over time are all consistent for a given construct (WT or ∆107). The two LPRs for an individual construct match within error, as the differences in overall charge movement and transported charge over time are independent of pre-steady-state proton release from the transporter at high pH.

      (4) A related question, how does the protonation of H110 influence the potential rate of proton transport between the two systems? Does the proton on H110 transfer to E14?

      The protonation of H110 will only influence the rate of transport of WT-EmrE as its protonation is required for formation of the hydrogen bonding network that coordinates gating. However, protonation of both E14s will influence the rate of proton transport of both systems as protonation state affects the rate of alternating access which is necessary for proton turnover. This is another reason we use the transported charge over time metric to compare mutants as it allows for a common metric for mutants with altered rates which are present in the same density and under the same gradient conditions. We do not have any evidence to support transfer of proton from H110 to E14, but there is also no evidence to exclude this possibility. We do not discuss this in the manuscript because it would be entirely speculative.

      (5) Is the pKa in the simulations (Figure 6B) consistent with the experiment?

      We calculated the pKa from this WT PMF and got a pKa of 7.1, which is in close proximity of the experimental value of 6.8

      (6) Why isn't the PMF for delta_107 compared to WT to corroborate the prediction that hydration sufficiently alters both the rate and pKa of E14?

      We appreciate the reviewer’s suggestion and agree that a direct comparison would be valuable. However, several factors limit the interpretability of such an analysis in this context:

      (a) Our data indicate that the primary difference in free energy barriers between WT and Δ107 lies in the hydration step rather than proton transport itself. To fully resolve this, a 2D PMF calculation via 2D umbrella sampling would be required which can be very expensive. Solely looking at the proton transport side of this PMF will not give much difference.

      (b) Given this, the aim for us to calculate this PMF is to support our conjecture that the bottleneck for such transport is the hydrophobic gate.

      (7) The authors suggest that A61 rotation 'controls the water wire formation' by measuring the distribution of water connectivity (water-water distances via logS) and average distances between A61 and I68/I67. Delta_107 has a larger inter-residue distance (Figure 6A) more probable small log S closer waters connecting E14 and two residues near the top of the protein (Figure 5A). However, it strikes me that looking at average distances and the distribution of log S is not the best way to do this. Why not quantify the correlation between log S and A61 orientation and/or A61-I68/I71 distances as well as their correlation to the proposed tail interactions (D84-R106 interactions) to directly verify the correlation (and suggest causation) of these interactions on the hydration in this region. Additionally, plotting the RMSD or probability of waters below I68 and I171 as a function of A61-I68 distances and/or numbers over time would support the log S analysis.

      The reviewer requested that we provide direct correlation analyses between A61 orientation, residue distances (A61-I68/I71), and water connectivity (logS) to better support the claim about water wire formation, rather than relying solely on average distances and distributions.

      We appreciate the reviewer’s suggestion to strengthen our analysis with direct correlations. However, due to the slow kinetics of hydration/dehydration events, unbiased simulation timescales do not permit sufficient sampling of multiple transitions to perform statistically robust dynamic correlation analyses. Instead, our approach focuses on equilibrium statistics, which reveal the dominant conformational states of WT- and Δ107-EmrE and provide meaningful insights into shifts in hydration patterns.

      (8) It looks like the D84-R106 salt bridge controls this A61-I68 opening. Could this also be quantifiably correlated?

      As discussed in response to the previous question, the unbiased simulation timescales do not permit sufficient sampling of multiple transitions to perform statistically robust dynamic correlation analyses.

      (9) The NMR results show that alternating access increases in frequency from ~4/s for WT at low and high pH to ~17/s for delta_107 only at high pH. They then go on to analyze potential titration changes in the delta_107 mutant, finding two residues with approximate pKa values of 5.6 and 7.1. The former is assigned to E14, consistent with WT. But the latter is suggested to be either D84, which salt bridges to R106, or the C-terminal carboxylate. If it is D84, why would deprotonation, which would be essential to form the salt bridge, increase the rate of alternating access relative to WT?

      We note that the faster alternating access rate was observed for TPP+-bound ∆107-EmrE, not the transporter in the absence of substrate. In the absence of substrate the relatively broad lines preclude quantitative determination of the alternating access rate by NMR making it difficult to judge the validity of the reviewers reasoning. Identification of which residue (D84 or H110) corresponds to the shifted pKa is ultimately of little consequence as this mutant does not reflect the native conditions of the transporter. It is far more important to acknowledge that both R106 and D84 are sensitive to this deprotonation as it indicates these residues are close in space and provides experimental support for the existence of the salt bridge identified in the MD simulations, as discussed in the manuscript.

      (10) In a more general sense, can the authors speculate why an efflux pump would evolve this type of secondary gate that can be thrown off by tight binding in the allosteric site such as that demonstrated by Harmane? What potential advantage is there to having a tail-regulated gate?

      This was likely a necessity to allow for better coupling as these transporters evolved to be more promiscuous. The C-terminal tail is absent in tightly coupled family members such as Gdx who are specific for a single substrate and have a better-defined transport stoichiometry. We have included this discussion in the main text and are currently investigating this phenomenon further. Those experiments are beyond the scope of the current manuscript.

      (11) It is hard to visualize the PT reaction coordinate. Is the e_PT unit vector defined for each window separately based on the initial steered MD pathway? If so, how reliant is the PT pathway on this initial approximate path? Also, how does this position for each window change if/when E14 rotates? This could be checked by plotting the x,y,z distributions for each window and quantifying the overlap between windows in cartesian space. These clouds of distributions could also be plotted in the protein following alignment so the reader can visualize the reaction coordinate. Does the CEC localization ever stray to different, disconnected regions of cartesian phase space that are hidden by the reaction coordinate definition?

      The unit vector e_PT is the same across all windows based on unbiased MD. Therefore, the reaction coordinate (a scalar) is the vector from the starting point to the CEC, projected on this unit vector. E14 rotation does not significantly change the window definition a lot unless the CEC is very close to E14, where we found this to be a better CV. For detailed discussions about this CV, especially a comparison between a curvilinear CV, please see J. Am. Chem. Soc. 2018, 140, 48, 16535–16543 “Simulations of the Proton Transport” and its SI Figure S1.In the Supplementary Information, we added figure 6.1 to show the average X, Y, Z coordinates of each umbrella window.

      (12) Lastly, perhaps I missed it, but it's unclear if the rate of substrate efflux is also increased in the delta_107 mutant. If this is also increased, then the overall rate of exchange is faster, including proton leak. This would be important to distinguish since the focus now is entirely on proton leaks. I.e., is it only leak or is it overall efflux and leak?

      We have amended SI figure 3.2 to include a gradient condition where an infinite drug gradient is created across the liposome. The infinite gradient allows for rapid transport of drug into the liposomes until charge build-up opposes further transport. This peak is at the same time for both LPRs of WT- and ∆107-EmrE suggesting the rate of substrate transport is similar. Differences in the peak heights across LPRs can be attributed to competition between drug and proton for the primary binding site such that more proton will be released for the higher density constructs as described above. This process does also create a proton gradient as drug moving in is coupled to two protons moving out so as charge build-up inhibits further drug movement, the building proton gradient will also begin to drive proton back in which is another example of uncoupled leak. Here, again we see that this back-flow of protons or leak is of greater magnitude for ∆107-EmrE proteoliposomes that for those with WT-EmrE. We have included this discussion in the SI and main text.

      Minor

      (1) Introduction - the authors describe EmrE as a model system for studying the molecular mechanism of proton-coupled transport. This is a rather broad categorization that could include a wide range of phenomena distal from drug transport across membranes or through efflux pumps. I suggest further specifying to not overgeneralize.

      We revised to note the context of multidrug efflux.

      Reviewer #2 (Recommendations for the authors):

      Simulations. The initial water wire analysis is based on 4 different 1 ms simulations presented in Figure 5. The 3 WT replicates show similar results for the tail-blocking water wire formation, but the details of the system build and loop/C-terminal tail placement are not clear. It does appear that a single C-terminal tail model was created for all WT replicates. Was there also modeling for any parts of the truncation mutant? Regardless, since these initial placements and uncertainties in the structures may impact the results and subsequent water wire formation, I would like a discussion of how these starting structures impacted the formation or not of wires. I think that another WT replicate should be run starting from a completely new build that places the tail in a different (but hopefully reasonable location). This could be built with any number of tools to generate reasonable starting structures. It's critical to ensure that multiple independent simulations across different initial builds show the same water wire behavior so that we know the results are robust and insensitive to the starting structure and stochastic variation.

      We thank Reviewer 2 for their suggestion regarding the discussion of the initial structure. In our simulations, the C-terminal tail was initially modeled in an extended conformation (solvent-exposed) to mimic its disordered state prior to folding. This approach resembles an annealing process, where the system evolves from a higher free-energy state toward equilibrium. Notably, across all three replicas, we observed consistent folding of the tail onto the protein surface, supporting the robustness of this conformational preference.

      For the Δ107 truncation mutant, minimal modeling was required, as most experimental structures resolve residues up to S105 or R106. To rigorously assess the influence of the starting configuration, we analyzed the tail’s dynamics using backbone dihedral angle auto- and cross-correlation functions (new Supplementary Figures 10.1 and 10.2). These analyses reveal rapid decay of correlations—consistent with the tail’s short length (5 residues) and high flexibility—indicating that the system "forgets" its initial configuration well within the simulation timescale. Thus, we conclude that our sampling is sufficient to capture equilibrium behavior, independent of the starting structure.

      What does the size of the barrier in the PMF (Figure 6B) imply about the rate of proton transfer/leak and can the pKa shift of the acidic residue be estimated with this energy value compared to bulk?

      We noticed this point aligns with a related concern raised by Reviewer 1. For a detailed discussion please refer to Point 5 in our response to Reviewer 1.

      Experimental validation. The hypotheses generated by this work would be better buttressed if there were some mutation work at the hydrophobic gate (61, 68, 71) to support it. I realize that this may be hard, but it would significantly improve the quality.

      Due to the small size of the transporter, any mutagenesis of EmrE should necessarily be accompanied by functional characterization to fully assess the effects of the mutation on rate-limiting steps. We have revised the manuscript to add a discussion of the challenges with analyzing simple point mutants and citing what is known from prior scanning mutagenesis studies of EmrE.

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Reviewer #1:

      The addition of the discussion about the two isomers of 18:1 didn't quite work in the place that the authors added. What the authors wrote on line 126 is true about 18:1 isomers in wild type worms. However, they are reporting their lipidomics results of the fat-2(wa17) mutant worms. In this case, a substantial amount of the 18:1 is the oleic acid (18:1n-9) isomer. The authors can check Table 2 in their reference [10] and see that wild type and other fat mutants indeed contain approximately 10 fold more cis vaccenic than oleic acid, the fat-2(wa17) mutants do accumulate oleic acid, because the wild type activity of FAT-2 is to convert oleic acid to linoleic acid, where it can be converted to downstream PUFAs. I suggest editing their sentence on line 126 to say that the high 18:1 they observed agrees with [10], and then comment about reference 10 showing the majority of 18:1 being the cis-vaccenic isomer in most strains, but the oleic acid isomer is more abundantly in the fat-2(wa17) mutant strain.

      We thank the reviewer for spotting that and sparing us a bit of embarrassment. We have now modified the text and hope we got it right this time:

      "Even though the lipid analysis methods used here are not able to distinguish between different 18:1 species, a previous study showed that the majority of the 18:1 fatty acids in the fat-2(wa17) mutant is actually 18:1n9 (OA) [10] and not 18:1n7 (vaccenic acid) as in most other strains [10,23]; this is because OA is the substrate of FAT-2 and thus accumulates in the mutant."

      Reviewer #2:

      I still do not agree with the answer to my previous comment 6 regarding Figure S2E. The authors claim that hif-1(et69) suppresses fat-2(wa17) in a ftn-2 null background (in Figure S2 legend for example). To claim so, they would need to compare the triple mutant with fat2(wa17);ftn-2(ok404) and show some rescue. However, we see in Figure 5H that ftn2(ok404) alone rescues fat-2(wa17). Thus, by comparing both figures, I see no additional effect of hif-1(et69) in an ftn-2(ok404) background. I actually think that this makes more sense, since the authors claim that hif-1(et69) is a gain-of-function mutation that acts through suppression of ftn-2 expression. Thus, I would expect that without ftn-2 from the beginning, hif-1(et69) does not have an additional effect, and this seems to be what we see from the data. Thus, I would suggest that the authors reformulate their claims regarding the effect of hif1(et69) in the ftn-2(ok404) background, which seems to be absent (consistently with what one would expect).

      We completely agree with the reviewer and indeed this is the meaning that we tried to convey all along. The text has now been modified as follows:

      "Lastly, ftn-2(et68) is still a potent fat-2(wa17) suppressor when hif-1 is knocked out (S2D Fig), suggesting that no other HIF-1-dependent functions are required as long as ftn-2 is downregulated; this conclusion is supported by the observation that the potency of the ftn2(ok404) null allele to act as a fat-2(wa17) suppressor is not increased by including the hif-1(et69) allele (compare Fig 5H and S2E Fig)."

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      In this manuscript, the authors present a novel CRISPR/Cas9-based genetic tool for the dopamine receptor dop1R2. Based on the known function of the receptor in learning and memory, they tested the efficacy of the genetic tool by knocking out the receptor specifically in mushroom body neurons. The data suggest that dop1R2 is necessary for longer-lasting memories through its action on ⍺/ß and ⍺'/ß' neurons but is dispensable for short-term memory and thus in ɣ neurons. The experiments impressively demonstrate the value of such a genetic tool and illustrate the specific function of the receptor in subpopulations of KCs for longer-term memories. The data presented in this manuscript are significant.

      Reviewer #2 (Public Review):

      Summary:

      This manuscript examines the role of the dopamine receptor, Dop1R2, in memory formation. This receptor has complex roles in supporting different stages of memory, and the neural mechanisms for these functions are poorly understood. The authors are able to localize Dop1R2 function to the vertical lobes of the mushroom body, revealing a role in later (presumably middle-term) aversive and appetitive memory. In general, the experimental design is rigorous, and statistics are appropriately applied. While the manuscript provides a useful tool, it would be strengthened further by additional mechanistic studies that build on the rich literature examining the roles of dopamine signaling in memory formation. The claim that Dop1R2 is involved in memory formation is strongly supported by the data presented, and this manuscript adds to a growing literature revealing that dopamine is a critical regulator of olfactory memory. However, the manuscript does not necessarily extend much beyond our understanding of Dop1R2 in memory formation, and future work will be needed to fully characterize this reagent and define the role of Dop1R2 in memory.

      Strengths:

      (1) The FRT lines generated provide a novel tool for temporal and spatially precise manipulation of Dop1R2 function. This tool will be valuable to study the role of Dop1R2 in memory and other behaviors potentially regulated by this gene.

      (2) Given the highly conserved role of Dop1R2 in memory and other processes, these findings have a high potential to translate to vertebrate species.

      Weaknesses:

      (1) The authors state Dop1R2 associates with two different G-proteins. It would be useful to know which one is mediating the loss of aversive and appetitive memory in Dop1R2 knockout flies.

      We thank you for the insightful comment. We agree that it would be very useful to know which G-proteins are transmitting Dop1R2 signaling. To that extent, we examined single-cell transcriptomics data to check the level of co-expression of Dop1R2 with G-proteins that are of interest to us. (Figure 1 S1)

      Lines 312-325

      “Some RNA binding proteins and Immediate early genes help maintain identities of Mushroom body cells and are regulators of local transcription and translation (de Queiroz et al., 2025; Raun et al., 2025). So, the availability of different G-proteins may change in different lobes and during different phases of memory. The G-protein via which GPCRs signal, may depend on the pool of available G-proteins in the cell/sub-cellular region (Hermans, 2003)., Therefore, Dop1R2 may signal via different G-proteins in different compartments of the Mushroom body and also different compartments of the neuron. We looked at Gαo and Gαq as they are known to have roles in learning and forgetting (Ferris et al., 2006; Himmelreich et al., 2017). We found that Dop1R2 co-expresses more frequently with Gαo than with Gαq (Figure 1 S1). While there is evidence for Dop1R2 to act via Gαq (Himmelreich et al., 2017). It is difficult to determine whether this interaction is exclusive, or if Dop1R2 can also be coupled to other G-proteins. It will be interesting to determine the breadth of G-proteins that are involved in Dop1R2 signaling.”

      (2) It would be interesting to examine 24hr aversive memory, in addition to 24hr appetitive memory.

      This is indeed an important point and we agree that it will complete the assessment of temporally distinct memory traces. We therefore performed the Aversive LTM experiments and include them in the results.

      Lines 208-228

      “24h memory is impaired by loss of Dop1R2

      Next, we wanted to see if later memory forms are also affected. One cycle of reward training is sufficient to create LTM (Krashes & Waddell, 2008), while for aversive memory, 5-6 cycles of electroshock-trainings are required to obtain robust long-term memory scores (Tully et al., 1994). So, we looked at both, 24h aversive and appetitive memory. For aversive LTM, the flies were tested on the Y-Maze apparatus as described in (Mohandasan et al., (2022).

      Flipping out Dop1R2 in the whole MB causes a reduced 24h memory performance (Figure 4A, E). No phenotype was observed when Ddop1R2 was flipped out in the γ-lobe (Figure 4B, F). However, similar to 2h memory, loss of Ddop1R2 in the α/β-lobes (Figure 4C, G) or the α’/β’-lobes (Figure 4D, H) causes a reduction in memory performance. Thus, Dop1R2 seems to be involved in aversive and appetitive LTM in the α/β-lobes and the α’/β’-lobes.

      Previous studies have shown mutation in the Dop1R2 receptor leads to improvement in LTM when a single shock training paradigm is used (Berry et al., 2012). As we found that it disrupts LTM, we wanted to verify if the absence of Dop1R2 outside the MB is what leads to an improvement in memory. To that extent, we tested panneuronal flip-out of Dop1R2 flies for 6hr and 24hr memory upon single shock using the elav-Gal4 driver. We found that it did not improve memory at both time points (Figure 4 S1). Confirming that flipping out Dop1R2 panneuronally does not improve LTM (Figure 4 S1C) and highlighting its irrelevance in memory outside the MB.”

      (3) The manuscript would be strengthened by added functional analysis. What are the DANs that signal through Dop1R. How do these knockouts impact MBONs?

      We thank you for this question. We indeed agree that it is a highly relevand and open question, how distinct DANs signal via distinct Dopamine receptors. Our work here uniquely focusses on Dop1R2 within the MB. We aim to investigate other DopRs and the connection between DANs in the future using similar approaches.

      (4) Also in Figure 2, the lobe-specific knockouts might be moved to supplemental since there is no effect. Instead, consider moving the control sensory tests into the main figure.

      We thank you for this suggestion and understand that in Figure 2 no significant difference is seen. However, we have emphasized in the text that the results from the supplementary figures are just to confirm that the modifications made at the Dop1R2 locus did not alter its normal function.

      Lines 156-162

      “We wanted to see if flipping out Dop1R2 in the MB affects memory acquisition and STM by using classical olfactory conditioning. In short, a group of flies is presented with an odor coupled to an electric shock (aversive) or sugar (appetitive) followed by a second odor without stimulus. For assessing their memory, flies can freely choose between the odors either directly after training (STM) or at a later timepoint.

      To ensure that the introduced genetic changes to the Dop1R2 locus do not interfere with behavior we first checked the sensory responses of that line”

      (5) Can the single-cell atlas data be used to narrow down the cell types in the vertical lobes that express Dop1R2? Is it all or just a subset?

      This is indeed an interesting question, and we thank you for mentioning it. To address this as best as we could, we analyzed the single cell transcriptomic data from (Davie et al., 2018) and presented it in Figure 1 S1.

      Reviewer #3 (Public Review):

      Summary:

      Kaldun et al. investigated the role of Dopamine Receptor Dop1R2 in different types and stages of olfactory associative memory in Drosophila melanogaster. Dop1R2 is a type 1 Dopamine receptor that can act both through Gs-cAMP and Gq-ERCa2+ pathways. The authors first developed a very useful tool, where tissue-specific knock-out mutants can be generated, using Crispr/Cas9 technology in combination with the powerful Gal4/UAS gene-expression toolkit, very common in fruit flies.

      They direct the K.O. mutation to intrinsic neurons of the main associative memory centre fly brain-the mushroom body (MB). There are three main types of MB-neurons, or Kenyon cells, according to their axonal projections: a/b; a'/b', and g neurons.

      Kaldun et al. found that flies lacking dop1R2 all over the MB displayed impaired appetitive middle-term (2h) and long-term (24h) memory, whereas appetitive short-term memory remained intact. Knocking-out dop1R2 in the three MB neuron subtypes also impaired middle-term, but not short-term, aversive memory.

      These memory defects were recapitulated when the loss of the dop1R2 gene was restricted to either a/b or a'/b', but not when the loss of the gene was restricted to g neurons, showcasing a compartmentalized role of Dop1R2 in specific neuronal subtypes of the main memory centre of the fly brain for the expression of middle and long-term memories.

      Strengths:

      (1) The conclusions of this paper are very well supported by the data, and the authors systematically addressed the requirement of a very interesting type of dopamine receptor in both appetitive and aversive memories. These findings are important for the fields of learning and memory and dopaminergic neuromodulation among others. The evidence in the literature so far was generated in different labs, each using different tools (mutants, RNAi knockdowns driven in different developmental stages...), different time points (short, middle, and long-term memory), different types of memories (Anesthesia resistant, which is a type of protein synthesis independent consolidated memory; anesthesia sensitive, which is a type of protein synthesis-dependent consolidated memory; aversive memory; appetitive memory...) and different behavioral paradigms. A study like this one allows for direct comparison of the results, and generalized observations.

      (2) Additionally, Kaldun and collaborators addressed the requirement of different types of Kenyon cells, that have been classically involved in different memory stages: g KCs for memory acquisition and a/b or a'/b' for later memory phases. This systematical approach has not been performed before.

      (3) Importantly, the authors of this paper produced a tool to generate tissue-specific knock-out mutants of dop1R2. Although this is not the first time that the requirement of this gene in different memory phases has been studied, the tools used here represent the most sophisticated genetic approach to induce a loss of function phenotypes exclusively in MB neurons.

      Weaknesses:

      (1) Although the paper does have important strengths, the main weakness of this work is that the advancement in the field could be considered incremental: the main findings of the manuscript had been reported before by several groups, using tissue-specific conditional knockdowns through interference RNAi. The requirement of Dop1R2 in MB for middle-term and long-term memories has been shown both for appetitive (Musso et al 2015, Sun et al 2020) and aversive associations (Plaçais et al 2017).

      Thank you for this comment. We believe that the main takeaway from the paper is the elegant tool we developed, to study the role of Dop1R2 in fruit flies by effectively flipping it out spatio-temporally. Additionally, we studied its role in all types of olfactory associative memory to establish it as a robust tool that can be used for further research in place of RNAi knockouts which are shown to be less efficient in insects as mentioned in the texts in line 394-398.

      “The genetic tool we generated here to study the role of the Dop1R2 dopamine receptor in cells of interest, is not only a good substitute for RNAi knockouts, which are known to be less efficient in insects (Joga et al., 2016), but also provides versatile possibilities as it can be used in combination with the powerful genetic tools of Drosophila.”

      (2) The approach used here to genetically modify memory neurons is not temporally restricted. Considering the role of dopamine in the correct development of the nervous system, one must consider the possible effects that this manipulation can have in the establishment of memory circuits. However, previous studies addressing this question restricted the manipulation of Dop1R2 expression to adulthood, leading to the same findings than the ones reported in this paper for both aversive and appetitive memories, which solidifies the findings of this paper.

      We thank you for this comment and we agree that it would be important to show a temporally restricted effect of Dop1R2 knockout. To assess this and rule out potential developmental defects we decided to restrict the knockout to the post-eclosion stage and to include these results.

      Lines 230-250

      “Developmental defects are ruled out in a temporally restricted Dop1R2 conditional knockout.

      To exclude developmental defects in the MB caused by flip-out of Dop1R2, we stained fly brains with a FasII antibody. Compared to genetic controls, flies lacking Dop1R2 in the mushroom body had unaltered lobes (Figure 4 S2C).

      Regardless, we wanted to control for developmental defects leading to memory loss in flip-out flies. So, we generated a Gal80ts-containing line, enabling the temporal control of Dop1R2 knockout in the entire mushroom body (MB). Given that the half-life of the receptor remains unknown, we assessed both aversive short-term memory (STM) and long-term memory (LTM) to determine whether post-eclosion ablation of Dop1R2 in the MB produced differences compared to our previously tested line, in which Dop1R2 was constitutively knocked out from fertilization. To achieve this, flies were maintained at 18°C until eclosion and subsequently shifted to 30°C for five to seven days. On the fifth day, training was conducted, followed by memory testing. Our results indicate that aversive STM was not significantly impaired in Dop1R2-deficient MBs compared to control flies (Figure 4 S3), consistent with our previous findings (Figure 2). However, aversive LTM was significantly impaired relative to control lines (Figure 4 S3), which also aligned with prior observations. These findings strongly indicate that memory loss caused by Dop1R2 flip-out is not due to developmental defects.”

      (3) The authors state that they aim to resolve disparities of findings in the field regarding the specific role of Dop1R2 in memory, offering a potent tool to generate mutants and addressing systematically their effects on different types of memory. Their results support the role of this receptor in the expression of long-term memories, however in the experiments performed here do not address temporal resolution of the genetic manipulations that could bring light into the mechanisms of action of Dop1R2 in memory. Several hypotheses have been proposed, from stabilization of memory, effects on forgetting, or integration of sequences of events (sensory experiences and dopamine release).

      We thank you for this comment. We agree that it would be interesting to dissect the memory stages by knocking out the receptor selectively in some of them (encoding, consolidation, retrieval). However, our tool irreversibly flips out Dop1R2 preventing us from investigating the receptor’s role in retrieval. Our results show that the receptor is dispensable for STM formation (Figure 2, Figure 4 Supplement 3), suggesting that it is not involved in encoding new information. On the other hand, it is instead involved in consolidation and/or retrieval of long-term and middle-term memories (Figure 3, Figure 4, Figure 5B).

      Overall, the authors generated a very useful tool to study dopamine neuromodulation in any given circuit when used in combination with the powerful genetic toolkit available in Drosophila. The reports in this paper confirmed a previously described role of Dop1R2 in the expression of aversive and appetitive LTM and mapped these effects to two specific types of memory neurons in the fly brain, previously implicated in the expression and consolidation of long-term associative memories.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) On the first view, the results shown here are different from studies published earlier, while in the same line with others (e.g. Sun et al, for appetitive 24h memories). For example, Berry et al showed that the loss of dop1R2 impairs immediate memory, while memory scores are enhanced 3h, 6h, and 24h after training. Further, they showed data that shock avoidance, at least for higher shock intensities, is reduced in mutant (damb) flies. All in all, this favors how important it is to improve the genetic tools for tissue-specific manipulation. Despite the authors nicely discussing their data with respect to the previous studies, I wondered whether it would be suitable to use the new tool and knock out dop1R2 panneuronally to see whether the obtained data match the results published by Berry et al.. Further, as stated in line 105ff: "As these studies used different learning assays - aversive and appetitive respectively as well as different methods, it is unclear if Dop1R2 has different functions for the different reinforcement stimulus" I wondered why the authors tested aversive and appetitive learning for STM and 2h memory, but only appetitive memory for 24h.

      Thank you for this comment. To that extent, as mentioned above in response to reviewer #2, we included in the results the aversive LTM experiment (Figure 4). Moreover, we performed experiments along the line of Berry et al. using our tool as shown in Figure 4 S1. Our results support that Dop1R2 is required for LTM, rather than to promote forgetting.

      (2) Line 165ff: I can´t find any of the supplementary data mentioned here. Please add the corresponding figures.

      Thank you for pointing this out. In that line we don’t refer to any supplementary data, but to the Figure 1F, showing the absence of the HA-tag in our MB knock-out line. We have clarified this in the text (lines 151-153)

      (3) I can't imagine that the scale bar in Figure 1D-F is correct. I would also like to suggest to show a more detailed analysis of the expression pattern. For example, both anterior and posterior views would be appropriate, perhaps including the VNC. This would allow the expression pattern obtained with this novel tool to be better compared with previously published results. Also, in relation to my comment above (1), it may help to understand the functional differences with previous studies, especially as the authors themselves state that the receptor is "mainly" expressed in the mushroom body (line 99). It would be interesting to see where else it is expressed (if so). This would also be interesting for the panneuronal knockdown experiment suggested under (1). If the receptor is indeed expressed outside the mushroom body, this may explain the differences to Berry et al.

      Thank you for noting this, there was indeed a mistake in the scale bar which we now fixed. Since with our HA-tag immunostaining we could not detect any noticeable signal outside of the MB, we decided to analyze previously existing single cell transcriptomics data that showed expression of the receptor in 7.99% of cells in the VNC and in 13.8% of cells outside the MB (lines 98-100) confirming its sparse expression in the nervous system. The lack of detection of these cells is likely due to the sparse and low expression of the protein. The HA-tag allows to detect the endogenous level of the locus (it is possible that a Gal4/UAS amplification of the signal might allow to detect these cells).

      Regarding the panneuronal knockout, we decided to try to replicate the experiment shown in Berry et al. in Figure 4 S1 and found that Dop1R2 is required for LTM.

      (4) Related to learning data shown in Figures 2-4, the authors should show statistical differences between all groups obtained in the ANOVA + PostHoc tests. Currently, only an asterisk is placed above the experimental group, which does not adequately reflect the statistical differences between the groups. In addition, I would like to suggest adding statistical tests to the chance level as it may be interesting to know whether, for example, scores of knockout flies in 3C and 3D are different from the chance level.

      Many thanks for this correction, we agree with the fact that the way significance scores were shown was not informative enough. We fixed the point by now showing significance between all the control groups and the experimental ones. We also inserted the chance level results in the figure legends.

      (5) Unfortunately, the manuscript has some typing errors, so I would like to ask the authors to check the manuscript again carefully.

      Some Examples:

      Line 31: the the

      Line 56: G-Protein

      Line 64: c-AMP

      Line 68: Dopamine

      Line 70: G-Protein (It alternates between G-protein and G-Protein)

      Line 76: References are formatted incorrectly

      Line 126: Ha-Tag (It alternates between Ha and HA)

      Line 248: missing space before the bracket...is often found

      Thank you for noticing these errors, we have now corrected the spelling throughout the manuscript.

      (6) In the figures the axes are labelled Preference Index (Pref"I"). In the methods, however, the calculation formula is defined as "PREF".

      We thank you for drawing attention to this. To avoid confusion, we changed the definition in the methods section so that it could be clear and coherent (“Memory tests” paragraph in the methods section).

      “PREF = ((N<sub>arm1</sub> - N<sub>arm2</sub>) 100) / N<sub>total</sub> the two preference indices were calculated from the two reciprocal experiments. The average of these two PREFs gives a learning index (LI). LI = (PREF<sub>1</sub> + PREF<sub>2</sub>) / 2.

      In case of all Long-term Aversive memory experiments, Y-Maze protocol was adapted to test flies 24 hours post training. Testing using the Y-Maze was done following the protocol as described in (Mohandasan et al., 2022) where flies were loaded at the bottom of 20-minutes odorized 3D-printed Y-Mazes from where they would climb up to a choice point and choose between the two odors. The learning index was then calculated after counting the flies in each odorized vial as follows: LI = ((N<sub>CS-</sub> - N<sub>CS+</sub>) 100) / N<sub>total</sub>. Where NCS- and NCS+ are the number of flies that were found trapped in the untrained and trained odor tube respectively.

      Reviewer #2 (Recommendations For The Authors):

      (1) In Figures 2 and 3, the legends running two different subfigures is confusing. Would be helpful to find a different way to present.

      Thank you for your suggestion. We modified how we present legends, placing them vertically so that it is clearer.

      (2) Use additional drivers to verify middle and long-term memory phenotypes.

      We agree that it would be interesting to see the role of Dop1R2 in other neurons. To that extent, we looked at long term aversive memory in flies where the receptor was panneuronaly flipped out, and did not find evidence that suggested involvement of Dop1R2 in memory processes outside the MB. (Figure 4 S1)

      (3) Additional discussion of genetic background for fly lines would be helpful.

      Thank you for your advice. We have mentioned the genetic background of flies in the key resources table of the methods sections. Additionally, we also included further explanation on how the lines were created and their genetic background (see “Fly Husbandry” paragraph in the methods section).

      “UAS-flp;;Dop1R2 cko flies and Gal4;Dop1R2<sup>cko</sup> flies were crossed back with ;;Dop<sup>cko</sup> flies to obtain appropriate genetic controls which were heterozygous for UAS and Gal4 but not Dop1R2<sup>cko</sup>.”

      Reviewer #3 (Recommendations For The Authors):

      Line 109 states that to resolve the problem a tool is developed to knock down Dop1R2 in s spatial and temporal specific manner- while I agree that this is within the potential of the tool, there is no temporal control of the flipase action in this study; at least I cannot find references to the use of target/gene switch to control stages of development or different memory phases. However the version available for download is missing supplementary information, so I did not have access to supplementary figures and tables.

      Thank you for the comment, as mentioned before it would be great to be able to dissect the memory phases. We show in lines 232 – 250 and Figure 4 S3 that the temporally restricted flip-out to the post-eclosion life stage gave us coherent results with the previous findings, ruling out potential developmental defects.

      In relation to my comment on the possible developmental effects of the loss of the gene, Figure 1F could showcase an underdeveloped g lobe when looking at the lobe profiles. I understand this is not within the scope of the figure, but maybe a different z projection can be provided to confirm there are no obvious anatomical alterations due to the loss of the receptor.

      We understand the doubt about the correct development of the MB and we thank you for your insightful comment. To that extent we decided to perform a FasII immunostaining that could show us the MB in the different lines (Figure 4 S2) and it appears that there are no notable differences in the lobes development in our knockout line.

      It seems that the obvious missing piece of the puzzle would be to address the effects of knocking out Dop1R2 in aversive LTM. The idea of systematically addressing different types of memory at different time points and in different KCs is the most attractive aspect of this study beyond the technical sophistication, and it feels that the aim of the study is not delivered without that component.

      We agree and we thank you for the clarification. As mentioned above in response to Reviewer #2, we decided to test aversive LTM as described in lines –208-228, Figure 4, Figure 4 S1.

      Some statements of the discussion seem too vague, and I think could benefit from editing:

      Line 284 "however other receptors could use Gq and mediate forgetting"- does this refer to other dopamine receptors? Other neuromodulators? Examples?

      Thank you for pointing this out. We Agree and therefore decided to omit this line.

      Line 289 "using a space training protocol and a Dop1R2 line" - this refers to RNAi lines, but it should be stated clearly.

      That is correct, we thank you for bringing attention to this and clarified it in the manuscript.

      –Lines 329-330

      “Interestingly, using a spaced training protocol and a Dop1R2 RNAi knockout line another study showed impaired LTM (Placais et al., 2017).”

      The paragraph starting in line 305 could be re-written to improve clarity and flow. Some statements seem disconnected and require specific citations. For example "In aversive memory formation, loss of Dop1R2 could lead to enhanced or impaired memory, depending on the activated signaling pathways and the internal state of the animal...". This is not accurate. Berry et al 2012 report enhanced LTM performance in dop1R2 mutants whereas Plaçais et al 2017 report LTM defects in Dop1R2 knock-downs, but these different findings do not seem to rely on different internal states or signaling pathways. Maybe further elaboration can help the reader understand this speculation.

      We agree and we thank you for this advice. We decided to add additional details and citations to validate our speculation

      Lines 350-353

      “In aversive memory formation, loss of Dop1R2 could lead to enhanced or impaired memory, depending on the activated signaling pathways. The signaling pathway that is activated further depends on the available pool of secondary messengers in the cell (Hermans, 2003) which may be regulated by the internal state of the animal.”

      "...for reward memory formation, loss of Dop1R2 seems to impair memory", this seems redundant at this point, as it has been discussed in detail, however, citations should be provided in any case (Musso 2015, Sun 2020)

      Thank you for noting this. We recognize the redundancy and decided to exclude the line.

      Finally, it would be useful to additionally refer to the anatomical terminology when introducing neuron names; for example MBON MVP2 (MBON-g1pedc>a/b), etc.

      Thank you for this suggestion. We understand the importance of anatomical terminologies for the neurons. Therefore, we included them when we introduce neurons in the paper.

      We thank you for your observations. We recognize their value, so we have made appropriate changes in the discussion to sound less vague and more comprehensive.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public review):

      Summary:

      Using highly specific antibody reagents for biological research is of prime importance. In the past few years, novel approaches have been proposed to gain easier access to such reagents. This manuscript describes an important step forward toward the rapid and widespread isolation of antibody reagents. Via the refinement and improvement of previous approaches, the Perrimon lab describes a novel phage-displayed synthetic library for nanobody isolation. They used the library to isolate nanobodies targeting Drosophila secreted proteins. They used these nanobodies in immunostainings and immunoblottings, as well as in tissue immunostainings and live cell assays (by tethering the antigens on the cell surface).

      Since the library is made freely available, it will contribute to gaining access to better research reagents for non-profit use, an important step towards the democratisation of science.

      Strengths:

      (1) New design for a phage-displayed library of high content.

      (2) Isolation of valuble novel tools.

      (3) Detailed description of the methods such that they can be used by many other labs.

      We are grateful for these supportive comments.

      Weaknesses:

      My comments largely concentrate on the representation of the data in the different Figures.

      We have made adjustments according to the reviewer’s recommendations.

      Reviewer #2 (Public review):

      Summary:

      In this study, the authors propose an alternative platform for nanobody discovery using a phage-displayed synthetic library. The authors relied on DNA templates originally created by McMahon et al. (2018) to build the yeast-displayed synthetic library. To validate their platform, the authors screened for nanobodies against 8 Drosophila secreted proteins. Nanobody screening has been performed with phage-displayed nanobody libraries followed by an enzyme-linked immunosorbent assay (ELISA) to validate positive hits. Nanobodies with higher affinity have been tested for immunostaining and immunoblotting applications using Drosophila adult guts and hemolymph, respectively.

      Strengths:

      The authors presented a detailed protocol with various and complementary approaches to select nanobodies and test their application for immunostaining and immunoblotting experiments. Data are convincing and the manuscript is well-written, clear, and easy to read.

      We thank the reviewer for these supportive comments.

      Weaknesses:

      On the eight Drosophila secreted proteins selected to screen for nanobodies, the authors failed to identify nanobodies for three of them. While the authors mentioned potential improvements of the protocol in the discussion, none of them have been tested in this manuscript.

      We prepared all eight antigens by single-step IgG purification (see Materials and Methods) without additional biophysical quality control (e.g., size-exclusion chromatography). Consequently, we cannot definitively determine whether the three “no-binder” cases resulted from the aggregation or misfolding of the antigens, versus gaps in our naive library’s sequence space. While approaches such as additional purification steps or affinity maturation of weak binders would likely rescue these difficult targets, comprehensive pipeline optimization is beyond the scope of establishing and validating the phage-displayed nanobody platform. We have clarified this limitation and suggested these strategies in third paragraph of the Discussion.

      The same comment applies to the experiments using membrane-tethered forms of the antigens to test the affinity of nanobodies identified by ELISA. Many nanobodies fail to recognize the antigens. While authors suggested a low affinity of these nanobodies for their antigens, this hypothesis has not been tested in the manuscript.

      We observed that several nanobodies with strong ELISA signals showed reduced binding to membrane-displayed antigens. This discrepancy may result from low affinity of the nanobodies or differences in post-translational modifications (e.g., glycosylation) and antigen context between secreted IgG-fusion proteins (used for panning/ELISA) and GPI- or mCD8-anchored proteins. In an ongoing work, we have performed affinity maturation of the nanobodies and successfully increased the affinity toward the target antigen. These results will be reported separately.

      Improving the protocol at each step for nanobody selection would greatly increase the success rate for the discovery of nanobodies with high affinity.

      We fully agree that systematic optimization—from antigen preparation (e.g., additional purification steps) through screening conditions (e.g., buffer composition, additional affinity-maturation steps)—could substantially increase the success rate and nanobody affinity. These represent important directions for future work.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Figure 3. The merge of two GFP channels does not make much sense. Can the authors not use artificial colours? And show the panels at higher resolution, such that a viewer can really see and judge what they are seeing? The same comments apply to all Supplementary Figures.

      We appreciate the reviewer’s comment. In the revised Figure 3, we have replaced the cyan/green overlay with red/green overlay and used enlarged pictures so that GFP-positive cells and corresponding nanobody staining are clearly visible. We applied the same layout to all relevant Supplementary Figures.

      (2) Figure 4. Also, in this Figure, it is not really possible to see what the authors say one should see. The resolution should be higher, and arrows or arrowheads should point to important structures.

      We appreciate the reviewer’s comment. In the revised Figure 4A, we have added arrows to point to the immunostaining signal in cells with smaller nuclei and added inset panels to show a closer view of representative NbMip-4G staining.

      Reviewer #2 (Recommendations for the authors):

      (1) Images are sometimes quite small and difficult to interpret. For example, Figures S2C-D.

      We thank the reviewer for this suggestion. In the revised figures, we have replaced the cyan/green overlay with red/green overlay and used enlarged pictures that clearly show GFP-positive cells alongside their corresponding nanobody staining.

      (2) Supplemental figures are not always cited in the text.

      Thank you for the comment. To eliminate this misunderstanding, we have updated the Nesfatin1 nanobody screen data as Supplementary Figure 1 and Mip nanobody screen data as Supplementary Figure 2. We have made the corresponding changes in the Results section.

    1. Author response:

      We were delighted by the reviewers' general comments. We thank the reviewers for their thoughtful reviews, constructive criticism, and analysis suggestions. We have carefully addressed each of their points during the revision of the manuscript.

      Unfortunately, after the paper was submitted to eLife, the first author, who ran all the analyses, left academia. We now realized that we currently do not have sufficient resources to perform all additional analyses as requested by the reviewers.

      The following is the authors’ response to the original reviews:

      Public Reviews:

      Reviewer #1 (Public Review):

      This study uses MEG to test for a neural signature of the trial history effect known as 'serial dependence.' This is a behavioral phenomenon whereby stimuli are judged to be more similar than they really are, in feature space, to stimuli that were relevant in the recent past (i.e., the preceding trials). This attractive bias is prevalent across stimulus classes and modalities, but a neural source has been elusive. This topic has generated great interest in recent years, and I believe this study makes a unique contribution to the field. The paper is overall clear and compelling, and makes effective use of data visualizations to illustrate the findings. Below, I list several points where I believe further detail would be important to interpreting the results. I also make suggestions for additional analyses that I believe would enrich understanding but are inessential to the main conclusions.

      (1) In the introduction, I think the study motivation could be strengthened, to clarify the importance of identifying a neural signature here. It is clear that previous studies have focused mainly on behavior, and that the handful of neuroscience investigations have found only indirect signatures. But what would the type of signature being sought here tell us? How would it advance understanding of the underlying processes, the function of serial dependence, or the theoretical debates around the phenomenon?

      Thank you for pointing this out. Our MEG study was designed to address two questions: 1) we asked whether we could observe a direct neural signature of serial dependence, and 2) if so, whether this signature occurs at the encoding or post-encoding stage of stimulus processing in working memory. This second question directly concerns the current theoretical debate on serial dependence.

      Previous studies have found only indirect signatures of serial dependence such as reactivations of information from the previous trial or signatures of a repulsive bias, which were in contrast to the attractive bias in behavior. Thus, it remained unclear whether an attractive neural bias can be observed as a direct reflection of the behavioral bias. Moreover, previous studies observed the neuronal repulsion during early visual processes, leading to the proposal that neural signals become attracted only during later, post-encoding processes. However, these later processing stages were not directly accessible in previous studies. To address these two questions, we combined MEG recordings with an experimental paradigm with two items and a retro-cue. This design allowed to record neural signals during separable encoding and post-encoding task phases and so to pinpoint the task phase at which a direct neural signature of serial dependence occurred that mirrored the behavioral effect.

      We have slightly modified the Introduction to strengthen the study motivation.

      (1a) As one specific point of clarification, on p. 5, lines 91-92, a previous study (St. JohnSaaltink et al.) is described as part of the current study motivation, stating that "as the current and previous orientations were either identical or orthogonal to each other, it remained unclear whether this neural bias reflected an attraction or repulsion in relation to the past." I think this statement could be more explicit as to why/how these previous findings are ambiguous. The St. John-Saaltink study stands as one of very few that may be considered to show evidence of an early attractive effect in neural activity, so it would help to clarify what sort of advance the current study represents beyond that.

      Thank you for this comment. In the study by St. John-Saaltink et al. (2016), two gratings oriented at 45° and 135° were always presented to either the left or right side of a central fixation point in a trial (90° orientation difference). As only the left/right position of the 45° and 135° gratings varied across trials, the target stimulus in the current trial was either the same or differed by exactly 90° from the previous trial. In consequence, this study could not distinguish whether the observed bias was attractive or repulsive, which concerned both the behavioral effect and the V1 signal. Furthermore, the bias in the V1 signal was partially explained by the orientation that was presented at the same position in the previous trial, which could reflect a reactivation of the previous orientation rather than an actual altered orientation.

      We have changed the Introduction accordingly.

      References:

      St. John-Saaltink E, Kok P, Lau HC, de Lange FP (2016) Serial Dependence in Perceptual Decisions Is Reflected in Ac6vity Pa9erns in Primary Visual Cortex. Journal of Neuroscience 36: 6186–6192.

      (1b) The study motivation might also consider the findings of Ranieri et al (2022, J. Neurosci) Fornaciai, Togoli, & Bueti (2023, J. Neurosci), and Lou& Collins (2023, J. Neurosci) who all test various neural signatures of serial dependence.

      Thank you. As all listed findings showed neural signatures revealing a reactivation of the previous stimulus or a response during the current trial, we have added them to the paragraph in the Introduction referring to this class of evidence for the neural basis for serial dependence.

      (2) Regarding the methods and results, it would help if the initial description of the reconstruction approach, in the main text, gave more context about what data is going into reconstruction (e.g., which sensors), a more conceptual overview of what the 'reconstruction' entails, and what the fidelity metric indexes. To me, all of that is important to interpreting the figures and results. For instance, when I first read, it was unclear to me what it meant to "reconstruct the direction of S1 during the S2 epoch" (p. 10, line 199)? As in, I couldn't tell how the data/model knows which item it is reconstructing, as opposed to just reporting whatever directional information is present in the signal.

      (2a) Relatedly, what does "reconstruction strength" reflect in Figure 2a? Is this different than the fidelity metric? Does fidelity reflect the strength of the particular relevant direction, or does it just mean that there is a high level of any direction information in the signal? In the main text explain what reconstruction strength and what fidelity is?

      Thank you for pointing this out. We applied the inverted encoding model method to MEG data from all active sensors (271) within defined time-windows of 100 ms length. MEG data was recorded in two sessions on different days. Specifically, we constructed an encoding model with 18 motion direction-selective channels. Each channel was designed to show peak sensitivity to a specific motion direction, with gradually decreasing sensitivity to less similar directions. In a training step, the encoding model was fiCed to the MEG data of one session to obtain a weight matrix that indicates how well the sensor activity can be explained by the modeled direction. In the testing step, the weight matrix was inverted and applied to the MEG data of the other session, resulting in a response profile of ‘reconstruction strengths’, i.e., how strongly each motion direction was present in a trial. When a specific motion direction was present in the MEG signal, the reconstruction strengths peaked at that specific direction and decreased with increasing direction difference. If no information was present, reconstruction strengths were comparable across all modeled directions, i.e., the response profile was flat. To integrate response profiles across trials, single trial profiles were aligned to a common center direction (i.e., 180°) and then averaged.

      To quantify the accuracy of each IEM reconstruction, i.e., how well the response profile represents a specific motion direction relative to all other directions we computed the ‘reconstruction fidelity’. Fidelity was obtained by projecting the polar vector of the reconstruction at every direction angle (in steps of 1°) onto the common center (180°) and averaging across all direction angles (Rademaker et al 2019, Sprague, Ester & Serences, 2016). As such, ‘reconstruction fidelity’ is a summary metric with fidelity greater than zero indicating an accurate reconstruction.

      How does the model know which direction to reconstruct? Our modelling procedure was informed about the stimulus in question during both the training and the testing step. Specifically, we informed our model during the training step about e.g., the current S2. Then, we fit the model to training data from the S2 epoch and applied it to testing data from the S2 epoch. Crucially, during the testing step the motion direction in question, i.e., current S2, becomes relevant again. For example, when S2 was 120°, the reconstructions were shifted by 60° in order to align with the common center, i.e., 180°. In addition, we also tested whether we could reconstruct the motion direction of S1 during the S2 epoch. Here, we used again the MEG data from the S2 epoch but now for S1 training. i.e., the model was informed about S1 direction. Accordingly, the recentering step during testing was done with regard to the S1 direction. Similarly, we also reconstructed the motion direction of the previous target (i.e., the previous S1 or S2), e.g., during the S2 epoch.

      Together, the multi-variate pattern of MEG activity across all sensors during the S2 epoch could contain information about the currently presented direction of S2, the direction of the preceding S1 and the direction of the target stimulus from the previous trial (i.e., either previous S1 or previous S2) at the same time. An important exception from this regime was the cross-reconstruction analysis (Appendix 1—figure 2). Here we trained the encoding model on the currently relevant item (S1 during the S1 epoch, S2 during the S2 epoch and the cued item during the retro-cue epoch) of one MEG session and reconstructed the previous target on the other MEG session.

      Finally, to examine shifts of the neural representation, single-trial reconstructions were assigned to two groups, those with a previous target that was oriented clockwise (CW) in relation to the currently relevant item and those with a previous target that was oriented counter-clockwise (CCW). The CCW reconstructions were flipped along the direction space, hence, a negative deviation of the maximum of the reconstruction from 180° indicated an attraction toward the previous target, whereas a positive deviation indicated a repulsion. Those reconstructions were then first averaged within each possible motion direction and then across them to account for different presentation numbers of the directions, resulting in one reconstruction per participant, epoch and time point. To examine systematic shifts, we then tested if the maximum of the reconstruction was systematically different from the common center (180°). For display purposes, we subtracted the reconstructed maximum from 180° to compute the direction shifts. A positive shift thus reflected attraction and a negative shift reflected repulsion.

      We have updated the Results accordingly.

      References:

      Rademaker RL, Chunharas C, Serences JT (2019) Coexisting representations of sensory and mnemonic information in human visual cortex. Nature Neuroscience. 22: 1336-1344.

      Sprague TC, Ester EF, Serences JT (2016) Restoring Latent Visual Working Memory Representations in Human Cortex. Neuron. 91: 694-707

      (3) Then in the Methods, it would help to provide further detail still about the IEM training/testing procedure. For instance, it's not entirely clear to me whether all the analyses use the same model (i.e., all trained on stimulus encoding) or whether each epoch and timepoint is trained on the corresponding epoch and timepoint from the other session. This speaks to whether the reconstructions reflect a shared stimulus code across different conditions vs. that stimulus information about various previous and current trial items can be extracted if the model is tailored accordingly.

      As reported above, our modeling procedure was informed about same stimulus during both the training and the testing step, except for the cross-reconstruction analysis.

      Regarding the training and testing data, the model was always trained on data from one session and tested on data from the other session, so that each MEG session once served as the training data set and once as the test data set, hence, training and test data were independent. Importantly, training and testing was always performed in an epoch- and time point-specific way: For example, the model that was trained on the first 100-ms time bin from the S1 epoch of the first MEG session was tested on the first 100-ms time bin from the S1 epoch of the second MEG session.

      Specifically, when you say "aim of the reconstruction" (p. 31, line 699), does that simply mean the reconstruction was centered in that direction (that the same data would go into reconstructing S1 or S2 in a given epoch, and what would differentiate between them is whether the reconstruction was centered to the S1 or S2 direction value)?

      As reported above, during testing the reconstruction was centered at the currently relevant direction. The encoding model was trained with the direction labels of S1, S2 or the target item, corresponding to the currently relevant direction, i.e., S1 in S1 epochs, S2 in S2 epochs and target item (S1 or S2) in the retro-cue epoch. The only exception was the reconstruction of S1 during the S2 epoch. Here the encoding model was trained on the S1 direction, but with data from the S2 epoch and then applied to the S2 epoch data and recentered to the S1 direction. So here, S1 and S2 were indeed trained and tested separately for the same epoch.

      (4) I think training and testing were done separately for each epoch and timepoint, but this could have important implications for interpreting the results. Namely if the models are trained and tested on different time points, and reference directions, then some will be inherently noisier than others (e.g., delay period more so than encoding), and potentially more (or differently) susceptible to bias. For instance, the S1 and S2 epochs show no attractive bias, but they may also be based on more high-fidelity training sets (i.e., encoding), and therefore less susceptible to the bias that is evident in the retrocue epoch.

      Thanks for pointing this out. Training and testing were performed in an epoch- and time point-specific way. Thus, potential differences in the signal-to-noise ratio between different task phases could cause quality differences between the corresponding reconstructed MEG signals. However, we did not observe such differences. Instead, we found comparable time courses of the reconstruction fidelities and the averaged reconstruction strengths between epochs (Figure 2b and 2c, respectively). Fig. 2b, e.g., shows that reconstruction fidelity for motion direction stimuli built up slowly during the stimulus presentation, reaching its maximum only after stimulus offset. This observation may contrast to different stimulus materials with faster build-ups, like the orientation of a Gabor.

      We agree with the reviewer that, regardless of the comparable but not perfectly equal reconstruction fidelities, there are good arguments to assume that the neural representation of the stimulus during its encoding is typically less noisy than during its post-encoding processing and that this difference could be one of the reasons why serial dependence emerged in our study only during the retro-cue epoch. However, the argument could also be reversed: a biased representation, which represents a small and hard-to-detect neural effect, might be easier to observe for less noisy data. So, the fact that we found a significant bias only during the potentially “noisier” retro-cue epoch makes the effect even more noteworthy.

      We mentioned the limitation related to our stimulus material already at the end of the Discussion. We have now added a new paragraph to the Discussion to address the two opposing lines of reasoning.  

      (4) I believe the work would benefit from a further effort to reconcile these results with previous findings (i.e., those that showed repulsion, like Sheehan & Serences), potentially through additional analyses. The discussion attributes the difference in findings to the "combination of a retro-cue paradigm with the high temporal resolution of MEG," but it's unclear how that explains why various others observed repulsion (thought to happen quite early) that is not seen at any stage here. In my view, the temporal (as well as spatial) resolution of MEG could be further exploited here to better capture the early vs. late stages of processing. For instance, by separately examining earlier vs. later time points (instead of averaging across all of them), or by identifying and analyzing data in the sensors that might capture early vs. late stages of processing. Indeed, the S1 and S2 reconstructions show subtle repulsion, which might be magnified at earlier time points but then shift (toward attraction) at later time points, thereby counteracting any effect. Likewise, the S1 reconstruction becomes biased during the S2 epoch, consistent with previous observations that the SD effects grow across a WM delay. Maybe both S1 and S2 would show an attractive bias emerging during the later (delay) portion of their corresponding epoch? As is, the data nicely show that an attractive bias can be detected in the retrocue period activity, but they could still yield further specificity about when and where that bias emerges.

      We are grateful for this suggestion. Before going into detail, we would like to explain our motivation for choosing the present analysis approach that included averaging time points within an epoch of interest.

      Our aim was to detect a neuronal signature of serial dependence which is manifested as an attractive shift of about 3.5° degrees within the 360° direction space. To be able to detect such a small effect in the neural data and given the limited resolution of the reconstruction method and the noisy MEG signals, we needed to maximize the signal-to-noise ratio. A common method to obtain this is by averaging data points. In our study we asked subjects to perform 1022 trials, down-sampled the MEG data from the recorded sampling rate of 1200 Hz to 10 Hz (one data point per 100 ms) that we used for the estimation of reconstruction fidelity and calculated the final neural shift estimates by averaging time points that showed a robust reconstruction fidelity, thus representing interpretable data points.

      Our procedure to maximize the signal-to-noise ratio was successful as we were able to reliably reconstruct the presented and remembered motion direction in all epochs (Figure 1a and 1b in the manuscript). However, the reconstruction did not work equally well for all time points within each epoch. In particular, there were time points with a non-significant reconstruction fidelity. In consequence, for the much smaller neural shift effect we did not expect to observe reliable time-resolved results, i.e., when considering each time point separately. Instead, we used the reconstruction results to define the time window in order to calculate the neural shift, i.e., we averaged across all time points with a significant reconstruction fidelity.

      Author response image 1 depicts the neural shift separately for each time point during the retro-cue epoch. Importantly, the gray parts of the time courses indicate time points where the reconstruction of the presented or cued stimulus was not significant. This means that the reconstructed maxima at those time points were very variable/unreliable and therefore the neural shifts were hardly interpretable.

      Author response image 1.

      Time courses of the reconstruction shift reveal a tendency for an attractive bias during the retrocue phase. Time courses of the neural shift separately for each time point during the S1 (left panel), S2 (middle panel) and retro-cue epochs (right panel). Gray lines indicate time points with non-significant reconstruction fidelities and therefore very variable and non-interpretable neural reconstruction shifts. The colored parts of the lines correspond to the time periods of significant reconstruction fidelities with interpretable reconstruction shifts. Error bars indicate the middle 95% of the resampling distribution. Time points with less than 5% (equaling p < .05) of the resampling distribution below 0° are indicated by a colored circle. N = 10.

      First, the time courses in the Author response image 1 show that the neural bias varied considerably between subjects, as revealed by the resampling distributions, at given time points. In this resampling procedure, we drew 10 participants in 10.000 iterations with replacement and calculated the reconstruction shift based on the mean reconstruction of the resampled participants. The observed variability stresses the necessity to average the values across all time points that showed a significant reconstruction fidelity to increase the signal-to-noise ratio.

      Second, despite this high variability/low signal-to-noise ratio, Author response image 1 (right panel) shows that our choice for this procedure was sensible as it revealed a clear tendency of an attractive shift at almost all time points between 300 through 1500 ms after retro-cue onset with only a few individual time-points showing a significant effect (uncorrected for multiple comparisons). It is worth to mention that this time course did not overlap with the time course of previous target cross-reconstruction (Appendix 1—figure 2, right panel), as there was no significant target cross-reconstruction during the retro-cue epoch with an almost flat profile around zero. Also, there was no overlap with previous target decoding in the retro-cue epoch (Figure 5 in the manuscript). Here, the previous target was reactivated significantly only at early time points of 200 and 300 ms post cue onset (i.e., at time points with a non-significant reconstruction fidelity and therefore no interpretable neural shift), while the nominally highest values of the attractive neural shift were visible at later time points that also showed a significant reconstruction fidelity (Figure 2b in the manuscript).

      Third, Author response image 1 (left and middle panel) shows the time courses of the neural shift during the S1 and S2 epochs. While no neural shift could be observed for S1, during the S2 epoch the time-resolved analysis indicated an initial attractive shift followed by a (nonsignificant) tendency for a repulsive shift. After averaging neural shifts across time points with a significant reconstruction fidelity, there was no significant effect with an overall tendency for repulsion, as reported in the paper. The attractive part of the neural shift during the S2 epoch was nominally strongest at very early time points (at 100-300 ms after S2 onset) and overlapped perfectly with the reactivation of the previous target as shown by the cross-reconstruction analysis (Appendix 1—figure 2, middle panel). This overlap suggests that the neural attractive shift did not reflect an actual bias of the early S2 representation, but rather a consequence of the concurrent reactivation of the previous target in the same neural code as the current representation. Finally, this neural attractive shift during S2 presentation did not correlate with the behavioral error (single trial-wise correlation: no significant time points during S2 epoch) or the behavioral bias (subject-wise correlation). In contrast, for the retro-cue epoch, we observed a significant correlation between the neural attractive shift and behavior.

      Together, the time-resolved results show a clear tendency for an attractive neural bias during the retro-cue phase, thus supporting our interpretation that the attractive shift during the retro-cue phase reflects a direct neuronal signature of serial dependence. However, these additional analyses also demonstrated a large variability between participants and across time points, warranting a cautious interpretation. We conclude that our initial approach of averaging across time points was an appropriate way of reducing the high level of noise in the data and revealed the reported significant and robust attractive neural shift in the retrocue phase.

      (5) A few other potentially interesting (but inessential considerations): A benchmark property of serial dependence is its feature-specificity, in that the attractive bias occurs only between current and previous stimuli that are within a certain range of similarity to each other in feature space. I would be very curious to see if the neural reconstructions manifest this principle - for instance, if one were to plot the trialwise reconstruction deviation from 0, across the full space of current-previous trial distances, as in the behavioral data. Likewise, something that is not captured by the DoG fivng approach, but which this dataset may be in a position to inform, is the commonly observed (but little understood) repulsive effect that appears when current and previous stimuli are quite distinct from each other. As in, Figure 1b shows an attractive bias for direction differences around 30 degrees, but a repulsive one for differences around 170 degrees - is there a corresponding neural signature for this component of the behavior?

      We appreciate the reviewer's idea to split the data. However, given that our results strongly relied on the inclusion of all data points, i.e., including all distances in motion direction between the current S1, S2 or target and the previous target and requiring data averaging, we are concerned that our study was vastly underpowered to be able to inform whether the attractive bias occurs only within a certain range of inter-stimulus similarity. To address this important question, future studies would require neural measurements with much higher signal-to-noise-ratio than the present MEG recordings with two sessions per participant and 1022 trials in total.

      Reviewer #2 (Public Review):

      Summary:

      The study aims to probe the neural correlates of visual serial dependence - the phenomenon that estimates of a visual feature (here motion direction) are attracted towards the recent history of encoded and reported stimuli. The authors utilize an established retro-cue working memory task together with magnetoencephalography, which allows to probe neural representations of motion direction during encoding and retrieval (retro-cue) periods of each trial. The main finding is that neural representations of motion direction are not systematically biased during the encoding of motion stimuli, but are attracted towards the motion direction of the previous trial's target during the retrieval (retro-cue period), just prior to the behavioral response. By demonstrating a neural signature of attractive biases in working memory representations, which align with attractive behavioral biases, this study highlights the importance of post-encoding memory processes in visual serial dependence.

      Strengths:

      The main strength of the study is its elegant use of a retro-cue working memory task together with high temporal resolution MEG, enabling to probe neural representations related to stimulus encoding and working memory. The behavioral task elicits robust behavioral serial dependence and replicates previous behavioral findings by the same research group. The careful neural decoding analysis benefits from a large number of trials per participant, considering the slow-paced nature of the working memory paradigm. This is crucial in a paradigm with considerable trial-by-trial behavioral variability (serial dependence biases are typically small, relative to the overall variability in response errors). While the current study is broadly consistent with previous studies showing that attractive biases in neural responses are absent during stimulus encoding (previous studies reported repulsive biases), to my knowledge it is the first study showing attractive biases in current stimulus representations during working memory. The study also connects to previous literature showing reactivations of previous stimulus representations, although the link between reactivations and biases remains somewhat vague in the current manuscript. Together, the study reveals an interesting avenue for future studies investigating the neural basis of visual serial dependence.

      Weaknesses:

      (1) The main weakness of the current manuscript is that the authors could have done more analyses to address the concern that their neural decoding results are driven by signals related to eye movements. The authors show that participants' gaze position systematically depended on the current stimuli's motion directions, which together with previous studies on eye movement-related confounds in neural decoding justifies such a concern. The authors seek to rule out this confound by showing that the consistency of stimulus-dependent gaze position does not correlate with (a) the neural reconstruction fidelity and (b) the repulsive shift in reconstructed motion direction. However, both of these controls do not directly address the concern. If I understand correctly the metric quantifying the consistency of stimulus-dependent gaze position (Figure S3a) only considers gaze angle and not gaze amplitude. Furthermore, it does not consider gaze position as a function of continuous motion direction, but instead treats motion directions as categorical variables. Therefore, assuming an eye movement confound, it is unclear whether the gaze consistency metric should strongly correlate with neural reconstruction fidelity, or whether there are other features of eye movements (e.g., amplitude differences across participants, and tuning of gaze in the continuous space of motion directions) which would impact the relationship with neural decoding. Moreover, it is unclear whether the consistency metric, which does not consider history dependencies in eye movements, should correlate with attractive history biases in neural decoding. It would be more straightforward if the authors would attempt to (a) directly decode stimulus motion direction from x-y gaze coordinates and relate this decoding performance to neural reconstruction fidelity, and (b) investigate whether gaze coordinates themselves are history-dependent and are attracted to the average gaze position associated with the previous trials' target stimulus. If the authors could show that (b) is not the case, I would be much more convinced that their main finding is not driven by eye movement confounds.

      The reviewer is correct that our eye-movement analysis approach considered gaze angle (direction) and not gaze amplitude. We considered gaze direction to be the more important feature to control for when investigating the neural basis of serial dependence that manifests, given the stimulus material used in our study, as a shift/deviation of angle/direction of a representation towards the previous target motion direction. To directly relate gaze direction and MEG data to each other we equaled the temporal resolution of the eye tracking data to match that of the MEG data. Specifically, our analysis procedure of gaze direction provided a measure indicating to which extent the variance of the gaze directions was reduced compared with random gaze direction patterns, in relation to the specific stimulus direction within each 100 ms time bin. Importantly, this procedure was able to reveal not only systematic gaze directions that were in accordance with the stimulus direction or the opposite direction, but also picked up all stimulus-related gaze directions, even if the relation differed across participants or time.

      Our analysis approach was highly sensitive to detect stimulus-related gaze directions during all task phases (Appendix 1—figure 3). As expected, we found systematic gaze directions when S1 and S2 were presented on the screen, and they were reduced thereafter, indicating a clear relationship between stimulus presentation and eye movement. Systematic gaze directions were also present in the retro-cue phase where no motion direction was presented. Here they showed a clearly different temporal dynamic as compared to the S1 and S2 phases. They appeared at later time points and with a higher variability between participants, indicating that they coincided with retrieving the target motion direction from working memory.

      To relate gaze directions with MEG results, we calculated Spearman rank correlations. We found that there was no systematic relationship at any time point between the stimulus related reconstruction fidelity and the amount of stimulus-related gaze direction. Even more, the correlation varied strongly from time point to time point revealing its random nature. In addition to the lack of significant correlations, we observed clearly distinct temporal profiles for gaze direction (Appendix 1—figure 3a and Appendix 1—figure 3b) and the reconstruction fidelities (Figure 2b in the manuscript, Appendix 1—figure 3c), in particular in the critical retro-cue phase.

      We favored this analysis approach over one that directly decoded stimulus motion direction from x-y gaze coordinates, as we considered it hardly feasible to compute an inverted encoding model with only two eye-tracker channels as an input (in comparison to 271 MEG sensors), and to our knowledge, this has not been done before. Other decoding methods have previously been applied to x-y gaze coordinates. However, in contrast to the inverted encoding model, they did not provide a measure of the representation shift which would be crucial for our investigation of serial dependence.

      We appreciate the suggestion to conduct additional analyses on eye tracking data (including different temporal and spatial resolution and different features) and their relation to MEG data. However, the first author, who ran all the analyses, has in the meantime left academia. Unfortunately, we currently do not have sufficient resources to perform additional analyses.

      While the presented eye movement control analysis makes us confident that our MEG finding was not crucially driven by stimulus-related gaze directions, we agree with the reviewer that we cannot completely exclude that other eye movement-related features could have contributed to our MEG findings. However, we would like to stress that whatever that main source for the observed MEG effect was (shift of the neuronal stimulus representation, (other) features of gaze movement, or shift of the neuronal stimulus representation that leads to systematic gaze movement), our study still provided clear evidence that serial dependence emerged at a later post-encoding stage of object processing in working memory. This central finding of our study is hard to observe with behavioral measures alone and is not affected by the possible effects of eye movements.

      We have slightly modified our conclusion in the Results and Appendix 1. Please see also our response to comment 1 from reviewer 3.

      (2) I am not convinced by the across-participant correlation between attractive biases in neural representations and attractive behavioral biases in estimation reports. One would expect a correlation with the behavioral bias amplitude, which is not borne out. Instead, there is a correlation with behavioral bias width, but no explanation of how bias width should relate to the bias in neural representations. The authors could be more explicit in their arguments about how these metrics would be functionally related, and why there is no correlation with behavioral bias amplitude.

      We are grateful for this suggestion. We correlated the individual neuronal shift with the two individual parameter fits of the behavior shift, i.e., amplitude (a) and tuning width (w). We found a significant correlation between the individual neural bias and the w parameter (r = .70, p = .0246) but not with the a parameter (r = -.35, p = .3258) during the retro-cue period (Appendix 1—figure 1). This indicates that a broader tuning width of the individual bias (as reflected by a smaller w parameter) was associated with a stronger individual neural attraction.

      It is important to note that for the calculation of the neural shift, all trials entered the analysis to increase the signal-to-noise ratio, i.e., it included many trials where current and previous targets were separated by, e.g., 100° or more. These trials were unlikely to produce serial dependence. Subjects with a more broadly tuned serial dependence had more interitem differences that showed a behavioral attraction and therefore more trials affected by serial dependence that entered the calculation of the neural shift. In contrast, individual differences in the amplitude (a) parameter were most likely too small, and higher individual amplitude did not involve more trials as compared to smaller amplitude to affect the neural bias in a way to be observed in a significant correlation.

      We have added this explanation to Appendix 1.  

      (3) The sample size (n = 10) is definitely at the lower end of sample sizes in this field. The authors collected two sessions per participant, which partly alleviates the concern. However, given that serial dependencies can be very variable across participants, I believe that future studies should aim for larger sample sizes.

      We want to express our appreciation for raising this issue. We apologize that we did not explicitly explain and justifythe choice for the sample size used in our paper, in particular, as we had in fact performed a formal a-priori power analysis.

      At the time of the sample size calculation, there were no comparable EEG or MEG studies to inform our power calculation. Thus, we based our calculation merely on the behavioral effect reported in the literature and, in particular, observed in a behavioral study from our lab that included four different experiments with overall more than 100 participants with 1632 trials each (see Fischer et al., 2020), in which the behavioral serial dependence effect (target vs. nontarget) was very robust. Based on the contrast between target and non-target with an effect size of 1.359 in Experiment 1, a power analysis with 80% desired power led to a small, estimated sample size of 6 subjects.

      However, we expected that the detection of the neural signature of this effect would require more participants. Therefore, we based our power calculation on a much smaller behavioral effect, i.e. the modulation of serial dependence by the context-feature congruency that we observed in our previous study (Fischer et al., 2020). In particular, we focused on Experiment 1 of the previous study that used color as the feature for retro-cueing, as we planned to use exactly the same paradigm for the MEG study. In contrast to the serial dependence effect, its modulation by color resulted in a more conservative power estimate: Based on an effect size of 0.856 in that experiment, a sample size of n = 10 should yield a power of 80% with two MEG sessions per subject.

      At the time when we conducted our study, two other studies were published that investigated serial dependence on the neural level. Both studies included a smaller number of data points than our study: Sheehan & Serences (2022) recorded about 840 trials in each of 6 participants, resulting in fewer data points both on the participant and on the trial level. Hajonides et al. (2023) measured 20 participants with 400 trials each, again resulting in fewer datapoints than our study (10 participants with 1022 trials each). Taken together, our a-priori sample size estimation resulted in comparable if not higher power as compared to other similar studies, making us feel confident that the estimated sample was sufficient to yield reliable results.

      We have now included this description and the results of this power analysis in the Materials and Methods section.

      Despite this, we fully agree with the reviewer that our study would profit from higher power. With the knowledge of the results from this study, future projects should attempt to increase substantially the signal-to-noise-ratio by increasing the number of trials in particular, in order to observe, e.g., robust time-resolved effects (see our comments to review 1).

      References:

      Fischer C, Czoschke S, Peters B, Rahm B, Kaiser J, Bledowski C (2020) Context information supports serial dependence of multiple visual objects across memory episodes. Nature Communication 11: 1932.

      Sheehan TC, Serences JT (2022) Attractive serial dependence overcomes repulsive neuronal adaptation PLOS Biology 20: e3001711.

      Hajonides JE, Van Ede F, Stokes MG, Nobre AC, Myers NE (2023) Multiple and Dissociable Effects of Sensory History on Working-Memory Performance Journal of Neuroscience 43: 2730–2740.

      (4) It would have been great to see an analysis in source space. As the authors mention in their introduction, different brain areas, such as PPC, mPFC, and dlPFC have been implicated in serial biases. This begs the question of which brain areas contribute to the serial dependencies observed in the current study. For instance, it would be interesting to see whether attractive shifts in current representations and pre-stimulus reactivations of previous stimuli are evident in the same or different brain areas.

      We appreciate this suggestion. As mentioned above, we currently do not have sufficient resources to perform a MEG source analysis.

      Reviewer #3 (Public Review):

      Summary:

      This study identifies the neural source of serial dependence in visual working memory, i.e., the phenomenon that recall from visual working memory is biased towards recently remembered but currently irrelevant stimuli. Whether this bias has a perceptual or postperceptual origin has been debated for years - the distinction is important because of its implications for the neural mechanism and ecological purpose of serial dependence. However, this is the first study to provide solid evidence based on human neuroimaging that identifies a post-perceptual memory maintenance stage as the source of the bias. The authors used multivariate pattern analysis of magnetoencephalography (MEG) data while observers remembered the direction of two moving dot stimuli. After one of the two stimuli was cued for recall, decoding of the cued motion direction re-emerged, but with a bias towards the motion direction cued on the previous trial. By contrast, decoding of the stimuli during the perceptual stage was not biased.

      Strengths:

      The strengths of the paper are its design, which uses a retrospective cue to clearly distinguish the perceptual/encoding stage from the post-perceptual/maintenance stage, and the rigour of the careful and well-powered analysis. The study benefits from high within participant power through the use of sensitive MEG recordings (compared to the more common EEG), and the decoding and neural bias analysis are done with care and sophistication, with appropriate controls to rule out confounds.

      Weaknesses:

      A minor weakness of the study is the remaining (but slight) possibility of an eye movement confound. A control analysis shows that participants make systematic eye movements that are aligned with the remembered motion direction during both the encoding and maintenance phases of the task. The authors go some way to show that this eye gaze bias seems unrelated to the decoding of MEG data, but in my opinion do not rule it out conclusively. They merely show that the strengths of the gaze bias and the strength of MEGbased decoding/neural bias are uncorrelated across the 10 participants. Therefore, this argument seems to rest on a null result from an underpowered analysis.

      Our MEG as well eye-movement analysis showed that they were sensitive to pick up robustly stimulus-related effects, both for presented and remembered motion directions. When relating both signals to each other by correlating MEG reconstruction strength with gaze direction, we found a null effect, as pointed out by the reviewer. Importantly, there was also a null effect when the shift of the reconstruction (representing our main finding) was correlated with gaze direction. Furthermore, an examination of the individual time courses of gaze direction and individual MEG reconstruction strength revealed that the lack of a relationship between MEG and gaze data did not rest on a singular observation but was present across all time points. Even more, the temporal profile of the correlation varied strongly from time point to time point revealing its random nature and indicating that there was no hint of a pattern that just failed to reach significance. Taking these observations together, our MEG findings were unlikely to be explained by eye position.

      Nevertheless, we agree with the reviewer that there is general problem of interpreting a null effect with a limited number of observations (and an analysis approach that focused on one out of many possible features of the gaze movement). Thus, we admit that there is a (slight) possibility that eye movements contributed to the observed MEG effects. This possibility, however, did not affect our novel finding that serial dependence occurred during the postencoding stage of object processing in working memory.

      Please see also our response to point 1 from reviewer 2.

      Impact:

      This important study contributes to the debate on serial dependence with solid evidence that biased neural representations emerge only at a relatively late post-perceptual stage, in contrast to previous behavioural studies. This finding is of broad relevance to the study of working memory, perception, and decision-making by providing key experimental evidence favouring one class of computational models of how stimulus history affects the processing of the current environment.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      Minor concerns:

      The significance statement opens "Our perception is biased towards sensory input from the recent past." This is a semantic point, but it seems a somewhat odd statement, given there is so much debate about whether serial dependence is perceptual vs. decisional, and that the current work indeed claims that it emerges at a late, post-encoding stage.

      Thank you for this point. We agree. “Visual cognition is biased towards sensory input from the recent past.” would be a more appropriate statement. According to the Journal's guidelines, however, the paragraph with the Significant Statement will be not included in the final manuscript.

      It would be preferable for data and code to be available at review so that reviewers might verify some procedural points for clarity.

      Code and preprocessed data used for the presented analyses are now available on OSF via http://osf.io/yjc93/. Due to storage limitations, only the preprocessed MEG data for the main IEM analyses focusing on the current direction are uploaded. For access to additional data, please contact the authors.

      For instance, I could use some clarification on the trial sequence. The methods first say the direction was selected randomly, but then later say each direction occurred equally often, and there were restrictions on the relationships between current and previous trial items. So it seems it couldn't have truly been random direction selection - was the order selected randomly from a predetermined set of possibilities?

      For the S1/S2 stimuli in a trial the dots moved fully coherent in a direction randomly drawn from a pool of directions between 5° and 355° spaced 10° from one another, therefore avoiding cardinal directions. Across trials, there was a predetermined set of possible differences in motion direction between the current and the previous target. This set included 18 motion direction differences, ranging from -170° to 180°, in steps of 10°. Trial sequences were balanced in a way that each of these differences occurred equally often during a MEG session.

      I could also use some additional assurance the sample size (participants or data points) is sufficient for the analysis approach deployed here.

      We performed a formal a-priori power analysis to justify our choice for the sample size. Please see our response to reviewer 2, point 3, where we explained the procedure of the apriori power analysis in detail. We have now included this description and the results of this power analysis in the Materials and Methods.

      Did you consider a decoding approach, instead of reconstruction, to test what information predominates the signal, in an unbiased way?

      Thank you for this argument. With our analysis approach based on the inverted encoding model, we believe to be unbiased, since we first reconstructed whether the MEG signal contained information about the presented and remembered motion direction. Only in the next step, we tested whether this reconstructed signal showed an offset and if so, whether this offset was biased towards or away from the previous target. A decoding approach aims to answer classification questions and is not suitable to reveal the actual shifts of the neural information. In our study, we could decode, e.g., the current direction or the previous target, but this would not answer the question of whether and at which stage of object processing the current representation was biased towards the past. Moreover, in a decoding approach to reveal which information predominates in the signal, we would have to classify different options (e.g. current information vs previous), thereby biasing the possible set of results more than in our chosen analysis.

      I think the claim of a "direct" neural signature may come off as an overstatement when the spatial and temporal aspects of the attractive bias are still so coarsely specified here.

      Thank you for pointing this out. We agree that the term “direct neural signature” can be seen as an overstatement when it is interpreted to indicate a narrowly defined activity of a brain region (ideally via “direct” invasive recordings) that reflects serial dependence. Our definition of the term “direct” referred to the observation of an attractive shift in a neural representation of the current target motion direction item towards the previous target. This was in contrast to previous “indirect” evidence for the neural basis of serial dependence based on either repulsive shifts of neural representations that were opposite to the attractive bias in behavior or on a reactivation of previous information in the current trial without presenting evidence for the actual neural shift. With this definition in mind, we consider the title of our study a valid description of our findings.

      Reviewer #2 (Recommendations For The Authors):

      I was wondering why the authors chose a bootstrap test for their neural bias analysis instead of a permutation test, similar to the one they used for their behavioral analysis. As far as I know, bootstrap tests do not provide guaranteed type-1 error rate control. The procedure for the permutation test would be quite straightforward here, randomly permuting the sign of each participant's neural shift and recording the group-average shift in a permutation distribution. This test seems more adequate and more consistent with the behavioral analysis.

      Thank you for this comment. We adapted a resampling approach (bootstrapping) that was similar to that by Ester et al. (2020) who also investigated categorical biases and also applied a reconstruction method (Inverted Encoding Model) to assess significance of a bias of the reconstructed orientation against zero in a certain direction. The bootstrapping method relied on a) detecting an offset against zero and b) evaluating the robustness of the observed effect across participants. In contrast, a permutation approach, as suggested by the reviewer, assesses whether an empirical neural shift is more extreme than the permutation distribution. The permutation approach seems more suited to assess the magnitude of the shift which in our study was not a priority. Therefore, we reasoned that the bootstrapping for our inference statistics was better suited to assess the direction of the neural shift and its robustness across participants.

      We have added this additional information to the Materials and Methods:

      References:

      Ester EF, Sprague TC, Serences JT (2020) Categorical biases in human occipitoparietal cortex. Journal of Neuroscience 40:917–931.

      The manuscript could be improved by more clearly spelling how the training and testing data were labelled, particularly for the reactivation analyses. If I understood correctly, in the first reactivation analysis the authors train and test on current trial data, but label both training and testing data according to the previous trial's motion direction. In the second analysis, they label the training data according to the current motion direction, but label the testing data according to the previous motion direction. Is that correct?

      Yes, this is correct. Please see also our response to reviewer 1, point 2 and 3, for a detailed description.

      I was surprised to see that the shift in the reconstructed direction is about three times larger than the behavioral attraction bias. Would one not expect these to be comparable in magnitude? It would be helpful to address and discuss this in the discussion section.

      Thank you for pointing this out. We agree with the reviewer that as both measures provided an identical metric (angle degree), one would expect that their magnitudes should be directly comparable. However, we speculate that these magnitudes inform only about the direction of the bias and their significant difference from zero, thus they operate on different scales and are not directly comparable. For example, Hallenbeck et al. (2022) showed that fMRI-based reconstructed orientation bias and behavioral bias correlated on both individual and group level, despite strong magnitude differences. This is in line with our observation and supports the speculation that the magnitudes of neural and behavioral biases operate on different scales and, thus, are not directly comparable.

      We have updated to the Discussion accordingly.

      References:

      Hallenbeck GE, Sprague TC, Rahmati M, Sreenivasan KK, Curtis CE (2022) Working memory representations in visual cortex mediate distraction effects Nature Communications 12: 471.

      Reviewer #3 (Recommendations For The Authors):

      (1) It may be worth showing that the gaze bias towards the current/cued stimulus is not biased towards the previous target. One option might be to run the same analysis pipeline used for the MEG decoding but on the eye-tracking data. Another could be to remove all participants with significant gaze bias, but given the small sample size, this might not be feasible.

      We appreciate this suggestion. However, as mentioned above, we currently do not have sufficient resources to conduct additional analyses on the eye tracking data.

      (2) Minor typo: Figure 3c - bias should be 11.7º, not -11.7º.

      Corrected. Thank you!

      Note on data/code availability: The authors state that preprocessed data and analysis code will be made available on publication, but are not available yet.

      Code and preprocessed data used for the present analyses are now available on OSF via http://osf.io/yjc93/. Due to storage limitations, only the preprocessed MEG data for the main IEM analyses focusing on the current direction are uploaded. For access to additional data, please contact the authors.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Participants in this study completed three visits. In the first, participants received experimental thermal stimulations which were calibrated to elicit three specific pain responses (30, 50, 70) on a 0-100 visual analogue scale (VAS). Experimental pressure stimulations were also calibrated at an intensity to the same three pain intensity responses. In the subsequent two visits, participants completed another pre-calibration check (Visit 2 of 3 only). Then, prior to the exercise NALOXONE or a SALINE placebo-control was administered intravenously. Participants then completed 1 of 4 blocks of HIGH (100%) or LOW (55%) intensity cycling which was tailored according to a functional threshold power (FTP) test completed in Visit 1. After each block of cycling lasting 10 minutes, participants entered an MRI scanner and were stimulated with the same thermal and pressure stimulations that corresponded to 30, 50, and 70 pain intensity ratings from the calibration stage. Therefore, this study ultimately sought to investigate whether aerobic exercise does indeed incur a hypoalgesia effect. More specifically, researchers tested the validity of the proposed endogenous pain modulation mechanism. Further investigation into whether the intensity of exercise had an effect on pain and the neurological activation of pain-related brain centres were also explored.

      Results show that in the experimental visits (Visit 2 and 3), when participants exercised at two distinct intensities as intended. Power output, heart rate, and perceived effort ratings were higher during the HIGH versus LOW-intensity cycling. In particular. HIGH intensity exercise was perceived as "hard" / ~15 on the Borg (1974, 1998) scale, whereas LOW intensity exercise was perceived as "very light" / ~9 on the same scale.

      The fMRI data from Figure 1 indicates that the anterior insula, dorsal posterior insula, and middle cingulate cortex show pronounced activation as stimulation intensity and subsequent pain responses increased, thus linking these brain regions with pain intensity and corroborating what many studies have shown before.

      Results also showed that participants rated a higher pain intensity in the NALOXONE condition at all three stimulation intensities compared to the SALINE condition. Therefore, the expected effect of NALOXONE in this study seemed to occur whereby opioid receptors were "blocked" and thus resulted in higher pain ratings compared to a SALINE condition where opioid receptors were "not blocked". When accounting for participant sex, NALOXONE had negligible effects at lower experimental nociceptive stimulations for females compared to males who showed a hyperalgesia effect to NALOXONE at all stimulation intensities (peak effect at 50 VAS). Females did show a hyperalgesia effect at stimulation intensities corresponding to 50 and 70 VAS pain ratings. The fMRI data showed that the periaqueductal gray (PAG) showed increased activation in the NALOXONE versus SALINE condition at higher thermal stimulation intensities. The PAG is well-linked to endogenous pain modulation.

      When assessing the effects of NALOXONE and SALINE after exercise, results showed no significant differences in subsequent pain intensity ratings.

      When assessing the effect of aerobic exercise intensity on subsequent pain intensity ratings, authors suggested that aerobic exercise in the form of a continuous cycling exercise tailored to an individual's FTP is not effective at eliciting an exercise-induced hypoalgesia response irrespective of exercise intensity. This is because results showed that pain responses did not differ significantly between HIGH and LOW intensity exercise with (NALOXONE) and without (SALINE) an opioid antagonist. Therefore, authors have also questioned the mechanisms (endogenous opioids) behind this effect.

      Strengths:

      Altogether, the paper is a great piece of work that has provided some truly useful insight into the neurological and perceptual mechanisms associated with pain and exercise-induced hypoalgesia. The authors have gone to great lengths to delve into their research question(s) and their methodological approach is relatively sound. The study has incorporated effective pseudo-randomisation and conducted a rigorous set of statistical analyses to account for as many confounds as possible. I will particularly credit the authors on their analysis which explores the impact of sex and female participants' stage of menses on the study outcomes. It would be particularly interesting for future work to pursue some of these lines of research which investigate the differences in the endogenous opioid mechanism between sexes and the added interaction of stage of menses or training status.

      There are certainly many other areas that this article contributes to the literature due to the depth of methods the research team has used. For example, the authors provide much insight into: the impact of exercise intensity on the exercise-induced hypoalgesia effect; the impact of sex on the endogenous opioid modulation mechanism; and the impact of exercise intensity on the neurological indices associated with endogenous pain modulation and pain processing. All of which, the researchers should be credited for due to the time and effort they have spent completing this study. Indeed, their in-depth analysis of many of these areas provides ample support for the claims they make in relation to these specific questions. As such, I consider their evidence concerning the fMRI data to be very convincing (and interesting).

      Weaknesses:

      Although the authors have their own view of their results, I do however, have a slightly different take on what the post-exercise pain ratings seem to show and its implications for judging whether an exercise-induced hypoalgesia effect is present or not. From what I have read, I cannot seem to find whether the authors have compared the post-exercise pain ratings against any data that was collected pre-exercise/at rest or as part of the calibration. Instead, I believe the authors have only compared post-exercise pain ratings against one another (i.e., HIGH versus LOW, NALOXONE versus SALINE). In doing so, I think the authors cannot fully assume that there is no exercise-induced hypoalgesia effect as there is no true control comparison (a no-exercise condition).

      In more detail, Figure 6A appears to show an average of all pain ratings combined per participant (is this correct?). As participants were exposed to stimulations expected to elicit a 30, 50, or 70 VAS rating based on pre-calibration values, therefore the average rating would be expected to be around 50. What Figure 6A shows is that in the SALINE condition, average pain ratings are in fact ~10-15 units lower (~35) and then in the NALOXONE condition, average pain ratings are ~5 units lower (~45) for both exercise intensities. From this, I would surmise the following:

      It appears there is an exercise-induced hypoalgesia effect as average pain ratings are ~30% lower than pre-calibrated/resting pain ratings within the SALINE condition at the same temperature of stimulation (it would also be interesting to see if this effect occurred for the pressure pain).

      It appears there is evidence for the endogenous opioid mechanism as the NALOXONE condition demonstrates a minimal hypoalgesia effect after exercise. I.e., NALOXONE indeed blocked the opioid receptors, and such inhibition prevented the endogenous opioid system from taking effect.

      It appears there is no effect of exercise intensity on the exercise-induced hypoalgesia effect.

      That is, participants can cycle at a moderate intensity (55% FTP) and incur the same hypoalgesia benefits as cycling at an intensity that demarcates the boundary between heavy and severe intensity exercise (100%FTP). This is a great finding in my mind as anyone wishing to reduce pain can do so without having to engage in exercise that is too effortful/intense and therefore aversive - great news! This likely has many applications within the field of public health.

      I will very slightly caveat my summaries with the fact that a more ideal comparison here would be a control condition whereby participants did the same experimental visit but without any exercise prior to entering the MRI scanner. I consider the overall strength of the evidence to be solid, with the answer to the primary research question still a little ambiguous.

      Reviewer #2 (Public review):

      Summary:

      This interesting study compared two different intensities of aerobic exercise (low-intensity, high-intensity) and their efficacy in inducing a hypoalgesic reaction (i.e. exercise-induced hypoalgesia; EIH). fMRI was used to identify signal changes in the brain, with the infusion of naloxone used to identify hypoalgesia mechanisms. No differences were found in postexercise pain perception between the high-intensity and low-intensity conditions, with naloxone infusion causing increased pain perception across both conditions which was mirrored by activation in the medial frontal cortex (identified by fMRI). However, the primary conclusion made in this manuscript (i.e. that aerobic exercise has no overall effect on pain in a mixed population sample) cannot be supported by this study design, because the methodology did not include a baseline (i.e. pain perception following no exercise) to compare high/low-intensity exercise against. Therefore, some of the statements/implications of the findings made in this manuscript need to be very carefully assessed.

      Strengths:

      (1) The use of fMRI and naloxone provides a strong approach by which to identify possible mechanisms of EIH.

      (2) The infusion of naloxone to maintain a stable concentration helps to ensure a consistent effect and that the time course of the protocol won't affect the consistency of changes in pain perception.

      (3) The manipulation checks (differences in intensity of exercise, appropriate pain induction) are approached in a systematic way.

      (4) Whilst the exploratory analyses relating to the interactions for fitness level and sex were not reported in the study pre-registation, they do provide some interesting findings which should be explored further.

      Weaknesses:

      (1) Given that there is no baseline/control condition, it cannot be concluded that aerobic exercise has no effect on pain modulation because that comparison has not been made (i.e. pain perception at 'baseline' has not been compared with pain perception after high/lowintensity exercise). Some of the primary findings/conclusions throughout the manuscript state that there is 'No overall effect of aerobic exercise on pain modulation', but this cannot be concluded.

      (2) Across the manuscript, a number of terms are used interchangeably (and applied, it seems, incorrectly) which makes the interpretation of the manuscript difficult (e.g. how the author's use the term 'exercise-induced pain').

      (3) There is a lack of clarity on the interventions used in the methods, for example, it is not exactly clear the time and order in which the exercise tasks were implemented.

      (4) The exercise test (functional threshold power) used to set the intensity of the low/high exercise bouts is not an accurate means of demarcating steady state and non-steady state exercise. As a result, at the intensity selected for the high-intensity exercise in this study, it is likely that the challenge presented for the high-intensity exercise would have been very different between participants (e.g. some would have been in the 'heavy' domain, whereas others would be in the 'severe' domain).

      (5) It is likely that participants did not properly understand how to use the 6-20 Borg scale to rate their perceived effort, and so caution must be taken in how this RPE data is used/interpreted.

      (6) Although interesting, the secondary analyses (relating to the interaction effects of fitness level and sex) were not included in the study pre-registration, and so the study was not designed to undertake this analysis. These findings should be taken with caution.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Participants in this study completed three visits. In the first one, participants received experimental thermal stimulations which were calibrated to elicit three specific pain responses (30, 50, 70) on a visual analogue scale (VAS). Experimental pressure stimulations were also calibrated at an intensity to the same three pain intensity responses. In the subsequent two visits, participants completed another pre-calibration check (Visit 2 of 3 only). Then, prior to the exercise NALOXONE or a SALINE placebo-control was administered intravenously. Participants then completed 1 of 4 blocks of HIGH (100%) or LOW (55%) intensity cycling which was tailored according to a functional threshold power (FTP) test completed in Visit 1. After each block of cycling lasting 10 minutes, participants entered an MRI scanner and were stimulated with the same thermal and pressure stimulations that corresponded to 30, 50, and 70 pain intensity ratings from the calibration stage. Therefore, this study ultimately sought to investigate whether aerobic exercise does indeed incur a hypoalgesia effect. More specifically, researchers tested the validity of the proposed endogenous pain modulation mechanism.

      Further investigation into whether the intensity of exercise had an effect on pain and the neurological activation of pain-related brain centres was also explored.

      Results show that in the experimental visits (Visit 2 and 3) when participants exercised at two distinct intensities as intended. Power output, heart rate, and perceived effort ratings were higher during the HIGH versus LOW-intensity cycling. In particular, HIGH intensity exercise was perceived as "hard" / ~15 on the Borg (1974) scale, whereas LOW intensity exercise was perceived as "very light" / ~9 on the Borg (1974) scale.

      The fMRI data from Figure 1 indicates that the anterior insula, dorsal posterior insula, and middle cingulate cortex show pronounced activation as stimulation intensity and subsequent pain responses increase, thus linking these brain regions with the percept of pain intensity and corroborating what many studies have shown before.

      Results also showed that participants rated a higher pain intensity in the NALOXONE condition at all three stimulation intensities compared to the SALINE condition. Therefore, the expected effect of NALOXONE in this study seemed to occur whereby opioid receptors were "blocked" and thus resulted in higher pain ratings compared to a SALINE condition where opioid receptors were "not blocked". When accounting for participant sex, NALOXONE had negligible effects at lower experimental nociceptive stimulations for females compared to males who showed a hyperalgesia effect to NALOXONE at all stimulation intensities (peak effect at 50 VAS). Females did show a hyperalgesia effect at stimulation intensities corresponding to 50 and 70 VAS pain ratings. The fMRI data showed that the periaqueductal gray (PAG) showed increased activation in the NALOXONE versus SALINE condition at higher thermal stimulation intensities. The PAG is well-linked to endogenous pain modulation.

      When assessing the effects of NALOXONE and SALINE after exercise, results showed no significant differences in subsequent pain intensity ratings.

      When assessing the effect of aerobic exercise intensity on subsequent pain intensity ratings, authors suggested that aerobic exercise in the form of a continuous cycling exercise tailored to an individual's FTP is not effective at eliciting an exercise-induced hypoalgesia response irrespective of exercise intensity. This is because results showed that pain responses did not differ significantly between HIGH and LOW-intensity exercise with (NALOXONE) and without (SALINE) an opioid antagonist. Therefore, authors have also questioned the mechanisms (endogenous opioids) behind this effect.

      Altogether, the paper is a great piece of work that has provided some truly useful insight into the neurological and perceptual mechanisms associated with pain and exercise-induced hypoalgesia. The authors have gone to great lengths to delve into their research question(s) and their methodological approach is relatively sound. Although the authors have their own view of their results, I do however, have a slightly different take on what the post-exercise pain rating seems to show and its implications for judging whether an exercise-induced hypoalgesia effect is present or not. From what I have read, I cannot seem to find whether the authors have compared the post-exercise pain ratings against any data that was collected preexercise/at rest or as part of the calibration. Instead, I believe the authors have only compared post-exercise pain ratings against one another (i.e., HIGH versus LOW, NALOXONE versus SALINE). In doing so, I think the authors cannot fully question whether there is an exerciseinduced hypoalgesia effect as there is no true control comparison (a no-exercise condition). Nevertheless, there are certainly many other areas that this article contributes to the literature due to the depth of methods the research team has used. For example, the authors provide much insight into: the impact of exercise intensity on the exercise-induced hypoalgesia effect; the impact of sex on the endogenous opioid modulation mechanism; and the impact of exercise intensity on the neurological indices associated with endogenous pain modulation and pain processing. All of which, the researchers should be credited for due to the time and effort they have spent completing this study.

      I have provided some specific comments for the authors to consider. They are organised to correspond to each section as it is presented, and I have denoted the line I am referring to each time.

      To conclude, thank you to the authors for their work, and thank you to the editor for the opportunity to contribute to the review of this paper. I hope my comments are seen as useful and I look forward to seeing the authors' responses.

      We sincerely appreciate the reviewer's insightful comments, which highlight the strengths of our study. In response to the concerns raised, we have made several key revisions to the original manuscript to address the reviewers’ comments. As for the lack of a resting control condition, we acknowledge that our study was not designed to test the overall effect of exercise versus no exercise. However, our primary objective was to compare different exercise intensities, hypothesising that low-intensity (LI) exercise would induce less pain modulation as compared to high-intensity (HI) exercise. By exploring this, we aimed to enhance understanding of the dose-response relationship between exercise and pain modulation. To better reflect this focus, we have revised the misleading phrasing regarding the ‘overall’ effect of exercise to clearly emphasize our primary aim: comparing HI and LI exercise.

      This reviewer suggests an interesting interpretation of the data suggesting that exercise induced hypoalgesia might have occurred for both exercise intensities since the pain ratings provided were lower than the anticipated intensities as determined by the calibration. Given that this difference is lower in the naloxone (NLX) condition could provide evidence of opioidergic mechanisms underlying this effect. Unfortunately, the current study is not designed to comprehensively answer this question since there was no resting control condition. In particular, the lower pain ratings under SAL (Figure 6) could be due to exercise triggering the descending pain modulatory system (DPMS), but equally due to the default activation of the DPMS. Only an additional “no exercise” condition could disentangle this. Furthermore, habituation to noxious stimuli can influence pain ratings, resulting in lower pain ratings during the experiment as compared to the calibration. We have now provided a more detailed overview of the pain ratings at different stimulus intensities after HI and LI exercise in both drug treatment conditions for heat and pressure pain ratings. We elaborated on the specific comments raised in more detail in the following sections.

      Specific Comments

      (1) Abstract

      Line 25 - "we were unable to"... personal preference but this wording is a little 'weighted' in my view. I personally do not think researchers search to prove hypotheses correct, rather we search to prove hypotheses wrong, and therefore only through repeated attempts of falsification can we surmise that something holds true.

      We agree with the reviewer that the chosen wording can be perceived as weighted and have rephrased the sentence.

      Line 33 to 35 - the "...but individual factors... might play a role" is a crucial caveat to this sentence for me. Whilst I can understand that the results of the authors' study indicate that prior assumptions about exercise-induced hypoalgesia and its opioidergic mechanisms may be questioned, I think a little more evidence is needed to finally decide whether aerobic exercise has no overall effect on experimental pain responses. (see more in the Results comments below).

      We thank the reviewer for their comment. We agree that no claims can be made regarding the effect of aerobic exercise per se on pain modulation compared to no exercise based on the current data. Furthermore, we agree that more research is needed to further advance our understanding of (non-)opioidergic mechanisms in exercise-induced pain modulation. However, based on the data presented in this study we propose that the involvement of endogenous opioids in exercise-induced hypoalgesia could be influenced by sex and fitness levels since we could show differences in opioidergic involvement between males and females of different fitness levels. Future studies should account for the fitness levels and sex of the sample investigated.

      (2) Introduction

      Line 48 - please predefine anterior cingulate cortex here.

      We thank the reviewer for detecting this and have introduced the abbreviation for the anterior cingulate cortex in the referenced line.

      Line 49 - please predefine periaqueductal gray here instead of line 52.

      We have introduced the abbreviation for periaqueductal grey in the referenced line.

      Line 47 to 54 - when discussing the descending pain modulatory systems, authors seem to be relating specifically to the intensity/magnitude of pain experiences. However, the different brain regions that are mentioned may have varying "roles" according to which dimension of pain is of focus.

      Hofbauer et al. (2001) - https://doi.org/10.1152/jn.2001.86.1.402

      Rainville et al. (1997) - https://doi.org/10.1126/science.277.5328.968

      The two above studies provide some nice earlier findings on the brain regions - some of which are mentioned by the authors in this section - associated with the processing of pain quality in addition to the intensity of pain... simply attach here if they are of interest to the authors.

      The studies by Hofbauer et al. (2001) and Rainville et al. (1997) provide interesting findings on the effect of hypnotic suggestions on pain affect and the perceived intensity of a painful stimulus. However, these studies did not investigate exercise-induced changes in brain regions of the DPMS. The studies referenced in the relevant section of the manuscript are (one of the few) imaging studies that have indeed investigated brain structures of the DPMS in the context of exercise and pain modulation and, thus, were included in this paragraph to focus on the findings of these studies as well as emphasise the scarcity of imaging studies investigating exercise-induced pain modulation. Given these divergent research topics of the proposed studies, we suggest not including them in this paragraph to maintain a clearer line of argument and focus on exercise-induced pain modulation in brain regions of the DPMS.

      L59 to 61 - a minor comment about the phrasing within this sentence and a recommended change is provided below for the flow of the sentence/paragraph.

      "...there are instances where administration of µ-opioid antagonists has decreased exerciseinduced pain modulation (Droste et al. 1988; etc.) whereas in others there has been little effect (Droste et al. 1988; etc.).

      We have altered the sentence based on the reviewers' suggestions to improve the flow and coherence of the sentence.

      L56 to 72 - Whilst the current version of this paragraph scans well enough, I find that the narrative flits between the mechanisms being discussed and the rationale/shortcomings of current research. I think that the original content of this paragraph can be structured into:

      A- The endogenous opioid system is a likely candidate to explain how exercise elicits a hypoalgesia response.

      B- Citation(s) of the imaging studies (Boecker et al., 2008, etc.) and earlier literature which support A (e.g., Janal et al. 1984).

      C- Further support of this theory as µ-opioid antagonists like naloxone seem to counteract the endogenous opioid effect (Haier et al., 1981).

      D- Introduction of the caveats of previous research such as the studies that observed that µ-opioids did not impact the endogenous pain modulation system during exercise (e.g., Droste et al., 1991, etc.) and the range of different interventions and exercise modalities which make it difficult to draw clear conclusions of the pain modulation effect.

      To me, this structure would set out the details you have already put together in a more orderly and systematic way and also will lead nicely into your ensuing paragraph (Line 74 onwards).

      We appreciate the reviewers' constructive comments on structuring this paragraph. We agree that the proposed version eases the readability and comprehension of the paragraph and have, thus, adapted the restructured paragraph according to the reviewer’s suggestion.

      L75 - Why are single-arm pre-post measures and designs an issue? If you can elaborate a little more this would be very insightful for a reader.

      Single-arm pre-post measurement studies involve participants being assigned to a single experimental condition, with pain assessments conducted only once before and once following an intervention. This study design presents some limitations, particularly in the context of examining exercise-induced modulation of pain (Vaegter and Jones, 2020). Such designs are potentially confounded by the effects of habituation to noxious stimuli, as highlighted by Vaegter and Jones (2020). Incorporating randomised controlled trials with multiple measurement blocks not only mitigates these limitations but also provides a clearer understanding of how individual bouts of exercise influence pain perception. We have now added this to the paper.

      L80 - The reference for the functional threshold power assessment is provided as a number. Please could the authors change to reflect which study/studies they are referring to here (I presume it is the Borszcz and/or the McGrath studies?).

      We apologise for this oversight and have now updated the reference to be displayed correctly. The reviewer is correct in assuming that Borszcz et al. (2018) is the referenced study here.

      L88 - Did participants also receive pressure pain stimulations in addition to the thermal stimuli, as the figure suggests?

      Note Since read on to L102-104 and understood why pressure pain was included but not mentioned due to results. However, I would still recommend including pressure pain stimulations in this line, if possible, to be consistent with what Figure 1 shows and later text in the Methods section also shows.

      We thank the reviewer for their suggestion to mention pressure pain at the referenced line to increase the clarity and consistency of the experimental paradigm. Pressure and heat pain were applied in alternating fashion during scanning. Whilst the results of pressure pain are not included in this study we agree with the reviewer that it should be mentioned again as part of the methods and have added this.

      L94 - I really like Figure 1. Great job.

      Could the authors please define the inter-trial interval (ITI) in the legend? And please could the authors clarify what unit the 30, 50, and 70 figures in the "18 trials per block" section refer to.

      We thank the reviewer for their positive feedback. We have now included a definition of inter-trial-interval (ITI) in the figure legend. Furthermore, we adapted Figure 1 so that the units of the stimulus intensities (30, 50, 70) on the Visual Analog Scale (VAS) are included in the figure allowing for a clearer identification.

      (3) Results

      General comment for figures ... is there a specific reason the authors chose for error bars to be represented by an SE value as opposed to an SD value?

      The reason I ask is that participant responses seem to vary (See Figure 2A and 2E-G as an example). Error bars showing SD values would perhaps do justice to the variability in participant response(s), whereas the SE may be a better representation of the variability in responses due to the assessor's methods of collection. Whilst the SE error bars are narrow (great job on that!), the individual responses are clearly varied which I speculate could be because of the interventions that have been implemented (i.e., exercise intensity).

      The use of Standard Error (SE) is more common in the cognitive neuroscience literature.

      However, as this reviewer noted, we have also included individual data points alongside the SE, thereby providing a comprehensive view that allows for a thorough interpretation of the data distribution.

      L102 to 104 - In fact, it is interesting that exercise did not impact the pressure pain ratings whereas the same cannot be said for thermal pain. In line with some of my comments below about the impact of exercise on pain intensity responses, I would be intrigued to see the results of the pressure pain ratings in more detail.

      Another note on this... Whilst the results for the pressure pain may be beyond the scope of this paper and will be reported separately, knowing of this data is tantalising for a reader. I would suggest to: A) either mention the pressure pain and include the analysis of the data; or B) not mention the pressure pain altogether and save it for the subsequent paper. Either way, I look forward to seeing further discussion on this in future work.

      We have now summarised the behavioural results of exercise on pressure pain ratings below in Supplemental Figure S1.

      There was no hypoalgesic effect evident in the behavioural pain ratings comparing HI to LI exercise in the saline (SAL) condition (β = 0.57, CI [-1.73, 2.86], SE = 1.17, t(1354) = 0.48, P = 0.63; Supplemental Figure S1A, blue bars) as well as no interaction of drug treatment and exercise intensity on pressure pain ratings (β = -1.43, CI [-4.87, 2.01], SE = 1.75, t(2756.02) = -0.82, P = 0.42; Supplemental Figure S1). Post-hoc paired t-tests (Bonferroni-corrected) confirmed there to be no significant differences between the drug treatment conditions at LI (P = 0.18) or HI (P = 0.85) and no significant difference between the exercise intensities in the SAL (P = 0.65) and NLX (P = 0.48) conditions, confirming no significant differences in drug treatment between the exercise intensities.

      Furthermore, there was no significant effect of fitness level on differences in pain ratings (LI – HI exercise) in the SAL condition (β = 3.16, CI [-1.64, 7.97], SE = 2.37, t(38) = 1.34, P = 0.19; Supplemental Figure S1B) and no significant correlation between fitness level and difference pain ratings (r = 0.25, P = 0.13). Finally, there was no significant interaction of drug treatment, exercise intensity, and sex on difference pain ratings (β =-7.97, CI [-18.67, 2.73], SE = 5.51, t(190) = -1.45, P = 0.15; Supplemental Figure S1C-D).

      Exercise did not appear to affect pressure pain ratings and we have now added this to the discussion and in the methods section. However, we think that the figure should be part of the supplements.

      L112 to 113 - Fantastic work for including this analysis in your study. Great job.

      We appreciate the reviewers’ positive feedback on conducting these crucial analyses when investigating sex and gender differences in pain.

      L186 to 189 - It is fascinating that there appears to be no effect of NALOXONE on pain ratings within female participants at a VAS rating of 30 for thermal pain as well as a much diminished hyperalgesia effect at a VAS rating of 50 compared to males. Meanwhile, at higher intensity stimulations corresponding to a VAS rating of 70, females in fact demonstrate a more pronounced hyperalgesia effect compared to males. In addition, the hyperalgesia effect of NALOXONE for males seems to "peak" at a VAS rating of 50. The mechanisms behind these findings alone would be incredibly exciting to explore... but maybe in another study.

      We agree with the reviewer that the differences in males and females are fascinating results and concur that this may hint at varying degrees of opioidergic involvement at different stimulus intensities. This finding is intriguing and potentially clinically relevant, warranting further investigation in future research, although it lies beyond the scope of the current paper.

      L189 - To double check... Figures 4A and 4B refer to the entire cohort (male and female responses combined) whereas C-E are separated by sex?

      In addition, as there are no annotations to the top of Figures 4C-E were no significant differences observed between saline and naloxone conditions per each stimulus intensity? i.e., similar tests to what are shown in Table S6 but separated for each sex.

      Without getting too carried away, there may be something here that indicates a difference between sexes concerning the opioid-driven pain modulation response on a neurological level (i.e., brain region activation).

      The reviewer is correct in assuming that Figures 4A and 4B refer to the entire cohort whilst Fig. 4C – 4E are split for males and females. The full output of the analyses for Fig. 4A and 4B are reported in Supplemental Tables S5 – S7. Furthermore, the full output of the LMER analyses for Fig. 4E is reported in Supplemental Table S10. We agree with the reviewer that additional annotations in Fig. 4C – Fig. 4E ease interpretation and have, thus, added them to the respective figures, denoting the significance of the interaction term stimulus intensity and drug treatment for females (Fig. 4C) and males (Fig. 4D), respectively. For completeness, we now report the post-hoc paired samples t-tests for females and males in the Supplemental Tables S8 and S9, respectively.

      L254 to 258 - "we could not establish an overall hypoalgesia effect of exercise...". Do the results of the exercise intensity x drug treatment provide an answer for this exact hypothesis? After checking the methods section, I cannot seem to find whether the statistical analysis has involved a comparison of the pain ratings after the high (alone), low (alone), or high and low (combined) exercise compared to ratings during control or pre-calibration as part of precalibration (i.e., pain ratings in a rested state without any exercise yet completed).

      We concur with the reviewer's assessment that the study design and statistical analyses cannot address the ‘overall’ effect of exercise compared to no exercise. Please refer back to our general response before comment 1, where we have addressed this point.

      As it seems that the analysis assesses the differences between high and low-intensity exercise, to me, the results of the exercise intensity x drug treatment analysis do not assess whether there is an exercise-induced hypoalgesia effect or not. Instead, it seems to assess whether the intensity of exercise is a differentiating factor in the expected exercise-induced hypoalgesia effect to subsequent pain intensity ratings to experimental pain stimulation. For the authors to judge whether aerobic exercise does or does not have a hypoalgesia effect, then the exercise conditions (either combined or standalone) would have to be compared to a control condition or a data set that involved pain ratings from a pre-exercise timepoint.

      We thank the reviewer for their comment. We would like to point out the we concluded there to be no hypoalgesic effect between the LI and HI exercise based on the LMER model comparing the behavioural pain ratings between the exercise conditions in the SAL condition (β = 1.19, CI [-1.85, 4.22], SE = 1.55, t(1354) = 0.77, P = 0.44; Figure 6A, blue bars and Table S9). The statistical model investigating the interaction of exercise intensity and drug treatment served to show that NLX did not modulate pain differently between the LI and HI exercise conditions.

      Given that our experiment involved different exercise levels in a randomized order, a simple pre vs post analysis is not straightforward. Nevertheless, we have set up a model where we take into account the rating time point (pain ratings provided before each exercise block (prepain ratings) and following each exercise block (post-pain ratings)) at each stimulus intensity (VAS 30, 50, 70) and exercise intensity (LI and HI). The model also takes into account the exercise intensity performed in the previous block, the overall block number as well as the varying subject intercepts. The analysis was completed for heat (Author response image 1A) and pressure (Author response image 1B) pain ratings in the SAL condition to establish whether there was a significant effect of exercise intensity on the changes from pre to post-pain ratings. The model for heat pain yielded a significant main effect for stimulus intensity (β = 1.43, CI [1.34, 1.52], SE = 0.05, t(2054.95) = 31.61, P < 0.001) but no significant interaction of exercise intensity, rating time point, and stimulus intensity (P = 0.14). The model for pressure pain in the SAL condition yielded a significant main effect of stimulus intensity (β = 1.00, CI [0.92, 1.08], SE = 0.04, t(2054.99) = 24.68, P < 0.001) and block number (β = 1.14, CI [0.35, 1.94], SE = 0.41, t(2055.98) = 2.80, P = 0.005) but not interaction of exercise intensity, rating time point, and stimulus intensity (P = 0.38).

      Author response image 1.

      Heat (A) and Pressure (B) pain ratings in the saline (SAL) condition for pre (purple) and post (turquoise) exercise pain ratings at LI and HI exercise and all stimulus intensities (VAS 30, 50, 70). The bars depict the mean pain rating pre and post-exercise and the dots depict the subject-specific mean ratings. The error bars depict the SEM.

      Another point of consideration is that Figure 6A appears to show an average of all pain ratings combined per participant (is this correct?). As participants were exposed to stimulations expected to elicit a 30, 50, or 70 VAS rating based on pre-calibration values, therefore the average rating would be expected to be around 50. What Figure 6A shows is that in the SALINE condition, average pain ratings are in fact ~10-15 units lower (~35) and then in the NALOXONE condition, average pain ratings are ~5 units lower (~45) for both exercise intensities. From this, I would surmise the following:

      • It appears there is an exercise-induced hypoalgesia effect as average pain ratings are ~30% lower than pre-calibrated/resting pain ratings within the SALINE condition at the same temperature of stimulation (it would also be interesting to see if this effect occurred for the pressure pain).

      • It appears there is evidence for the endogenous opioid mechanism as the NALOXONE condition demonstrates a minimal hypoalgesia effect after exercise. I.e., NALOXONE indeed blocked the opioid receptors, and such inhibition prevented the endogenous opioid system from taking effect.

      • It appears there is no effect of exercise intensity on the exercise-induced hypoalgesia effect. That is, participants can cycle at a moderate intensity (55% FTP) and incur the same hypoalgesia benefits as cycling at an intensity that demarcates the boundary between heavy and severe intensity exercise (100%FTP). This is a winner in my mind. Anyone wishing to reduce pain can do so without having to engage in exercise that is too effortful and therefore aversive - great news!

      I will very slightly caveat my summaries with the fact that a more ideal comparison here would be a control condition whereby participants did the same experimental visit but without any exercise prior to entering the MRI scanner.

      As a result of this interpretation of your findings, I do not think that aerobic exercise as a means to cause subsequent hypoalgesia to experimental thermal nociception can be fully discounted. On the contrary, I think your results showed in Figure 6A are evidence for it.

      The reviewer is correct in assuming that Figure 6A shows the averaged pain ratings across all stimulus intensities (VAS 30, 50, and 70) for each subject. To provide more details, we have split Figure 6A by stimulus intensity, now depicting the pain ratings for LI and HI exercise and treatment condition (SAL and NLX) at VAS 30, 50, and 70 (Supplemental Fig. S8). The LMER was extended to include the stimulus intensity and yielded a significant main effect of stimulus intensity (β = 1.39, CI [1.31, 1.47], SE = 0.04, t(2753.12) = -34.082, P < 0.001) and a significant interaction of stimulus intensity and drug treatment (β = 0.12, CI [0.01, 0.24], SE = 0.06, t(2751) = 2.13, P = 0.03) but no significant interaction of exercise intensity, drug treatment, and stimulus intensity (β = -0.05, CI [-0.20, 0.11], SE = 0.08, t(2751) = -0.56, P = 0.58).

      The reviewer further suggests that the average pain ratings in the SAL condition are lower than the anticipated stimulus intensity, thus, indicating exercise-induced hypoalgesia. While this interpretation is one possibility, there is an alternative explanation: the lower pain ratings may stem from habituation to heat pain (Greffrath et al., 2007; Jepma et al., 2014; May et al., 2012). To support this perspective, we have visualised data from other studies in our lab that have been conducted with the same thermode head and device (TSA-2), using the same calibration procedure and aiming for the same stimulus intensities (VAS 30, 50, and 70). In both studies (Author response image 2A: Study 1: Behavioural sample; Author response image 2B: Study 2: fMRI sample; Author response image 2C: Original Exercise Study), participants did not engage in an exercise task and the pain ratings at VAS 30 and VAS 50 were lower than the anticipated intensities (VAS 30: 11.1/13.4; VAS 50: 35.0/35.9). Furthermore, in a previous study by (Wittkamp et al., 2024), the authors showed that, despite calibrating the heat stimuli at VAS 60, participants rated the pain stimuli with M = 48.58 (SD = 13.79).

      This discrepancy observed between calibrated intensities and ratings provided could be attributable to habituation effects, especially at low-intensity stimuli. Moreover, we would like to point the reviewer to the highest stimulus intensity at VAS 70 (Author response image 2C), where no habituation in all three data sets (including the current study) has taken place. This consistency suggests that exercise-induced hypoalgesia may not be present in our findings or potentially confounded by habituation effects.

      Author response image 2.

      Heat pain ratings at different intensities (30, 50, and 70 VAS) in different study samples. Bars depict the mean ratings in the saline (SAL) condition. Individual data points depict subject-specific mean pain ratings. Error bars depict the SEM.

      The reviewer further suggests that there is evidence for endogenous opioidergic modulation since the pain ratings in the NLX condition are lower than the anticipated intensities. We fully agree but, again, would argue that the DPMS can exert its effects on painful stimuli in a default manner, i.e. irrespective of any exercise effect.

      We concur with the reviewer’s interpretation that there is no effect of exercise intensity on exercise-induced hypoalgesia since the ratings between both exercise intensities are not significantly different.

      Finally, we agree that our data does not allow for the interpretation of an ‘overall’ effect of exercise-induced hypoalgesia and would like to point out that we did not aim to claim this. Rather, the data suggests there to be no effect of LI vs. HI aerobic exercise on pain modulation. We acknowledge, however, that the phrasing involving ‘overall’ can be misleading and have revised this to focus on the comparison between LI and HI exercise, thereby enhancing precision and clarity.

      Note This is also where it would be really interesting to see the pain pressure data if it were to be included. Mainly to see whether it coheres with what the thermal stimulation stuff shows.

      We have provided the ratings for the pressure pain ratings in the SAL condition below (Author response image 3).

      Author response image 3.

      Pressure pain ratings in the SAL condition at stimulus intensity (VAS 30, 50, and 70). Bars depict the mean ratings in the saline (SAL) condition. Individual data points depict subject-specific mean pain ratings. Error bars depict the SEM.

      L259 - As mentioned in the comment above. Could the authors distinguish what is being shown in Figure 6A? Are the data presented as the pooled mean for all stimulation intensities? If not, what data is displayed per bar/column?

      We thank the reviewer for their comment. The reviewer is correct in assuming that the bars in Figure 6A depict the pooled means across all stimulus intensities (VAS 30, 50, 70) for each drug treatment condition and exercise intensity. To allow for a more detailed comprehension of the data, we have split Figure 6A by stimulus intensity, now depicting the pain ratings for LI and HI exercise and treatment condition (SAL and NLX) at VAS 30, 50, and 70 (Supplemental Figure S8). The LMER was extended to include the stimulus intensity and yielded a significant main effect of stimulus intensity (β = 1.39, CI [1.31, 1.47], SE = 0.04, t(2753.12) = -34.082, P < 0.001) and a significant interaction of stimulus intensity and drug treatment (β = 0.12, CI [0.01, 0.24], SE = 0.06, t(2751) = 2.13, P = 0.03) but no significant interaction of exercise intensity, drug treatment, and stimulus intensity (β = -0.05, CI [-0.20, 0.11], SE = 0.08, t(2751) = -0.56, P = 0.58).

      L278 - Can the authors please provide a reference that explains how W.kg-1 at FTP is a measure of fitness level?

      We thank the reviewer for their comment. The obtained FTP value was corrected for the weight of each participant (Watt/kg), yielding a weight-corrected fitness measure that allows for better comparison between subjects. We denoted this in the figures as W*kg-1 which serves to be the equivalent term.

      L296 - Take the line away from Figure 7A... Does the individual data show a positive relation between pain rating changes and W.kg-1? Besides the three data points (1 on the far right of the figure and the two on the far left), I find it hard to see any real trend.

      We acknowledge the reviewers’ concern regarding the regression line and the visual clarity of the individual data points. However, it is important to note that the significant main effect of fitness level on differences in pain ratings in the SAL condition (β = 6.45, CI [1.25, 11.65], SE = 2.56, t(38) = 2.52, P = 0.02) supports the assertion that higher fitness levels are associated with greater hypoalgesia following HI exercise compared to LI exercise. While the trend may not be visible for all data points, the statistical analysis provides a robust basis for the observed relationship (r = 0.33, P = 0.038).

      We have conducted an additional LMER model where we have excluded the subjects with the highest and lowest FTP values (sub-28 with 3.19 W/kg and sub-06 with 0.76 W/kg, respectively.) The LMER still yields a significant main effect of fitness level (β = 6.82, CI [1.25, 11.65], SE = 3.18, t(34) = 2.14, P = 0.039; Author response image 4) and a positive correlation between the difference ratings and fitness level approaching significance (r = 0.32, P = 0.057).

      Author response image 4.

      Fitness level on difference pain ratings (LI-HI exercise) without subjects with highest and lowest FTP (N = 37). (A) Subject-specific differences in heat pain ratings (dots) between LI and HI exercise conditions (LI – HI exercise pain ratings) and corresponding regression line pooled across all stimulus intensities in the SAL condition. Fitness level (FTP) showed a significant positive relation to heat pain ratings with a significant main effect of FTP (P = 0.039) on difference ratings.

      (4) Discussion

      L356 to 358 - Exactly. What you write here, I agree with. Your testing allowed you to judge whether there is an effect of aerobic exercise intensity on pain modulation. However, I think this has been a little conflated with the idea that there is "no overall effect of aerobic exercise on pain modulation" in other areas of the article (L358-361, Results, and Abstract). As per my previous comment, I am not sure this (no overall effect) is true.

      We agree with the reviewer and have adapted the manuscript so that the misleading phrase including ‘overall’ is removed.

      L358 to 365 - One addition to this debate about whether this is a hypoalgesia effect of aerobic exercise. In 358 - 361 (particularly the end of 361) there is a strong conclusion that there is no direct involvement of the endogenous opioid system. Then glance onto L364 to 365 and there is then an almost conflicting summary that a hypoalgesia effect driven by opioidergic regions of the brain (and ergo endogenous opioids) is in effect. If there were no direct endogenous opioid involvement, then differences between NALOXONE (blockade of the opioid mechanism) and SALINE conditions would not exist.

      We thank the reviewer for their comment. The structure of this paragraph aimed to guide the reader towards a more nuanced understanding of the possible mechanisms and caveats in exercise-induced pain modulation. Whilst our data suggest an effect of NLX on pain ratings where we showed significantly higher pain ratings in the NLX condition compared to the SAL condition we could not identify an interaction between treatment and exercise intensity. This suggests that there is no significant difference in opioidergic involvement between HI and LI exercise. Our exploratory analyses, however, show an effect of endogenous opioids involved as an underlying mechanism dependant on sex and fitness level.

      My perspective is that an exercise-induced hypoalgesia effect has occurred (based on the data in Figure 6A) but that this effect is certainly caveated by the sex and fitness levels that this study has observed (and kudos for it).

      As mentioned above, based on the current data we cannot untangle whether the reduced pain ratings in the SAL condition are due to habituation to noxious stimuli or an actual hypoalgesic effect of exercise (or potentially a mix of both). However, we fully agree with the reviewer that exercise-induced pain modulation is influenced by fitness level and sex.

      L390 - "endogenous pain modulation through μ-opioid receptors increases with increasing pain intensity". Aside from the general discussion about whether aerobic exercise causes a post-exercise hypoalgesia effect. This finding is also interesting for the pain incurred during exercise in the form of naturally occurring muscle pain and may also be clinically relevant as it could be that the endogenous pain modulation "system" could be primed through repeated exercise as your results show that the fitness level (i.e., a close correlate of how much someone has engaged in exercise and therefore 'activated' the endogenous pain modulation system) is associated with a more pronounced post-exercise hypoalgesia effect.

      This is an interesting aspect. With regards to the pain induced by exercise itself (i.e. muscle pain) we did not gather any data on this type of pain and interpreting this would be mere speculation. However, it is an interesting hypothesis to investigate in future studies whether the pain induced by exercise is potentially influenced by the endogenous opioid system. We agree with the reviewers’ interpretation that repeated exercise might prime the endogenous opioid system, especially in fitter individuals who engage more frequently in exercise and, thus, ‘train’ the endogenous opioid system. We have included this line of interpretation in the original manuscript, where we suggest that the mFC, a brain region with high µ-opioid receptor density, might be ‘trained’ by repeated exercise and, therefore, shows increase activation in fitter individuals after short bouts of exercise.

      L404 to 405 - "a resting baseline does not control for unspecific factors such as attentional load or distraction (Brooks et al., 2017; Sprenger et al., 2012) through exercise." I am not sure I agree. A control condition allows one to truly deduce whether exercise causes a hypoalgesia effect or not. The attentional load may be a factor, but I would argue this is distinct from endogenous pain modulation - unless there is a study that shows cognitive load alone can elicit endogenous opioids like exercise. About distraction, this would be the case if the pain measures were taken during the exercise. However, as the pain measures taken in the MRI were post-exercise and there was no added distraction related to the exercise present anymore, then I do not think any added effect of distraction due to the exercise and its effect on postexercise pain measure is relevant any longer.

      We agree with the reviewer that a resting baseline condition in the context of exercise induced pain modulation would allow for the investigation of a potential hypoalgesic effect of exercise compared to no exercise. It is important to note that both studies (Brooks et al., 2017; Sprenger et al., 2012) have indeed shown that the effect of cognitive pain modulation is mediated by endogenous opioids.

      L406 - I do not think a low-intensity exercise is a true "control" condition. It certainly does allow the study to compare the dose-response relationship but as the individual is exercising (even at a moderate physiological intensity) then comparison of HIGH vs LOW does not tell us whether exercise does or does not cause hypoalgesia. In contrast, the results from Figure 6A seem to show that even LOW intensity exercise has a hypoalgesia effect and this is a good thing for those who cannot exercise at high intensities (e.g., chronic populations).

      Please refer back to our general response before comment 1, where we have addressed this point.

      L410 - A small digression in relation to the exercise intensities:

      The intensity domains (moderate - heavy - severe) are not truly controlled within this study (mainly for the LOW condition), and therefore some participants could have exercised within different exercise intensity domains than others. To explain, the exercise intensity domains are distinguishable by the physiological responses associated with the boundaries of each of these domains. The FTP is believed to be a demarcation point between heavy and severe intensity domains (though kinesiologists debate the validity of this). Other concepts similar to FTP are Critical Power or the Respiratory Compensation Point. Ultimately, the boundary between heavy and severe intensity domains is characterised by the highest possible intensity by which a steady-state in oxygen kinetics (V̇ O2) occurs (Burnley & Jones, 2018). If this is expressed as a power output (Watts) and then a percentage of this power output is used to prescribe exercise intensity, then the physiological response is not always as expected. The reason is that for some people the gaseous exchange threshold (the demarcation point between the moderate and heavy intensity domains) is not always the same percentage between resting and FTP/Critical Power/Respiratory Compensation Point for each person. As a result, some individuals who are prescribed an intensity of 55% FTP/Critical Power/Respiratory Compensation Point may subsequently exercise within the moderate intensity domain (most people did based on the heart rate and RPE responses) whilst some others might actually exercise more within the heavy intensity domain. A quick check of Figures 3B-C could indicate that this might have been the case for two or three participants, but that is inference and speculation as we cannot truly know unless gas parameters were taken (which is perfectly understandable that they have not been taken because this study has done so much else). However, the importance of this for this study is that if some participants did indeed exercise at a slightly higher physiological intensity, this undermines the LOW condition as a "control" as the physiological stimulus between conditions (Brownstein et al., 2023). It means that the proposed differences in endogenous opioids (Vaegter et al., 2015; 2019) between exercise intensities may not have been present and therefore summarising a lack of an exercise induced hypoalgesia effect is slightly confounded. This is one factor contributing to my scepticism about the conclusion that there is a lack of an exercise-induced hypoalgesia response.

      We thank the reviewer for their comment as it touches upon the challenges of estimating exercise intensities precisely. It is, indeed, crucial to consider the boundaries between moderate, heavy, and severe intensity domains, as delineated by physiological markers such as the Functional Threshold Power (FTP), Critical Power, and the Respiratory Compensation Point (VO2max) (Burnley & Jones, 2018). Previous research has shown that the FTP and FTP20 tests are reliable and convenient methods to estimate approximate measures of VO2max (Denham et al., 2020) and that the FTP test is a useful test for performance prediction in moderately trained cyclists (Sørensen et al., 2019).

      We acknowledge that without direct measurements of VO2max, it is challenging to determine the precise intensity domain in which each participant was operating. While the RPE and HR might suggest that some participants performed in the moderate intensity domain in the LI exercise condition, we could still ascertain there to be a significant difference in the relative power (%FTP), heart rate (HR), and rating of perceived exertion (RPE) between the LI and HI exercise conditions. In the overall sample, the consistency in relative power, heart rate, and RPE responses among participants suggests that the exercise doses were effectively communicated and adhered to; therefore, the validity of the LI exercise condition remains robust.

      While we did not include metabolic assessments in our protocol, our study focused on providing a comprehensive analysis of the exercise-induced hypoalgesia phenomenon across two distinct exercise intensities. Additionally, the rationale for selecting specific exercise intensities was grounded in the existing literature, which indicates significant differences in the hypoalgesic response between exercise intensity levels (Jones et al., 2019; Vaegter et al., 2014).

      According to the reviewer, the potential lack of difference between the exercise conditions might contribute to the fact that there was no difference in endogenous opioid release and, thus, no difference in pain ratings between the exercise conditions. However, our data still suggests that there is an influence of endogenous opioids in the HI exercise condition in males with higher fitness levels. Together with recent findings on the association of µ-opioid receptor activation and fitness levels in men (Saanijoki et al., 2022), as well as the difference in µ-opioid receptor availability between high and moderate aerobic exercise (Saanijoki et al., 2018), we would hypothesise that the release of endogenous opioids after short HI bouts of exercise depend on fitness levels (and potentially sex).

      Finally, we propose that discussing exercise intensity domains within the context of our study enriches the understanding of exercise-induced hypoalgesia without undermining the integrity of our findings. We have, therefore, included this in the discussion of the manuscript.

      L417 - For some reason I am doubting this value (r = 0.61). Could this be checked? I think it is higher in their study. r = 0.88?

      Also, as someone with a kinesiology background, I would argue this is a given anyway. The maximum power one can cycle for 20 minutes is related to the maximum power one can cycle for 60 minutes, this is expected. (That is no slight on the authors of this study, more a remark that readers could look and figure that for themselves if they needed to know).

      We thank the reviewer for their comment. We have carefully re-checked the correlation coefficient between the FTP20 and FTP60 tests in the study by Borsczc et al. (2018) and have corrected the correlation coefficient to r = 0.88. We thank the reviewer for detecting this. Whilst we agree that it seems somehow intuitive that the FTP20 and FTP60 should correlate highly, we wanted to provide the reader with a better understanding of where the FTP20 tests originated from and how it is suitable to assess aerobic fitness levels without having to maintain a steady power output for 60 minutes.

      L428 - Kudos to the authors for taking a standardised approach to this. Hopefully, my comment earlier might provide some extra food for thought about exercise intensity. I think there are several other ways future research could prescribe exercise without the need for expensive and cumbersome bits of equipment to know how hard people are exercising.

      We strongly agree with the reviewer and hope that our study can inspire future research to implement more convenient and inexpensive ways to establish aerobic (and anaerobic) fitness levels.

      L456 to 458 - Would it be possible to revisit this and check whether the pooled mean of all stimulation intensities for pain intensity ratings after pressure pain is lower than 50? If so, I think it can also be assumed that there is a slight hypoalgesia effect occurring for pressure pain too.

      We have revisited the pressure pain ratings pooled across all stimulus intensities (VAS 30,50, and 70). Indeed, the ratings are below 50 VAS (Supplemental Figure S1A) in the SAL and NLX conditions. As mentioned before lower pain ratings after LI exercise cannot be taken as evidence for exercise-induced analgesia.

      L495 to L499 - I find this fascinating. Great finding.

      We thank the reviewer for their positive feedback.

      (5) Methods

      L650 - "Watts"

      We have changed the sentence accordingly.

      L651 - beats per minute can also be represented as b.min-1 and cadence as revolutions.min-1.

      To allow for easier interpretation of the results in a broader readership we would like to propose to maintain the original abbreviations.

      L678 - Just to check what the authors mean by "on the second experimental day", they are actually referring to Visit 2 of 3 (first experimental visit of 2) as it is shown in Figure 1?

      We apologise for the lack of clarity. Indeed, the second experimental day refers to the third visit in the study. We have added this to the sentence to increase clarity.

      L708 - would change the end of the sentence to "and remained blinded throughout the study"

      We have changed the sentence accordingly.

      L742 - comma after "in one participant".

      We have added the missing comma.

      L746 - slight mistype... RPE in brackets instead of PRE

      We have changed the abbreviation to RPE.

      L747 - In case the authors are interested in affective measures in future studies... Hardy and Rejeski (1989) have a 9-point Likert scale rating affective valence which might be useful to check out.

      Thank you. The scale by Hary and Rejeski (1989) is a very relevant measure of affective valence during exercise, and we will consider this in future studies.

      L755 - Four squares for the thermode to be applied were drawn on the arm but through the methods I can only seem to see that the thermode was applied to the second square during calibration. During the MRI scan, did someone move the thermode to different squares for different stimulations?

      We appreciate the reviewers' question. Indeed, the heat calibration and recalibration on the first and second day, respectively, have always been completed on the same skin patch (patch 2) to allow for comparability of calibration across days. During the experimental sessions, the thermode head was repositioned in a randomised order across participants (i.e., skin patch 14-3-2) before each block. This was done manually before the MRI block commenced. The order of thermode head position was kept constant within participants across experimental days (day 2 and day 3).

      L764 - ITI predefined?

      We thank the reviewer for their comment and would like to point to line 130 in the revised manuscript where the abbreviation for inter-trial-interval (ITI) was first introduced.

      (6) Other Sections + Supplementary Materials

      L891 - I apologise in advance for this comment as it is the most trivial comment you will ever receive, but there is an extra "." On this line after J.N. initials for methodology.

      We have changed the punctuation accordingly.

      Table S1 - Strictly speaking, some of the intensity denominations in this table are not exactly an "intensity".

      Iannetta et al. (2020) - https://doi.org/10.1249/mss.0000000000002147 provides a commentary on intensity domains as well as Burnley and Jones (2018) - https://doi.org/10.1080/17461391.2016.1249524

      Likewise in this table - the term "without fatigue" in the description column is not strictly true as participants will naturally fatigue but authors are referring more to a "steady state".

      We have changed the name of the column to ‘Description’ to describe the test phase as proposed by Allen and Coggen (2012) and previously implemented by McGrath et al. (2019) and not the ‘intensity domains’ (as specified by Iannetta et al. (2020)). Further, we have refined the wording in Table S1 and replaced the term ‘without fatigue’ with ‘steady state’.

      Once again, thank you to the authors for their great work on this project and to the editor for the chance to review this paper.

      We would like to thank this reviewer for their very insightful and important comments and for pointing out the strengths of the manuscript. We believe the suggestions will help to improve the quality of the manuscript.

      Reviewer #2 (Recommendations for the authors):

      Summary:

      This interesting study compared two different intensities of aerobic exercise (low-intensity, high-intensity) and their efficacy in inducing a hypoalgesic reaction (i.e. exercise-induced hypoalgesia; EIH). fMRI was used to identify signal changes in the brain, with the infusion of naloxone used to identify hypoalgesia mechanisms. No differences were found in postexercise pain perception between the high-intensity and low-intensity conditions, with naloxone infusion causing increased pain perception across both conditions which was mirrored by activation in the medial frontal cortex (identified by fMRI). However, the primary conclusion made in this manuscript (i.e. that aerobic exercise has no overall effect on pain in a mixed population sample) cannot be supported by this study design, because the methodology did not include a baseline (i.e. pain perception following no exercise) to compare high/low-intensity exercise against. Therefore, some of the statements/implications of the findings made in this manuscript need to be very carefully assessed.

      Strengths:

      (1) The use of fMRI and naloxone provides a strong approach by which to identify possible mechanisms of EIH.

      (2) The infusion of naloxone to maintain a stable concentration helps to ensure a consistent effect and that the time course of the protocol won't affect the consistency of changes in pain perception.

      (3) The manipulation checks (differences in intensity of exercise, appropriate pain induction) are approached in a systematic way.

      (4) Whilst the exploratory analyses relating to the interactions for fitness level and sex were not reported in the study pre-registation, they do provide some interesting findings which should be explored further.

      Weaknesses:

      (1) Given that there is no baseline/control condition, it cannot be concluded that aerobic exercise has no effect on pain modulation because that comparison has not been made (i.e. pain perception at 'baseline' has not been compared with pain perception after high/low intensity exercise). Some of the primary findings/conclusions throughout the manuscript state that there is 'No overall effect of aerobic exercise on pain modulation', but this cannot be concluded.

      (2) Across the manuscript, a number of terms are used interchangeably (and applied, it seems, incorrectly) which makes the interpretation of the manuscript difficult (e.g. how the author's use the term 'exercise-induced pain').

      (3) There is a lack of clarity on the interventions used in the methods, for example, it is not exactly clear the time and order in which the exercise tasks were implemented.

      (4) The exercise test (functional threshold power) used to set the intensity of the low/high exercise bouts is not an accurate means of demarcating steady state and non-steady state exercise. As a result, at the intensity selected for the high-intensity exercise in this study, it is likely that the challenge presented for the high-intensity exercise would have been very different between participants (e.g. some would have been in the 'heavy' domain, whereas others would be in the 'severe' domain).

      (5) It is likely that participants did not properly understand how to use the 6-20 Borg scale to rate their perceived effort, and so caution must be taken in how this RPE data is used/interpreted.

      (6) Although interesting, the secondary analyses (relating to the interaction effects of fitness level and sex) were not included in the study pre-registration, and so the study was not designed to undertake this analysis. These findings should be taken with caution.

      We thank the reviewer for their insightful comments that contribute to improving the quality of the manuscript. In response to the identified weaknesses, we have made key revisions to enhance clarity and rigor. Regarding the lack of a resting control condition, we acknowledge that our study does not assess the overall effect of exercise versus no exercise. Our primary objective was to compare high- (HI) and low-intensity (LI) exercise on pain modulation, hypothesizing that lower intensities would have minimal effects. We revised the manuscript to eliminate misleading phrases about an "overall" effect, clearly emphasizing our aim to investigate the comparative effects of different exercise intensities. To address terminology inconsistencies, we have adopted "exercise-induced pain modulation," reflecting existing literature that recognizes both hypoalgesia and hyperalgesia associated with exercise (Vaegter and Jones, 2020). We clarified this terminology in the introduction and specified the pain modalities used in our study. We also improved methodological transparency by better describing the timing and order of exercise and drug treatment interventions. Concerning exercise intensity estimation, we acknowledge the complexities in classifying moderate, heavy, and severe domains. We added the study by Wong et al. (2023) to discuss the potential limitations of the FTP estimation protocol. Although direct measures of VO2max or blood lactate are absent in our study, our findings, including perceived exertion (RPE) scores and relative power data, support that participants were primarily in the heavy-intensity domain during HI exercise. To clarify RPE ratings, we adjusted the presentation to align with the Borg scale's intended anchor points, ensuring greater accuracy in reported exertion levels. Statistical analyses confirm significant differences in RPE between exercise intensities. These revisions aim to clarify our intent and methodologies, ultimately strengthening the contribution of our research to understanding exercise-induced pain modulation.

      (1) Lines 27-33 - please present some data and accompanying statistical output in the results section of the abstract.

      We thank the reviewer for their comment. In the results section of the abstract, we report whether the findings are (not) significant using the general threshold of P < 0.05. However, we prefer not to include more detailed data and statistical outputs here, as these are thoroughly presented in the results section and do not contribute to the abstract’s primary purpose of providing a concise summary.

      (2) Line 29 - please indicate how fitness level was quantified.

      The functional threshold power (FTP) adjusted for weight served as an indication of cardiovascular fitness level. We have now included this in the abstract.

      (3) Line 35 - please include a sentence detailing the implications of your findings.

      We have now included a sentence on the implications of our findings in the abstract.

      (4) Introduction general - I appreciate that it was an exploratory analysis, however, the introduction does not particularly lay the groundwork for this (e.g., the influence of fitness level, sex, etc) - please include some background within the introduction to establish the role level of fitness/exercise/training/physical activity on pain modulation.

      A paragraph detailing the role of fitness level and sex in the context of exercise-induced pain modulation and endogenous opioid release was part of the introduction of our manuscript but has been removed as per the reviewing editor’s request (as the inclusion of sex and fitness level was not part of the preregistration). We have now re-included a shortened version of this paragraph to provide some background on these potentially crucial factors in exercise-induced pain modulation.

      (5) Lines 40-41 - reference needed.

      We thank the reviewer for detecting this and have now included references concerning the release of endogenous opioids and the term exercise-induced hypoalgesia.

      (6) Lines 48-49 - please provide the full terms for ACC and PAG (PAG has been provided on line 52, but should be presented earlier).

      We thank the reviewer for detecting this. We now introduce the abbreviations for the periaqueductal grey (PAG) and anterior cingulate cortex (ACC) in the correct lines.

      (7) Line 49 - the term exercise-induced pain is often used interchangeably (incorrectly) with many different types of pain experienced during/after exercise (e.g. muscle burn/ache, DOMS, injury etc.). Please see O'Malley et al 2024 (doi: 10.1113/EP091687).

      We thank the reviewer for their comment. Despite the distinction between different types of pain induced by exercise being important, this is less relevant for the current study. We would like to point out that the full term used is exercise-induced pain modulation, referring to the modulation of (experimental) pain through exercise. We have deliberately chosen this term as it summarises exercise-induced hypoalgesia as well as hyperalgesia. Therefore, we did not refer to pain induced by exercise and would disagree that this term has been used interchangeably with different types of pain in the current manuscript.

      (8) Line 57 - neither of these studies looked at exercise-induced pain, rather they examined experimentally induced pain (e.g. cold pressor test) or chronic pain and how exercise might exacerbate it. This leads back to the previous comment - it is important to define what is meant by exercise-induced pain (EIP) from the offset, and then remain consistent in the reference to this.

      We agree with the reviewer and have cited the studies accordingly. We would like to point out that the current study does not investigate exercise-induced pain but the modulation of experimental pain through exercise and have used the term exercise-induced pain modulation consistently in the manuscript to describe this.

      (9) Line 61 - Droste et al and Olausson et al are missing from the reference list.

      We apologise for this oversight and have now updated the reference list to include the studies by Droste et al. (1991) and Olaussen et al. (1986).

      (10) Line 61 - Do you mean exercise-induced hypoalgesia, or modulation of exercise-induced pain - it is not clear? EIH is introduced in Line 40 and in consistent with what the Koltyn study explored. Conversely, Koltyn induced pain using heat and pressure, rather than exercise.

      In this manuscript, we have opted for the term ‘exercise-induced pain modulation’ since previous research has shown that exercise can elicit hypoalgesia as well as hyperalgesia (for review see Vaegter and Jones (2020)). Thus, the term refers to the modulation of pain through exercise. We have now included a sentence detailing the use of the term ‘exercise-induced pain modulation’ in the first passage of the introduction. Corresponding to Koltyn et al. (2014), we have used heat and pressure stimuli to induce pain and investigate the modulating effect of different exercise intensities on these pain modalities.

      (11) Line 62 and 64 - Both the Janal study and Haier study are missing from the reference list.

      We apologise for this oversight and have now updated the reference list to include the studies by Janal et al. (1984) and Haier et al. (1981).

      (12) Line 62 and 64 - define long/short distance/duration.

      We have revised the terminology from "short-duration" to "short-distance" to facilitate a more precise comparison of the exercise protocols employed in the studies by Janal et al. (1984) and Haier et al. (1981). Specifically, the long-distance run conducted by Janal et al. (1984) spanned 6.3 miles (10.3 km), while the short-distance run executed by Haier et al. (1981) covered 1 mile (1.6 km).

      (13) Line 62 - what type of pain?

      Janal et al. (1984) implemented thermal, ischemic, and cold pressor pain in their study and observed a hypoalgesic effect in response to thermal and ischemic pain that was reversed under NLX administration. We have now specified this in the text.

      (14) Line 67 - please place "i.e., the insula, ACC and prefrontal regions" in parentheses.

      Done.

      (15) Lines 67-69 - please provide clarity on the nature of the interventions being employed. For example, are you referring to interventions to reduce/overcome pain? Or are you referring to approaches to experimentally induce or increase pain during exercise? In either case, please be specific on the interventions employed, and why this variation in approach may make it challenging to draw a conclusion

      The interventions employed by several studies aimed to investigate the pharmacological underpinnings of the pain modulatory effect of exercise and were, thus, pharmacological interventions. The primary objective of these interventions is usually not to reduce/induce/decrease/increase pain but to block a specific receptor type to infer the involvement/role of these receptor types in pain modulation through exercise. In the context of exercise and pain specifically, the most frequently used pharmacological intervention consists of administering a µ-opioid receptor antagonist (naltrexone/naloxone (NLX)). Depending on which type of µ-opioid receptor antagonist is used, different administration protocols are employed (i.e., oral or intravenous administration, different doses, only bolus without constant injection). This variability in the administration protocols of these pharmacological interventions can account for different findings of the extent of opioidergic involvement in exercise-induced pain modulation. We have now refined the according section to increase the precision and clarity of the interventions used.

      (16) Line 69 - administration of what?

      This passage refers to the variability of administration of µ-opioid receptor antagonists such as naloxone (NLX) or naltrexone. We have now specified this in the according line.

      (17) Line 74 - EIH?

      As described above, we have chosen the term 'exercise-induced pain modulation' as an umbrella term for both exercise-induced hypoalgesia and hyperalgesia. However, the reviewer is correct that specifically studies investigating exercise-induced hypoalgesia have been criticised. Still, the proposed criticism also applies to studies detecting hyperalgesia and we would, thus, argue to retain the term ‘exercise-induced pain modulation’ here for the sake of consistency.

      (18) Line 75 - please define "single-arm pre-post measurements"

      We appreciate the reviewers' comment. Single-arm pre-post measurement studies involve participants being assigned to a single experimental condition, with pain assessments conducted only once prior to and once following the intervention. This study design presents several limitations, particularly in the context of examining exercise-induced modulation of pain (Vaegter and Jones, 2020). Such designs do not consider the effects of habituation to noxious stimuli, as highlighted by Vaegter and Jones (2020). Consequently, when measuring pain levels with only one pre- and one post-intervention assessment, there is a risk of misinterpreting the outcomes where a reduction in post-intervention pain ratings might erroneously be credited to the exercise intervention itself, rather than being a result of habituation to the noxious stimuli experienced. Incorporating randomised controlled trials with multiple measurement blocks not only mitigates these limitations but also provides a clearer understanding of how individual bouts of exercise influence pain perception.

      (19) Line 84 - is (40) a reference?

      We apologise for this oversight and have now updated the reference by Borszcz et al. (2018) to be displayed correctly.

      (20) Line 86 - is that 10 min per block (i.e. 40 min exercise time), or 10 min in total? If the former please include "per block" at the end of the sentence (Line 87).

      The reviewer is correct in assuming that we employed 10 min of cycling per block, resulting in a total of 40 minutes of cycling. We have updated the sentence now including ‘per block’ as suggested by the reviewer.

      (21) Line 89 - when you refer to "painfulness" are you referring to the intensity of pain experienced? If so, I think "pain intensity" would be more appropriate.

      In the current study, participants were asked about the ‘painfulness’ of each stimulus based on previous studies (Horing et al., 2019; Horing & Büchel, 2022; Tinnermann et al., 2022). The term ‘painfulness’ is a composite measure of ‘pain intensity’ (sensory dimension) and ‘pain unpleasantness’ (affective dimension) (Talbot et al., 2019). Since unpleasantness is also a definitional criterion of pain (‘Terminology | International Association for the Study of Pain’, n.d.) and previous research shows a high correlation between ‘pain unpleasantness’ and ‘pain intensity’ (Granot et al., 2008; Talbot et al., 2019) we have opted for the term ‘painfulness’ as a more comprehensive measure. Inherently, these two measures are highly correlated.

      (22) Line 91-93 - the way this is written could be suggestive of this being separate to the cycling blocks. Please rephrase to confirm that this was administered prior to the commencement of the cycling blocks.

      We have refined the sentence to make it clearer that the drug treatment was administered before the cycling block commenced on each of the experimental days. We would like to further specify, that whilst the bolus dose of the treatment was administered prior to the experiment, a constant intravenous supply of SAL/NLX was maintained throughout the experiment using an infusion pump.

      (23) Methods general - why only 10 min of exercise? It is likely that there is a 'dose effect' of exercise on EIH, whereby the intensity of exercise and the duration of the exercise are important. Short-duration but high-intensity exercise can induce EIH, as can moderate duration low-intensity exercise. But, for this protocol, was the intensity high enough or long enough to meet the 'dose' needed?

      We thank the reviewer for their question. Our decision to employ 10-minute exercise blocks was rooted in both scientific evidence on exercise-induced hypoalgesia and the (clinical) applicability of the findings. Research has shown that exercise durations ranging from 8 minutes to 2 hours of aerobic exercise can induce hypoalgesia (for review see Koltyn (2002)). Specifically, several studies induce hypoalgesia at 10-15 minutes of aerobic exercise (Gomolka et al., 2019; Gurevich et al., 1994; Haier et al., 1981; Jones et al., 2019; Sternberg et al., 2001; Vaegter et al., 2015). Furthermore, many prior studies have employed exercise durations that are tailored to professional or amateur athletes which may not be practical for healthy individuals with lower fitness levels who may find it challenging to engage in longer sessions, such as an hour of running. When considering applying these findings to the clinical chronic pain population it is crucial to assess the manageability of proposed exercise protocols. We believe that 10 minutes of exercise, whilst being a relatively brief exercise duration, may still be sufficient to elicit exercise-induced hypoalgesia.

      (24) Methods general - what was the time gap between each round (i.e. after the fMRI, how long before the participant started the next cycling block?).

      After each fMRI run the participants were taken out of the MR scanner. The HR and SPO2 were measured and participants were given the chance to go to the restroom before positioning them on the bike and starting the next block. All in all, the time following the fMRI scan and before the new block commenced ranged between 5-10 minutes. We have now included this specification in the methods section.

      (25) Methods general - there is some evidence to show that the EIH effect is less consistently shown when heat is used to induce pain - was there a reason heat was used as the pain induction method here?

      We thank the reviewer for their comment. Indeed, previous meta-analyses by Naugle et al. (2012) report larger effect sizes for pressure pain (Cohen’s d = 0.69) closely followed by heat pain (d = 0.59). In light of this evidence, we included both pain modalities in the current study. Notably, we found no significant differences in pressure pain responses between LI and HI exercise. It is important to emphasise that the term "pressure pain" predominantly encompasses studies employing handheld pressure algometry, whereas our investigation utilised a pressure cuff. This methodological variation raises the possibility that our findings—and corresponding effect sizes—may not be directly comparable to prior pressure pain studies.

      (26) Methods general - please be consistent in the use of terminology. In some areas, you use the phrase "cycling block" whereas in other areas it is referred to as a "cycling run".

      We have revised the methods section to be more precise with the terms ‘run’ and ‘block’.

      (27) Line 571-573 - Please detail how participants were excluded based on scores from STAI and BDI-II.

      We apologise for the misspelling, as it should be that one participant was excluded based on a BMI (body mass index) below 18. No participant had to be excluded based on the STAI or BDI-II score in the current study. We have corrected this in the manuscript.

      (28) Line 636-651 - the FTP20 test has been shown not to be a valid marker of the separation between the heavy and severe exercise intensity domains (see Wong et al 2023 - https://doi.org/10.1080/02640414.2023.2176045). Given that participants completed the high intensity cycle in 'zone 4' (91-106% of FTP), it is probable that participants could have completed this 10 min in either the heavy or the severe exercise intensity domains, with significant implications for the relative challenge this 10 min of exercise. Why was zone 4 used? What are the implications of this? Please discuss and include this as a limitation.

      We thank the reviewer for their comment as it touches upon the challenges of accurately estimating exercise intensities. It is indeed crucial to consider the boundaries between moderate, heavy, and severe intensity domains, as delineated by physiological markers.

      The study by Wong et al. (2023) is interesting; it assesses blood lactate and VO2 levels at FTP and FTP+15 Watts. Despite being highly relevant for the field some of the findings should be interpreted with caution due to the low sample size of 13 participants, consisting of 11 male and only 2 female cyclists, which may limit generalisability. Additionally, the testing protocol implemented in the study to determine participants' FTP consisted of a 5-minute self paced pedalling at 100 Watts followed by a 20-minute maximal, self-paced time trial. This differs from the FTP20 test as implemented in the current study (see Supplemental Table S1) or by other studies (McGrath et al., 2019). The finding in Wong et al. (2023) that participants were only able to sustain cycling at FTP for an average of 33 minutes suggests that the deviating protocol overestimates FTP. Mackey and Horner (2021) propose that the validity of the FTP20 test might rely on the warm-up used before FTP20 testing and the training status of athletes.

      However, we acknowledge that without direct measurements of VO2max or blood lactate levels, it is challenging to determine the precise intensity domain in which each participant was operating in the current study. Still, the RPE (low: M = 8.59, SD = 1.32; high: M = 14.92, SD = 1.98) suggests that participants operated in the heavy-intensity domain in the HI exercise condition. This is further supported by the relative power (%FTP) maintained in the HI (M = 105; SD = 0.05; Author response image 5, purple) and LI (M = 58; SD = 0.06; Author response image 5, green) exercise conditions (difference: t(37) = 44.58, P < 2.2e-16, d = 6.46) confirming the accuracy of the implemented FTP test as well as the maintained power throughout the cycling blocks. Thus, we would argue that participants in the current study predominantly exercised the heavy domain during the HI exercise condition. We have included the relative Power in Figure 3A, replacing the absolute Power.

      Finally, we propose that discussing exercise intensity domains within the context of our study enriches the understanding of exercise-induced hypoalgesia without undermining the integrity of our findings. We have now included a discussion of the validity of the FTP20 test as a demarcation point concerning the intensity domains.

      Author response image 5.

      Raincloud plot of relative power (%FTP) during low (green) and high (purple) intensity exercise. Individual data points depict subject-specific averages across blocks.

      (29) Line 676 - please provide further information on each cycling run/block. Did each participant complete a total of 4 runs (i.e., a total of 40 minutes of exercise), with 2 runs completed at a high intensity and 2 runs completed at a low intensity in a randomised order (e.g., for one participant this could be 10 minutes at low, followed by 10 minutes at high, followed by 10 minutes a low, followed by 10 minutes at high)? Figure 1 details this nicely, however, it would be helpful to read in-text.

      The reviewer is correct in assuming that there were a total of 4 blocks on each experimental day. Participants completed cycling in 2 blocks at HI and in 2 blocks at LI in a pseudorandomised order. This order was kept constant across experimental days (i.e. completing the same block order on Day 2 and Day 3). We have detailed this further in the Methods section.

      (30) Discussion general - it is possible that EIH could be induced via different mechanisms and that these mechanisms are at least in part due to exercise intensity. For example, EIH from higher-intensity exercise might have some contribution from CPM.

      We thank the reviewer for their comment. Previous research aimed to disentangle the two seemingly similar mechanisms of exercise-induced hypoalgesia (EIH) and conditioned pain modulation (CPM) (Ellingson et al., 2014; Rice et al., 2019; Samuelly-Leichtag et al., 2018; Vaegter et al., 2014). CPM is typically induced by applying a tonic noxious stimulus that decreases pain sensitivity to another noxious stimulus applied simultaneously or shortly after at a distant body part (Graven-Nielsen & Arendt-Nielsen, 2010). Despite EIH and CPM showing distinct mechanisms, it cannot be completely ruled out that there are at least partially overlapping mechanisms driving the two phenomena (Rice et al., 2019). Due to our study design, where the time difference between cycling blocks and the applied pain was on average five minutes, it is unlikely that CPM is the driving pain modulatory mechanism in our study setup.

      (31) Line 101 - as this was preregistered, should the study design be followed and then reported?

      We have conducted the study adhering to the preregistered study design and now report the results for pressure pain (Supplemental Figure S1). Some of the preregistered analyses (i.e. directly comparing heat and pressure pain) were beyond the scope of the current study and will be reported separately.

      (32) Line 110 - please provide some data on the fitness levels and how this is classified as high/low.

      The FTP (relative to body weight) was used as an estimate of cardiovascular and endurance fitness (Valenzuela et al., 2018). We refrained from classifying the fitness levels dichotomously as low or high since this is a subjective measure in a sample of healthy individuals of diverse fitness levels. Instead, we utilised the FTP as a more nuanced metric for comparison.

      (33) Lines 159-160 - in the context of the difference in intensity between the sessions. But, it is likely that the high-intensity exercise would have posed quite different relative challenge between participants.

      We thank the reviewer for their comment. As described above, we did not obtain direct measurements of VO2max or blood lactate levels making it challenging to determine the precise intensity domain in which each participant was operating in the current study. However, all participants received the same instructions to the BORG rating scale ensuring the comparability of RPE across participants to a certain extent.

      (34) Figure 3C - what instructions and familiarisation were given to participants regarding the 6-20 Borg scale? In Figure 3C it looks as though several participants rated the low exercise intensity at 6. This would/should be equivalent to sitting quietly, so it looks as though at least several participants did not understand how to use the RPE - please discuss.

      Indeed, three participants rated the LI exercise condition at 6 due to an error in the translation of the scale instruction. Participants were instructed that the lower anchor point of the scale (6) referred to ‘extremely light’ instead of ‘no exertion’. Thus, we have rescaled the RPE ratings where a rating of 6 now corresponds to a 7 (‘extremely light’) on the BORG scale and again calculated the paired t-test. There is still a significant difference in the RPE between exercise intensities (t(38) = 19.65, P < 2.2e-16, d = 3.69; Author response image 6). We have corrected this in the manuscript accordingly and updated Figure 3C.

      Author response image 6.

      Raincloud plot of rating of perceived exertion (RPE) on the BORG scale during low (green) and high (purple) intensity exercise. Individual data points depict subject-specific averages across blocks. A rating of 6 reflects ‘no exertion’ and 20 reflects ‘maximal exertion’.

      (35) Line 171 - is (37, 38) a reference?

      We apologise for this oversight and have now updated the references to be displayed correctly.

      (36) Line 176-18 - is this interaction sufficiently powered? Differences between sexes are not mentioned in the pre-registered study

      We have conducted an additional post-hoc power analysis for the interaction of drug, fitness level, and sex on differential heat pain ratings. We employed the power analysis for mixed models implemented in R (powerCurve) with 1000 simulations. This revealed that with a power of α = 0.8, a sample size of n = 27 would have been sufficient to detect this effect (Author response image 7). Despite not having preregistered the factor ‘sex’, we believe that the observed results provide valuable insights that contribute to a deeper understanding of the data. We have established these analyses to be exploratory, emphasising the need for caution in their interpretation. However, we feel it is essential to report these findings to inform future studies, ensuring that such factors are adequately considered.

      Author response image 7.

      Post-hoc power analysis for behavioural effects from the linear mixed effects (LMER) model with interaction drug, fitness level, and sex using the R package powerCurve with α = 0.8 and 1000 simulations.

      (37) Line 227 - this is not what this analysis shows. The comparison is low vs high-intensity exercise on pain modulation, not exercise vs. no exercise. You cannot conclude that aerobic exercise has no effect on pain modulation because you did not do that comparison (i.e. no baseline (without exercise) for pain).

      We agree with the reviewer and have rephrased the sub-headline accordingly to reflect that there is no difference in exercise-induced hypoalgesia between HI and LI aerobic exercise.

      (38) Methods General - why was a control condition not used, or at least a baseline pain response, so that low/high-intensity exercise could be compared to a baseline? Given this, I'm not sure I agree with the study conclusions (abstract: 'These results indicate that aerobic exercise has no overall effect on pain in a mixed population sample') because you have compared high vs low-intensity exercise, not exercise vs. no exercise.

      As for the lack of a resting control condition, we acknowledge that our study was not designed to test the overall effect of exercise versus no exercise. However, our primary objective was to compare different exercise intensities, hypothesising that low-intensity (LI) exercise would induce less pain modulation as compared to high-intensity (HI) exercise. By exploring this, we aimed to enhance understanding of the dose-response relationship between exercise and pain modulation. To better reflect this focus, we have revised the misleading phrasing regarding the ‘overall’ effect of exercise to clearly emphasize our primary aim: comparing HI and LI exercise. This reviewer suggests an interesting interpretation of the data suggesting that exercise-induced hypoalgesia might have occurred for both exercise intensities since the pain ratings provided were lower than the anticipated intensities as determined by the calibration. Given that this difference is lower in the naloxone (NLX) condition could provide evidence of opioidergic mechanisms underlying this effect.

      Unfortunately, the current study is not designed to comprehensively answer this question since there was no resting control condition. In particular, the lower pain ratings under SAL (Figure 6) could be due to exercise triggering the descending pain modulatory system (DPMS), but equally due to the default activation of the DPMS. Only an additional “no exercise” condition could disentangle this. Furthermore, habituation to noxious stimuli can influence pain ratings, resulting in lower pain ratings during the experiment as compared to the calibration.

      (39) Line 285 - or that better-trained individuals have a greater EIH response to higher intensity exercise, but both those of low and high fitness have established EIH after low intensity exercise. Given there isn't a 'no exercise' baseline, it is hard to make conclusions about EIH effect generally, only comparisons between high/low exercise intensity.

      We thank the reviewer for their comment. We agree that we cannot establish whether all participants showed a hypoalgesic response to the LI exercise with the current study design. However, our results show that participants with higher fitness levels showed increased hypoalgesia after HI exercise compared to those with lower fitness levels. We have refined the sentence accordingly.

      (40) Figure 7A - the regression line here is not that convincing.

      We acknowledge the reviewers’ concern regarding the regression line. However, it is important to note that the significant main effect of fitness level on differences in pain ratings in the SAL condition (β = 6.45, CI [1.25, 11.65], SE = 2.56, t(38) = 2.52, P = 0.02) supports the assertion that higher fitness levels are associated with greater hypoalgesia following HI exercise compared to LI exercise. While the trend may not be visible for all data points, the statistical analysis provides a robust basis for the observed relationship (r = 0.33, P = 0.038).

      (41) Line 354 - the NLX infusion was double-blind, but what are the implications of participants knowing that they completed high/low-intensity exercise - this cannot be blinded.

      The reviewer is correct that the exercise intensities cannot be blinded. To account for potential expectation effects of exercise on several psychological and physiological domains (including pain), participants completed a questionnaire on the calibration day where they had to indicate their expectations of to what extent acute exercise affects several domains (Lindheimer et al., 2019). They could rate each domain on a Likert scale ranging from ‘large decrease’ (-3) to ‘large increase’ (3) with 0 denoting ‘no effect’. This format was chosen to allow measuring the direction and magnitude of expectation effects and to avoid being directive or suggestive (Lindheimer et al., 2019). Despite including other psychological and physiological domains in the questionnaire (i.e., stress, anxiety, energy, memory) we focused on the specific pain domains (muscle pain, joint pain, and whole body pain) to establish participant’s expectations regarding the effect of acute exercise on pain. We tested whether the expectation ratings for each pain type were significantly different from 0 (no effect) using a one-sample t-test.

      There was no significant effect for muscle pain (t(38) = 1.78, P = 0.08, M = 0.39, SE = 0.12), joint pain (t(38) = -0.12, P = 0.90, M = -0.03, SE = 0.11), or ‘whole-body pain (t(38) = -1.05, P = 0.30, M = -0.21, SE = 0.12) suggesting there to be no expectation effect on these pain domains in the overall sample (Supplemental Figure S10A). Since there is variation in the data we calculated the correlation of the expectation ratings in the different pain domains with the difference score between the pain ratings in the SAL condition (LI – HI rating; Supplemental Figure S10B). This analysis yielded no significant correlation in either of the pain domains (joint pain: r = 0.11, P = 0.49; muscle pain: r = -0.07, P = 0.68; whole-body pain: r = 0.07, P = 0.68).

      Moreover, given that we have not been able to show a difference between the exercise intensities on pain modulation, expectation effects are likely not to contribute to this null effect.

      (42) Line 356-358 - and this comparison (and primary hypothesis) is not blinded.

      While we agree with the reviewer that this comparison is not – and potentially cannot be – blinded, we would like to reiterate our results from the previous paragraph that indicate that such expectation effects of exercise on pain were not present in the sample and, thus, did not seem to have influenced the results. It is noteworthy that the double-blind design of our study design specifically pertains to the pharmacological intervention employed.

      (43) Line 358-360 - this could be explained by both types of exercise inducing EIH via the same mechanism (which is disrupted by NLX).

      We thank the reviewer for their comment and would like to refer back to the reviewer's comment number 38 for a response to this.

      (44) Line 360-361 - this conclusion cannot be drawn, because you have only compared high vs low intensity exercise. So, the conclusion should be 'These results suggest that there is no difference between high and low aerobic exercise intensity on heat-induced pain'.

      We agree with the reviewer and have rephrased the sentence to reflect the claim accurately.

      (45) Line 396 - as previously discussed, this conclusion cannot be drawn through this study design.

      We agree with the reviewer and have rephrased the sub-headline accordingly to reflect that there is no difference in exercise-induced hypoalgesia between HI and LI aerobic exercise.

      (46) Line 399 - please expand on this point - it is critical to the hypothesis and should also be included in the introduction. What intensities/duration/dose of aerobic exercise is generally established to cause EIH?

      We thank the reviewer and agree that this is a crucial aspect that requires further specification. Below we have expanded on the duration/intensities shown to elicit exercise-induced hypoalgesia and included a concise version of this detailed paragraph in the manuscript introduction.

      For aerobic exercise, different methods have been employed to determine exercise intensity levels i.e., through the VO2max, age-predicted HRmax, or incremental intensities (Koltyn, 2002). Most studies using VO2max as a measure of exercise intensity (Koltyn et al., 1996; Micalos & Arendt-Nielsen, 2016; Vaegter et al., 2014) were able to induce hypoalgesia with HI levels ranging between 65%-75% VO2max. When using the HRmax as a measure of determining exercise intensities, HI exercise at 70%-75% of the HRmax has been shown to produce greater hypoalgesia compared to moderate intensity at 50% HRmax (Naugle et al., 2014; Vaegter et al., 2014). Furthermore, previous research has suggested that HI exercise produces greater hypoalgesia compared to LI exercise (60-70% HRmax vs. light activity: M. D. Jones et al., 2019; 70% vs. 50% HRmax: Naugle et al., 2014; 75% vs. 50% VO2max: Vaegter et al., 2014).

      Furthermore, different durations can be regarded as suitable with durations between 8 minutes to 2 hours of aerobic exercise having been shown to induce hypoalgesia (for review see Koltyn (2002)). Hoffman et al. (2004) showed a hypoalgesic response after 30 minutes but not after 10 minutes at 75% VO2max of cycling. In contrast, other studies were able to induce hypoalgesia at 10-15 minutes of HI aerobic exercise (75% VO2may: Gomolka et al., 2019; 63% VO2max: Gurevich et al., 1994; self-paced: Haier et al., 1981; 60-70% HRmax: Jones et al., 2019; 85% HRmax: Sternberg et al., 2001; 75% VO2max: Vaegter et al., 2015).

      (47) Line 400-401 - please define high intensity.

      We thank the reviewer for their comment. The referenced studies by Vaegter et al. (2014) and Jones et al. (2019) based the estimation of HI and LI exercise on an age-related target heart rate corresponding to VO2max and HRmax, respectively. In Vaegter et al. (2014), the HI condition corresponded to 75% VO2max, while the LI to 50% VO2max. In Jones et al. (2019), the HI exercise condition corresponded to 60% and 70% of HRmax, while the LI condition was defined as pedalling slowly against a light resistance of 0.5 kg of force to maintain a rating of perceived exertion (RPE) not above resting. We have included this clarification in the relevant section to elucidate the intensities of the chosen exercise conditions.

      (48) Line 403-405 - I'm not sure I follow (perhaps I have misunderstood) - pain induction was completed after exercise in the MRI scanner, so there was no distraction effect of exercise in either condition. A baseline could have been established in the same way and there would be exactly the same conditions, just without prior exercise.

      We agree with the reviewer that a resting baseline condition in the context of exercise induced pain modulation allows for the investigation of a potential hypoalgesic effect of exercise compared to no exercise. Nevertheless, it is important to note that previous studies (Brooks et al., 2017; Sprenger et al., 2012) have shown that cognitive pain modulation is mediated by endogenous opioids. Therefore, tasks with different attentional loads potentially influence post-task pain ratings. Although, we agree with the reviewer that the effect of distraction or attentional load would be minimal in the MR scanner, there still could be an effect of different cognitive loads from exercise vs. no exercise. Nevertheless, we focus the discussion on investigating the dose-response relationship between different exercise intensities where an ‘active’ control condition might contribute to a more nuanced understanding of exercise-induced pain modulation.

      (49) Line 403-411 - this is fine (although I do not agree that this was the best methodological decision), however, it does limit the conclusions that can be drawn (as previously mentioned). That is, you cannot conclude that no EIH occurred, only that there was no difference between low and high-intensity exercise in post-exercise pain response.

      We agree with the reviewer that the comparison of HI vs. LI exercise does not allow for an interpretation of the overall effect of exercise as opposed to no exercise on pain modulation. The comparison of HI and LI exercise allows the investigation of a dose-response relationship of these distinct exercise intensities. While LI exercise might not be a 'pure' control condition in the traditional sense, it is valuable for exploring the complexities of exercise and pain interaction.

      (50) Line 419-422 - sorry I do not follow - you say that moderate intensity exercise most reliably induces EIH but then select exercise intensities that are likely to be in the heavy or severe intensity domain? Please also include in this discussion the limitations of FTP20 as a threshold marker (see Wong et al) and the implications on the results/conclusions.

      We thank the reviewer for their comment. In the referenced sentence, we have defined the HI exercise as described in the reviews. Specifically, Wewege and Jones (2020) reported hypoalgesia to be greater after higher-intensity exercise, although the intensity was not further specified. Naugle et al. (2012) noted that HI exercise (i.e., 75% of VO2max) produced greater hypoalgesia, while Koltyn (2002) indicated that hypoalgesia occurs at intensities ranging from 60% to 75% of VO2max but more reliably at 75% VO2max or higher. Consequently, we have removed the term ‘moderate’, as it does not accurately reflect what has been reported in the reviews and could be misleading. Moreover, we have clarified the specific criteria for what is considered high (or higher) intensity exercise in the referenced reviews.

      We kindly ask the reviewers to refer back to the previous comment (reviewer comment number 28) regarding the discussion of the intensity domains and the FTP20 test as demarcation point for these intensity domains.

      (51) Line 422-425 - indeed, pacing is an important element of this test, which inexperienced cyclists have difficulty with when they are not provided with proper familiarisation.

      We agree with the reviewer that the FTP20 test has mainly been validated and employed in experienced cyclists and requires further validation in non-athletes of both sexes. However, since we have used an extensive warm-up period and several paced steps (intervals, 5-minute time-trial) as well as recovery periods (Supplemental Table S1) based on McGrath et al. (2019) we propose that participants were thoroughly familiarised with the elements of pacing before the estimation of the FTP in the 20-minutes took place. On average, participants showed a variation of M = 21.80 Watts (SE = 1.44 Watts) during the 20-minute paced FTP20 test (Supplemental Figure S11A). Interestingly, our data suggests that participants with a higher FTP showed higher variation of power output (Watts) during the 20-minute FTP test compared to individuals with lower fitness levels (Supplemental Figure S11B).

      (52) Line 425-427 - please remove this, the RPE difference between exercise bouts is not evidence that participants cycled at FTP.

      We thank the reviewer for their comment. However, we would propose to include the rating of perceived exertion (RPE) since it shows that the exercise intensities have been perceived as significantly different by the participants. This behavioural measure of exertion is potentially important for a broader audience to understand the exercise implementation beyond physiological markers.

      (53) Line 432 - high vs. low-intensity aerobic exercise

      We have changed the sentence accordingly to support the claim of the study that there was no difference in exercise-induced pain modulation between HI and LI aerobic exercise.

      (54) Line 447-449 - this seems contradictory to the first line of this paragraph (430-432) - i.e. that the heterogenous sample may have caused the null finding. Why deliberately select a participant sample that is likely to lead to a null effect?

      In the current study, we aimed to include participants of diverse fitness levels and both sexes to verify the findings on exercise-induced pain modulation in a broader population. We consider this important concerning translational aspects of EIH. Indeed, our heterogeneous sample may have ‘caused’ the observed null effect, but at the same time, it suggests that more homogenous (sometimes composed solely of male athletes) samples employed in many earlier studies might have skewed the understanding of exercise-induced pain modulation and thus unintentionally suggested a (non-existing) generalisation of this effect to the general population.

      (55) Line 532-456 - although Koltyn found electrical pain to have the greatest effect?

      The review by Naugle et al. (2012) reported effect sizes for heat (Cohens d = 0.59) and pressure pain intensity (d = 0.69) following aerobic exercise but did not provide effect sizes for electrical pain intensity. They noted that the effect size for electrical pain intensity after isometric exercise was d = 0.40, which is lower than that for heat and pressure pain. While Koltyn (2002) stated that electrical and pressure stimuli induce exercise-induced hypoalgesia more consistently than thermal pain, the study did not clarify whether this applies to pain threshold, intensity, or tolerance, nor did they provide effect sizes. Given that electrical, pressure, and heat pain are the most commonly used methods to induce quantifiable pain in the context of exercise studies (Vaegter and Jones, 2020), we based our decision to use heat and pressure pain primarily on Naugle et al.'s findings.

      (56) Line 468-469 - why leave out content that was pre-registered (i.e. difference between pressure and heat pain) but includes analysis that wasn't (i.e. sex differences)? If a study is going to be pre-registered, then isn't it important to follow that design?

      We thank the reviewer for this comment. We have conducted the study adhering to the preregistered study design and now report the results for pressure pain (Supplemental Figure S1). Some of the preregistered analyses (i.e. directly comparing heat and pressure pain) were beyond the scope of the current study and will be reported separately.

      (57) Line 532-525 - and how could this have been accounted for?

      We apologise for any confusion, as we are unsure about the specific reference the reviewer is making based on the provided line numbers. We believe the question relates to how the potential effects of endocannabinoids were considered in the current study design, and we've addressed that in our response. In human studies, it is not possible to centrally block endocannabinoids, which makes it difficult to directly estimate their role in exercise-induced pain modulation in humans. Measuring endocannabinoids in the blood might not adequately capture changes in endocannabinoid levels in the brain throughout the different exercise intensity conditions. Despite these limitations, exploring the role of endocannabinoids in exercise-induced pain modulation presents a promising avenue for future research that could enhance our understanding of pain mechanisms and improve pain management strategies.

      58) Limitations General - please include the other limitations discussed in this review.

      Done.

      (59)Line 530 - please amend this conclusion, in line with previous comments.

      Done.

      We would like to thank the reviewer for critically evaluating the manuscript and providing insightful comments. We appreciate the reviewer recognising the strengths of our work and believe that their suggestions will contribute to improving the quality of the manuscript.

    1. Author response:

      Reviewer #1 (Public review):

      Summary:

      The manuscript "Rho-ROCK liberates sequestered claudin for rapid de novo tight junction formation" by Cho and colleagues investigates de novo tight junction formation during the differentiation of immortalized human HaCaT keratinocytes to granular-like cells, as well as during epithelial remodeling that occurs upon the apoptotic of individual cells in confluent monolayers of the representative epithelial cell line EpH4. The authors demonstrate the involvement of Rho-ROCK with well-conducted experiments and convincing images. Moreover, they unravel the underlying molecular mechanism, with Rho-ROCK activity activating the transmembrane serine protease Matriptase, which in turn leads to the cleavage of EpCAM and TROP2, respectively, releasing Claudins from EpCAM/TROP2/Claudin complexes at the cell membrane to become available for polymerization and de novo tight junction formation. These functional studies in the two different cell culture systems are complemented by localization studies of the according proteins in the stratified mouse epidermis in vivo.

      In total, these are new and very intriguing and interesting findings that add important new insights into the molecular mechanisms of tight junction formation, identifying Matriptase as the "missing link" in the cascade of formerly described regulators. The involvement of TROP2/EpCAM/Claudin has been reported recently (Szabo et al., Biol. Open 2022; Bugge lab), and Matriptase had been formerly described to be required for in tight junction formation as well, again from the Bugge lab. Yet, the functional correlation/epistasis between them, and their relation to Rho signaling, had not been known thus far.

      However, experiments addressing the role of Matriptase require a little more work.

      Strengths:

      Convincing functional studies in two different cell culture systems, complemented by supporting protein localization studies in vivo. The manuscript is clearly written and most data are convincingly demonstrated, with beautiful images and movies.

      Weaknesses:

      The central finding that Rho signaling leads to increased Matriptase activity needs to be more rigorously demonstrated (e.g. western blot specifically detecting the activated version or distinguishing between the full-length/inactive and processed/active version).

      We plan to provide more direct evidence that matriptase activation is regulated by the Rho-ROCK pathway, utilizing antibodies that specifically recognize the activated form of matriptase.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, the authors investigate how epithelia maintain intercellular barrier function despite and during cellular rearrangements upon e.g. apoptotic extrusion in simple epithelia or regenerative turnover in stratified epithelia like this epidermis. A fundamental question in epithelial biology. Previous literature has shown that Rho-mediated local regulation of actomyosin is essential not only for cellular rearrangement itself but also for directly controlling tight junction barrier function. The molecular mechanics however remained unclear. Here the authors use extensive fluorescent imaging of fixed and live cells together with genetic and drug-mediated interference to show that Rho activation is required and sufficient to form novo tight junctional strands at intercellular contacts in epidermal keratinocytes (HaCat) and mammary epithelial cells. After having confirmed previous literature they then show that Rho activation activates the transmembrane protease Matriptase which cleaves EpCAM and TROP2, two claudin-binding transmembrane proteins, to release claudins and enable claudin strand formation and therefore tight junction barrier function.

      Strengths:

      The presented mechanism is shown to be relevant for epithelial barriers being conserved in simple and stratifying epithelial cells and mainly differs due to tissue-specific expression of EpCAM and TROP2. The authors present careful state-of-the-art imaging and logical experiments that convincingly support the statements and conclusion. The manuscript is well-written and easy to follow.

      Weaknesses:

      Whereas the in vitro evidence of the presented mechanism is strongly supported by the data, the in vivo confirmation is mostly based on the predicted distribution of TROP2. Whereas the causality of Rho-mediated Matriptase activation has been nicely demonstrated it remains unclear how Rho activates Matriptase.

      As noted, while we have demonstrated that Rho activation is both necessary and sufficient to induce matriptase activation, the precise mechanism by which Rho mediates this activation remains unclear. As discussed in the manuscript, several potential molecular mechanisms could underlie the contribution of Rho to matriptase activation. As part of our future work, we intend to systematically investigate each of these mechanisms.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Recommendations for the authors:

      Reviewing Editor Comments:

      The resubmitted version of the manuscript adequately addressed several initial comments made by reviewing editors, including a more detailed analysis of the results (such as those of bilayer thickness). This version was seen by 2 reviewers. Both reviewers recognize this work as being an important contribution to the field of BK and voltage-dependent ion channels in general. The long trajectories and the rigorous/novel analyses have revealed important insights into the mechanisms of voltage-sensing and electromechanical coupling in the context of a truncated variant of the BK channel. Many of these observations are consistent with structural and functional measurements of the channel, available thus far. The authors also identify a novel partially expanded state of the channel pore that is accessed after gating-charge displacement, which informs the sequence of structural events accompanying voltage-dependent opening of BK.

      However, there are key concerns regarding the use of the truncated channel in the simulations. While many gating features of BK are preserved in the truncated variant, studies have suggested that opening of the channel pore to voltage-sensing domain rearrangement is impaired upon gating-ring deletion. So the inferences made here might only represent a partial view of the mechanism of electromechanical coupling.

      It is also not entirely clear whether the partially expanded pore represents a functionally open, sub-conductance, or another closed state. Although the authors provide evidence that the inner pore is hydrated in this partially open state, in the absence of additional structural/functional restraints, a confident assignment of a functional state to this structure state is difficult. Functional measurements of the truncated channel seem to suggest that not only is their single channel conductance lower than full-length channels, but they also appear to have a voltage-independent step that causes the gates to open. It is unclear whether it is this voltage-independent step that remains to be captured in these MD trajectories. A clean cut resolution of this conundrum might not be feasible at this time, but it could help present the various possibilities to the readers.

      We appreciate the positive comments and agree that there will likely be important differences between the mechanistic details of voltage activation between the Core-MT and full-length constructs of BK channels. We also agree that the dilated pore observed in the simulation may not be the fully open state of Core-MT.

      Nonetheless, the notion that the simulation may not have captured the full pore opening transition or the contribution of the CTD should not render the current work “incomplete”, because a complete understanding of BK activation would be an unrealistic goal beyond the scope of this work. We respectfully emphasize that the main insights of the current simulations are the mechanisms of voltage sensing (e.g., the nature of VSD movements, contributions of various charged residues, how small charge movements allow voltage sensing, etc.) as well as the role of the S4-S5-S6 interface in VSD-pore coupling. As noted by the Editor and reviewers, these insights represent important steps towards establishing a more complete understanding of BK activation.

      Below are the specific comments of the two experts who have assessed the work and made specific suggestions to improve the manuscript.

      Reviewer #1 (Recommendations for the authors):

      (1) Although the successful simulation of V-dependent K+ conduction through the BK channel pore and analysis of associated state dependent VSD/pore interactions and coupling analysis is significant, there are two related questions that are relevant to the conclusions and of interest to the BK channel community which I think should be addressed or discussed.

      One key feature of BK channels is their extraordinarily large conductance compared to other K+ selective channels. Do the simulations of K+ conductance provide any insight into this difference? Is the predicted conductance of BK larger than that of other K+ channels studied by similar methods? Is there any difference in the conductance mechanism (e.g., the hard and soft knock-on effects mentioned for BK)?

      The molecular basis of the large conductance of BK channels is indeed an interesting and fundamental question. Unfortunately, this is beyond the scope of this work and the current simulation does not appear to provide any insight into the basis of large conductance. It is interesting to note, though, the conductance is apparently related to the level of pore dilation and the pore hydration level, as increasing hydration level from ~30 to ~40 waters in the pore increases the simulated conductance from ~1.5 to 6 pS (page 8). This is consistent with previous atomistic simulations (Gu and de Groot, Nature Communications 2023; ref. 33) showing that the pore hydration level is strongly correlated with observed conductance. As noted in the manuscript, the conductance mechanism through the filter appears highly similar to previous simulations of other K+ channels (Page 8). Given the limit conductance events observed in the current simulations, we will refrain from discussing possible basis of the large conductance in BK channels except commenting on the role of pore hydration (page 8; also see below in response to #5).

      The pore in the MD simulations does not open as wide as the Ca-bound open structure, which (as the authors note) may mean that full opening requires longer than 10 us. I think that is highly likely given that the two 750 mV simulations yielded different degrees of opening and that in BK channels opening is generally much slower than charge movement. Therefore, a question is - do any of the conclusions illustrated in Figures 6, S5, S6 differ if the Ca-bound structure is used as the open state? For example, I expect the interactions between S5 and S6 might at least change to some extent as S6 moves to its final position. In this case, would conclusions about which residues interact, and get stronger or weaker, be the same as in Figures S6 b,c? Providing a comparison may help indicate to what extent the conclusions are dependent on achieving a fully open conformation.

      We appreciate the reviewer’s suggestion and have further analyzed the information flow and coupling pathways using the simulation trajectory initiated from the Ca2+-bound cryo-EM structure (sim 7, Table S1). The new results are shown in two new SI Figures S7 and S8, and new discussion has been added to pages 14-15. Comparing Figures 5 and S7, we find that dynamic community, coupling pathways, and information flow are highly similar between simulation of the open and closed states, even though there are significant differences in S5 contacts in the simulated open state vs Ca2+-bound open state (Figure S8). Interestingly, there are significant differences in S4-S5 packing in the simulated and Ca2+-bound open states (Figure S8 top panel), which likely reflect important difference in VSD/pore interactions during voltage vs Ca2+ activation.

      (2) P4 Significance -"first, successful direct simulation of voltage-activation"

      This statement may need rewording. As noted above Carrasquel-Ursulaez et al.,2022 (reference 39) simulated voltage sensor activation under comparable conditions to the current manuscript (3.9 us simulation at +400 mV), and made some similar conclusions regarding R210, R213 movement, and electric field focusing within the VSD. However, they did not report what happens to the pore or simulate K+ movement. So do the authors here mean something like "first, successful direct simulation of voltage-dependent channel opening"?

      We agree with the reviewer and have revised the statement to “ … the first successful direct simulation of voltage-dependent activation of the big potassium (BK) channel, ..”

      (3) P5 "We compare the membrane thickness at 300 and 750 mV and the results reveal no significant difference in the membrane thickness (Figure S2)" The figure also shows membrane thickness at 0 mV and indicates it is 1.4 Angstroms less than that at 300 or 750 mV. Whether or not this difference is significant should be stated, as the question being addressed is whether the structure is perturbed owing to the use of non-physiological voltages (which would include both 300 and 750 mV).

      We have revised the Figure S2 caption to clarify that one-way ANOVA suggest the difference is not significant.

      (4) P7 "It should be noted that the full-length BK channel in the Ca2+ bound state has an even larger intracellular opening (Figure 2f, green trace), suggesting that additional dilation of the pore may occur at longer timescales."

      As noted above, I agree it is likely that additional pore dilation may occur at longer timescales. However, for completeness, I suppose an alternative hypothesis should be noted, e.g. "...suggesting that additional dilation of the pore may occur at longer timescales, or in response to Ca-binding to the full length channel."

      This is a great suggestion. Revised as suggested.

      (5) Since the authors raise the possibility that they are simulating a subconductance state, some more discussion on this point would be helpful, especially in relation to the hydrophobic gate concept. Although the Magleby group concluded that the cytoplasmic mouth of the (fully open) pore has little impact on single channel conductance, that doesn't rule out that it becomes limiting in a partially open conformation. The simulation in Figure 3A shows an initial hydration of the pore with ~15 waters with little conductance events, suggesting that hydration per se may not suffice to define a fully open state. Indeed, the authors indicate that the simulated open state (w/ ~30-40 waters) has 1/4th the simulated conductance of the open structure (w/ ~60 waters). So is it the degree of hydration that limits conductance? Or is there a threshold of hydration that permits conductance and then other factors that limit conductance until the pore widens further? Addressing these issues might also be relevant to understanding the extraordinarily large conductance of fully open BK compared to other K channels.

      We agree with the reviewer’s proposal that pore hydration seems to be a major factor that can affect conductance. This is also well in-line with the previous computational study by Gu and de Groot (2023). We have now added a brief discussion on page 8, stating “Besides the limitation of the current fixed charge force fields in quantitively predicting channel conductance, we note that the molecular basis for the large conductance of BK channels is actually poorly understood (78). It is noteworthy that the pore hydration level appears to be an important factor in determining the apparent conductance in the simulation, which has also been proposed in a previous atomistic simulation study of the Aplysia BK channel (33).”

      Minor points

      (1) P5 "the fully relaxed pore profile (red trace in Figure S1d, top row) shows substantial differences compared to that of the Ca2+-free Cryo-EM structure of the full-length channel." For clarity, I suggest indicating which is the Ca-free profile - "... Ca2+-free Cryo-EM structure of the full-length channel (black trace)."

      We greatly appreciate the thoughtful suggestion. Revised as suggested.

      (2) P8 "Consistent with previous simulations (78-80), the conductance follows a multi-ion mechanism, where there are at least two K+ ions inside the filter" For clarity, I suggest indicating these are not previous simulations of BK channels (e.g., "previous simulations of other K+ channels ...").

      Revised as suggested. Thank you.

      (3) Figure 2, S1 - grey traces representing individual subunits are very difficult to see (especially if printed). I wonder if they should be made slightly darker. Similar traces in Figure 3 are easier to see.

      The traces in Figure S1 are actually the same thickness in Figure 3 and they appear lighter due to the size of the figure. Figure 2 panels a-c have been updated to improve the resolution.

      (4) Figure 2 - suggest labeling S6 as "S6 313-324" (similar to S4 notation) to indicate it is not the entire segment.

      Figure 2 panel d) has been updated as suggested.

      (5) Figure 2 legend - "Voltage activation of Core-MT BK channels. a-d)..."

      It would be easier to find details corresponding to individual panels if they were referenced individually. For example:

      "a-d) results from a 10-μs simulation under 750 mV (sim2b in Table S1). Each data point represents the average of four subunits for a given snapshot (thin grey lines), and the colored thick lines plot the running average. a) z-displacement of key side chain charged groups from initial positions. The locations of charged groups were taken as those of guanidinium CZ atoms (for Arg) and sidechain carboxyl carbons (for Asp/Glu) b) z-displacement of centers-of-mass of VSD helices from initial positions, c) backbone RMSD of the pore-lining S6 (F307-L325) to the open state, and d) tilt angles of all TM helices. Only residues 313-324 of S6 were included inthe tilt angle calculation, and the values in the open and closed Cryo-EM structures are marked using purple dashed lines. "

      We appreciate the thoughtful suggestion and have revised the caption as suggested.

      (6) Figure S1 - column labels a,b,c, and d should be referenced in the legend.

      The references to column labels have been added to Figure S1 caption.

      (7) References need to be double-checked for duplicates and formatting.

      a) I noticed several duplicate references, but did not do a complete search: Budelli et al 2013 (#68, 100), Horrigan Aldrich 2002 (#22,97), Sun Horrigan 2022 (#40, 86), Jensen et al 2012 (#56,81).

      b) Reference #38 is incorrectly cited with the first name spelled out and the last name abbreviated.

      We appreciate the careful proofreading of the reviewer. The duplicated references were introduced by mistake due to the use of multiple reference libraries. We have gone through the manuscript and removed a total of 5 duplicated references.

      Reviewer #2 (Recommendations for the authors):

      This manuscript has been through a previous level of review. The authors have provided their responses to the previous reviewers, which appear to be satisfactory, and I have no additional comments, beyond the caveats concerning interpretations based on the truncated channel, which are noted above.

      We greatly appreciate the constructive comments and insightful advice. Please see above response to the Reviewing Editor’s comments for response and changes regarding the caveats concerning interpretations of the current simulations.

    1. Author response:

      The following is the authors’ response to the original reviews.

      We deeply appreciate the reviewer comments on our manuscript. We have proceeded with all the minor changes mentioned. We also want to emphasize three major points:

      (1) Reversine has been shown to have several off-targets effects. Including inducing apoptosis (Chen et al. J Bone Oncol. 2024).

      (2) Hypoxia varies from 2% to 6%. Our definition of hypoxia is 5% concentration of oxygen with 5% concentration of CO<sub>2</sub>, taking into consideration the standard levels of oxygen in the IVF clinics. Physiological oxygen in mouse varies from ~1.5% to 8%.

      (3) Natale et al. 2004 (Dev Bio) and Sozen et al. 2015 (Mech of Dev) described that inhibition of p38 deeply affect the development of pre-implantation embryos after the 8-cell stage. For this reason, comprehensible dissect the interaction between p53, HIF1A and p38 during aneuploid stress is challenging. We do not discard a double function of p38 during lineage specification and in response to DNA damage.

      Reviewer #2 (Recommendations for the authors):

      (1) Line 69: Please add the species used in your cited publications (murine).

      Fixed

      (2) Line 72: Consider changing "Because" to "As".

      Fixed

      (3) Line 88: "from the nuclei" - please refer to where the reader may find the example provided (Figure S1A).

      Fixed

      (4) Line 89: This should be Figure S1B as no quantification is presented in S1A. S1A only contains examples of micronuclei.

      Fixed

      (5) Line 91: Refer to Figure S1A.

      Fixed

      (6) Line 91-93: Are these numbers correct? The query arises from the numbers presented in Figure S1B. Please define how the median was calculated; is it micronuclei CREST+ plus micronuclei CREST-?

      Fixed. We did not differentiate in these percentage the presence of CREST.

      (7) Line 95: extra/missing bracket?

      Fixed

      (8) Line 88-91:

      [a] Regarding the number of cells with micronuclei in this text, please clarify your sample size and how the percentages were calculated as they currently do not align (e.g., are these the total number of embryos from a single experimental replicate?).

      Also, different numbers are found here and in the figure legend: (DMSO-22/256 cells from 32 embryos; Rev-82/144 cells from 18 embryos; AZ-182/304 cells from 38 embryos) vs. Fig S1 legend (DMSO-n=128 cells; Rev-72 cells; AZ-152 cells).

      [c] Is the median calculated using the numbers presented above? If yes, then the numbers do not tally, please check (DMSO-22/256 cells=8.6%; Rev-82/144 cells=56.9%; AZ-182/304 cells =59.9%) vs. Line 91-93: DMSO=12.5%, Rev=75%; AZ=62.5% blastomeres had micronuclei.

      The percentage represents the average of aneuploidy per embryo after normalization.

      See table for DMSO. This number represents the average of aneuploid cells each aneuploid embryo has. Notice that some embryos are fully diploid. Some have more that 12.5% -> 25%. Most of the aneuploid embryos have 12.5% of aneuploidy. It is not black and white as how many aneuploid cell there is in the sample but a full understanding of how aneuploid are the aneuploid embryos in each sample.

      Author response image 1.

      (9) Line 108:

      [a] "n=28 per treatment" please clarify whether this refers to the number of embryos or cells and also add how many independent replicate experiments this data is representative of. as the text only refers to Figure 1C you can remove the P-values for ** and *.

      Number of embryos. Fixed

      (10) Line 111: Suggest citing Figure 1C at the end of the sentence.

      Fixed

      (11) Line 118-119: the reference to figures require updating to ensure they refer to the appropriate figure; ...decidua (Figure S1C)...viable E9.5 embryos (Figure S1D).

      Fixed

      (12) Line 126: A description of the data in Figures 1D and 1E is missing. Also, consider describing the DNA damage observed in the DMSO control group. Visually, it appears that DNA damage reduces from the 8-cell to the morula stage (Figure 1E) but increases at the blastocyst stage (Figure S2A)? Point for discussion for a normal rate of DNA damage?

      Agree, there is some DNA damage in the TE in blastocyst

      (13) Line 134: 8 EPI and 4 PE cells in what group?

      Fixed: DMSO-treated embryos

      (14) Line 137: Could this also suggest that AZ and reversine induce DNA damage through a different mechanism/pathway, resulting in the differential impact observed? Despite both being inhibitors of Mps1.

      This is a possibility.

      (15) Line 153: the legend for Figure 2A says the Welch t-test was performed, but the Mann-Whitney U-test was stated here. Which is correct?

      Welch’s t-test

      (16) Line 155: ...at the blastocyst stage. Compared to what?

      DMSO-treated embryos

      (17) Line 160: Data in Figure 2B requires the definition of P-values for , , . Please add one for and remove the one for **.

      Fixed

      (18) Line 173-174: Data in Fig. 4 requires the definition of the P-values for ****. Please remove the others.

      Fixed

      (19) Line 180: Instead of jumping across figures, this section would benefit from stating the numbers directly to allow for an accurate comparison, e.g. 64 and 7 in Figure 2D vs. X and Y in Figure 1C.

      (20) Line 187: Hif1a should be italicised.

      Fixed

      (21) Line 197: Based on the description here, I believe you are missing a reference to Figure 1A.

      Fixed

      (22) Line 203: Instead of jumping across figures, this section would benefit from stating the numbers directly to allow for accurate comparison, "particularly in the TE and PE" (67 vs 54; and 11 vs 6, respectively).

      (23) Line 209-210:

      [a] "...lowered the number of yH2AX foci..." is this a visual observation as quantification was performed for yH2AX intensity, not quantification of foci?

      A description for PARP1 levels in morula stage embryos was presented ("...relatively low in morula), but not for yH2AX levels at this stage of development. Missing description?

      Fixed

      (24) Line 235: This sentence would benefit from being specific about the environmental conditions...eg "Under normoxia, DMSO/AZ3146-treated...",

      (25) Line 238: The sentence should reference Figure 4F not 4G.

      Fixed

      (26) Line 242-243:

      [a] "slightly increased... in the TE (49.06%) and PE (50%) but, strikingly, reduced... EPI (33.3%)" compared to what and in which figure?

      Assuming you are comparing normoxia (4F) to hypoxia (4G), the numbers change for the TE (46.75% to 49.06%, respectively), EPI (42.88% to 33.3%, respectively), and PE (28.57% to 50%, respectively); yet these data were described as "strikingly different" for EPI (9.58 decrease) but only "slightly increased" for PE (21.42 increase). Suggest using appropriate adjectives to describe the results.

      Fixed

      (27) Line 256: It is stated in line 255 that treatment was performed at the zygote stage, yet this sentence says reversine treatment occurred at the 2-cell stage? Which is correct? Please amend appropriately. Refer to the comment below regarding adding a schematic to aid readers

      Fixed

      (28) Line 259: "n>27 per treatment" please clarify whether this refers to the number of embryos or cells and also add how many independent replicate experiments this data is representative of. Data in Figures S5A-B requires a definition of P-values for , . Please remove for *, *.

      Fixed

      (29) Line 261: AZ3146/reversine stated here, the figure shows Reversine/AZ3146. Please consider being consistent.

      Fixed

      (30) Line 263: "... normal morphology and cavitation (Figure S5D); however the image presented for Rev/DMSO and Rev/AZ3146 chimeras appear smaller with a distorted/weird shape when compared to DMSO/AZ. I believe the description does not match the images presented.

      Fixed

      (31) Line 267: "...similar results as 8-cell stage derived chimeras"; however, there is only a reference to Fig S5E which depicts 2-cell/zygote stage (see comment above for line 256 regarding required clarification of stage of treatment) derived chimeras. There is also a missing reference to Figure 4B, D, and/or F?

      Fixed

      (32) Line 271: add a reference to Figure S5E.

      Fixed

      (33) Line 283: "AZ3146/reversine" should be "Reversine/AZ3146" to match the figure.

      Fixed

      (34) Line 284: Figures 5E-F show both morphology and cavitation; the text should reflect this.

      Fixed

      (35) Line 281-285: I think this text requires editing to improve clarity. It is difficult for this reader to understand the authors' interpretation of the results....inhibiting HIF1A reduces morphology and cavitation. That's correct. However, this also diminished the contribution of AZ3146-treated cells to all 3 cell lineages; this is not quite accurate. AZ3146-treated cells were significantly reduced in total cell numbers because TE was significantly reduced. It is not appropriate to generalise this result to all 3 lineages, as EPI and TE appear to increase AZ's contribution following IDF treatment, albeit non-statistically significant.

      Fixed

      (36) Line 320: citation? ....reversine-treated embryos. Is this referring to your previous publication...Bolton 2016?

      Fixed

      (37) Line 344: missing space between 7.5 and IU.

      Fixed

      (38) Line 358: animal ethics approval number/code missing.

      Fixed

      (39) Line 397: missing space between "...previously" and "(Bermejo...".

      Fixed

      (40) Line 417: missing space between "...control" and "(Gu et...".

      Fixed

      (41) Line 421: missing space between "protocol" and "(Eakin...".

      Fixed

      (42) Line 427-429: Medium-grade mosaic chimeras were referred to as DMSO:AZ:Rev (3:3:2) here; but Figure 4 and associated legend says otherwise. Please amend appropriately. Were all medium mosaics generated in this manner? As I could only find Rev/AZ chimeras; my understanding of the Rev/AZ chimeras is 1:1 Rev:AZ instead of 3:2:3 DMSO:Rev:AZ.

      Fixed

      (43) Line 428: "reversine-treaded: please correct spelling.

      Fixed

      (44) Line 593: "n=28 per treatment" Please clarify whether this refers to the number of embryos or cells and also add how many independent replicate experiments this data is representative of.

      Fixed

      (45) Line 597: "through morula stage" when compared to what group?

      DMSO-treated embryos

      (46) Line 598: Data in Figure S5A-B requires the definition of P-values for , , **. Please remove for . Please define the error bars. SEM/95% confidence interval?

      Fixed

      (47) Line 604-607: Regarding 2B, no statistical test is stated yet Mann-Whitney was stated in Line 160 of the results section. Please confirm which test was used and include it in both sections for consistency.

      Fixed

      (48) Line 608: "Chemical downregulation of HIF1A"... this is not described in the results/methods section or shown in the figure. Please amend all sections for accuracy.

      Fixed

      (49) Line 613: please change "effect in" to "effect on".

      Fixed

      (50) Line 614: Please clarify the number of embryos or cells and also add how many independent replicate experiments this data is representative of. Data in Figure 2 also requires a definition of P-value for ****.

      Fixed

      (51) Line 625: Please clarify the number of embryos or cells and also add how many independent replicate experiments this data is representative of. Data in Figure 3 also requires a definition of P-value for ****.

      Fixed

      (52) Line 627: description requires editing to improve accuracy "...is only slightly increased at the 8-cell stage after exposure to reversine and AZ3146". However, the results show significantly higher DNA damage with Reversine treatment, but not with AZ when compared to DMSO. Please amend accordingly.

      Fixed

      (53) Line 629: Please define the error bars. SEM/95% confidence interval?

      Fixed

      (54) Line 634-635: it is written here that chimeras were made from 1:1 DMSO/AZ3146 and Reversine/DMSO; but Figure 4A shows 1:1 DMSO(grey):AZ3146(blue), and Reversine(red):AZ3146(blue), which contradicts the legend + method section; see comments for Line 427-429. Please amend these sections accordingly.

      Fixed

      (55) Line 648: reversine/AZ3146 chimeras? Refer to comments above.

      Fixed

      (56) Line 649-650: ...AZ-treated blastomeres contribute similarly to reversine-blastomeres to the TE and EPI but significantly increase contribution to the EPI? Please add the appropriate comparison group.

      Fixed

      (57) Line 652: Please clarify the number of embryos or cells and also add how many independent replicate experiments this data is representative of.

      Fixed

      (58) Line 664: Please clarify the number of embryos or cells and also add how many independent replicate experiments this data is representative of.

      Fixed

      (59) Line 675-677: FigS1B legend requires a definition of P-value for * and ****, can omit **

      Fixed

      (60) Line 678-680: FigS1C and S1D legend: sample size and replicates? Only mentioned in Lines 117-120, which requires back calculation.

      Fixed

      (61) Line 682-694: (1) Fig. S2B legend: missing P-value description for *** and ***; statistical test not stated, please add. Also, Figure S2E, only requires the definition for , and can omit others.

      Fixed

      (62) Line 702: FigS3B: missing description for ****, omit others.

      Fixed

      (63) Line 704-705: missing description for Rev/AZ group and hypoxia vs. normoxia conditions.

      Fixed

      (64) Line 712-713: "n>27 per treatment" Please clarify whether this refers to the number of embryos or cells and also add how many independent replicate experiments this data is representative of. Data in Figure S5 requires the definition of P-values for , . Please remove for *, *.

      Fixed

      (65) Line 713-715: could benefit from a description of which were marked from mTmG; e.g. why is DMSO, Rev, Rev in Green for [D]; does this mean 2-cell stage chimeras were only made with embryos treated with DMSO and Reversine? Has it been tested if you did this with AZ3146, do the proportions remain the same? This would be interesting to know.

      DMSO and reversine are in green because they are the cells mark with green in the chimeras. We also did chimeras with AZ3146. Hope this clarifies.

      (66) Line 719-721: why is there a difference between the proportion of aneuploid cells for the different chimeras? AZ in D/AZ, and R/AZ groups; while only R in D/R group? Is this because you only count those that were marked with mTmG (e.g. based on [Fig S5D])? (67) Line 724: low- and medium-grade chimeras would indicate quality, recommend adding low/medium grade aneuploid/mosaic chimeras.

      Fixed

      (68) Line 725-729: it may be my mistake, but I think the results description is not found within the Results section, but only here in the legend? Please include this detail also in the Results section.

      Fixed

      (69) Line 729: which is AZ or Rev cells?

      (70) References - Page number missing for some references; abbreviated version vs. non abbreviated version of journal titles used. Please be consistent/meet journal requirements.

      Fixed

      (71) Figures

      Figure 1: [C] both AZ-NANOG and DMSO-SOX17 have mean/median(?) of 11 cells (described in results), yet in this figure (on the same axis) these groups are not level. Are the numbers correct? This is also the case for Rev-SOX17 which is described in the results as having 8 cells yet appears to be above the 8 mark in the graphs; AZ-CDX2, which has 64 cells yet appears to be below the 60 mark; AZ-total, which has 82 cells yet appears to be below the 80 mark. In [E] the label orientation, "ns" has both horizontal and vertical orientation. Please make appropriate changes throughout to reflect accuracy.

      Figure 3: [C] As for Figure 1, DMSO-NANOG, which is described in results as having 14 cells, yet appears to be below the 13 mark in the graph; DMSO-SOX17, which has 6 cells yet appears to be above the 7 mark.

      These is due to average

      Figure 4: [D and E] random numerals appear in the bars on the graph. 9,10 and 7, 14? Are these sample size numbers? If they are, they should appear in all bars/groups or in the legend.

      Yes, these are sample sizes

      Figure 5: [D and G] same comment as for Fig 4 above, random numbers in the graph.

      Yes, these are sample sizes

      (72) Supplementary figures. Figure S2 [A] No quantification? This is important to add as representative images are only a 2D plane, which can be easily misinterpreted. [E] Should the y-axis label be written as "Number of cells normalised to DMSO group", or similar? Or is there a figure missing to depict the ratio of cells in each cell lineage normalised to the DMSO group, which is the description written in the legend? But I don't see a figure showing the ratio, just the absolute number of cells. Is this a missing figure or a mislabelled axis?

      Quantification at the blastocyst stage is misleading due to high cellular heterogeneity.

      Reviewer #3 (Recommendations for the authors):

      (1) The statement in the abstract: "embryos with a low proportion of aneuploid cells have a similar likelihood of developing to term as fully euploid embryos" Line 48-50 Capalbo does not really answer as the biopsy may not be reflective of ICM.

      This is a great point. Trophectoderm biopsies may not reflect the real proportion of aneuploidy in the ICM. We emphasize this in discussion and Fig. S4.

      (2) Line 69/70, at least 50% Singla et al/Bolton. It would be helpful to elaborate a bit more on this study. How can this be assessed when analysis results in destruction?

      (3) Differences in the developmental potential of reversine versus AZ-treated embryos. It is not entirely clear why. The differences in non-dividing cells if any are small, and the -crest cells are rather minor also. Could these drugs have other effects that are not evaluated in the study?

      Yes, specifically, reversine has been shown to have several off-targets effects. Including inducing apoptosis (Chen et al 2024).

      (4) Lines 45-46 understanding of reduction of aneuploidy should mention/discuss the paper of attrition/selection, of the kind by the Brivanlou lab for instance, or others. As well as allocation to specific lineages, including the authors' work.

      Dr. Brinvanlou experiments in gastruloids do not represent the same developmental stage of pre-implantation embryos. Comparison between models is debatable.

      (5) Line 53: human experiments are more limited due to access to samples. What does 'not allowed' mean? By who, where?

      NIH does not allow to experiment with human embryos for ethical reasons.

      (6) The figure callouts to S1A in lines 93,97. What is a non-dividing nucleus? For how long is it observed?

      A non-dividing nucleus is an accumulation of DNA in a round form without define separation of the chromosomes and their specific kinetochores (CREST antibody). The presence of non-dividing nucleus during the 4 -to-8 cell stage can indicate activation of the spindle assembly checkpoint during prometaphase. Example of non-dividing nucleus can be observed in Fig S1.B.

      (7) Line 108 A relatively minor effect on cell number and quality of blastocysts is observed. It is not surprising that thereafter, developmental potential is also high. At that stage, what are the individual cell karyotypes?

      Due to technical limitations, we can’t determine the specific karyotypes of these cells.

      (8) Line 153. The p53 increase of 1.3 fold is not dramatic.

      The levels of p53 at the morula stage is 7-fold differences. In contrast, at the blastocyst stage, a change in 1.3-fold is indeed less dramatic. This can be a result of the elimination of aneuploid cells or mechanism to counter the activation of the p53 pathway, like overexpression of the Hif1a pathway.

      (9) Line 155. Is there a more direct way to test for p38 activation?

      Natale et al 2004 (Dev Biol) and Sozen et al 2015 (Mech of Dev) described that inhibition of p38 deeply affect the development of pre-implantation embryos after the 8-cell stage. For this reason, comprehensible dissect the interaction between p53, HIF1A and p38 during aneuploid stress is challenging. We do not discard a double function of p38 during lineage specification and in response to DNA damage.

      (10) Line 191/192 Low oxygen conditions, is this equal to hypoxia? What is the definition of hypoxia here? The next sentence says physiological. Is that the same or different?

      Low oxygen can be defined as hypoxia. This varies from 2% to 6%. Our definition of hypoxia is 5% concentration of oxygen with 5% concentration of CO<sub>2</sub>, taking into consideration the standard levels of oxygen in the IVF clinics. Physiological oxygen in mouse varies from ~1.5% to 8%.

      (11) The question is whether there is something specific about HIF1 and aneuploidy, or whether another added stress would have similar effects on the competitiveness of treated cells.

      That is a great follow up of our work.

      (12) Line 300. Is p21 unregulated at the protein level or mRNA level? Please indicate.

      mRNA level.

      (13) Figure 1D/E H2Ax intensity is cell cycle phase-dependent. It might be meaningful to count foci by the nucleus and show both ways of analysis.

      (14) Check the spelling of phalloidin.

      Fixed in text and figures!

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The study by Deng et al reports single cell expression analysis of developing mouse hearts and examines the requirements for cardiac fibroblasts in heart maturation. The work includes extensive gene expression profiling and bioinformatic analysis. The prenatal fibroblast ablation studies show new information on the requirement of these cells on heart maturation before birth.

      The strengths of the manuscript are the new single cell datasets and comprehensive approach to ablating cardiac fibroblasts in pre and postnatal development in mice. Extensive data are presented on mouse embryo fibroblast diversity and morphology in response to fibroblast ablation. Histological data support localization of major cardiac cell types and effects of fibroblast ablation on cardiac gene expression at different times of development.

      A weakness of the study is that the major conclusions regarding collagen signaling and heart maturation are based on gene expression patterns and are not functionally validated.

      Reviewer #2 (Public review):

      This study aims to elucidate the role of fibroblasts in regulating myocardium and vascular development through signaling to cardiomyocytes and endothelial cells. This focus is significant, given that fibroblasts, cardiomyocytes, and vascular endothelial cells are the three primary cell types in the heart. The authors employed a Pdgfra-CreER-controlled diphtheria toxin A (DTA) system to ablate fibroblasts at various embryonic and postnatal stages, characterizing the resulting cardiac defects, particularly in myocardium and vasculature development. Single-cell RNA sequencing (scRNA-seq) analysis of the ablated hearts identified collagen as a crucial signaling molecule from fibroblasts that influences the development of cardiomyocytes and vascular endothelial cells.

      This is an interesting manuscript; however, there are several major issues, including an over-reliance on the scRNA-seq data, which shows inconsistencies between replicates.

      We thank the reviewer for carefully reading our revised manuscript. All of the questions listed below were raised in the previous round and have been addressed in the current revision. As noted in the “Recommendations for the Authors” section, the reviewer has no additional comments at this time.

      Some of the major issues are described below.

      (1) The CD31 immunostaining data (Figure 3B-G) indicate a reduction in endothelial cell numbers following fibroblast deletion using PdgfraCreER+/-; RosaDTA+/- mice. However, the scRNA-seq data show no percentage change in the endothelial cell population (Figure 4D). Furthermore, while the percentage of Vas_ECs decreased in ablated samples at E16.5, the results at E18.5 were inconsistent, showing an increase in one replicate and a decrease in another, raising concerns about the reliability of the RNA-seq findings.

      (2) Similarly, while the percentage of Ven_CMs increased at E18.5, it exhibited differing trends at E16.5 (Fig. 4E), further highlighting the inconsistency of the scRNA-seq analysis with the other data.

      (3) Furthermore, the authors noted that the ablated samples had slightly higher percentages of cardiomyocytes in the G1 phase compared to controls (Fig. 4H, S11D), which aligns with the enrichment of pathways related to heart development, sarcomere organization, heart tube morphogenesis, and cell proliferation. However, it is unclear how this correlates with heart development, given that the hearts of ablated mice are significantly smaller than those of controls (Figure 3E). Additionally, the heart sections from ablated samples used for CD31/DAPI staining in Figure 3F appear much larger than those of the controls, raising further inconsistencies in the manuscript.

      (4) The manuscript relies heavily on the scRNA-seq dataset, which shows inconsistencies between the two replicates. Furthermore, the morphological and histological analyses do not align with the scRNA-seq findings.

      (5) There is a lack of mechanistic insight into how collagen, as a key signaling molecule from fibroblasts, affects the development of cardiomyocytes and vascular endothelial cells.

      (6) In Figure 1B, Col1a1 expression is observed in the epicardial cells (Figure 1A, E11.5), but this is not represented in the accompanying cartoon.

      (7) Do the PdgfraCreER+/-; RosaDTA+/- mice survive after birth when induced at E15.5, and do they exhibit any cardiac defects?

      Reviewer #3 (Public review):

      Summary:

      The authors investigated fibroblasts' communication with key cell types in developing and neonatal hearts, with focus on critical roles of fibroblast-cardiomyocyte and fibroblast-endothelial cells network in cardiac morphogenesis. They tried to map the spatial distribution of these cell types and reported the major pathways and signaling molecules driving the communication. They also used Cre-DTA system to ablate Pdgfra labeled cells and observed myocardial and endothelial cell defects at development. They screened the pathways and genes using sequencing data of ablated heart. Lastly they reported a compensatory collagen expression in long term ablated neonate heart. Overall, this study provides us with important insight on fibroblasts' roles in cardiac development and will be a powerful resource for collagens and ECM focused research.

      Strengths:

      The authors utilized good analyzing tools to investigate on multiple database of single cell sequencing and Multi-seq. They identified significant pathways, cellular and molecular interactions of fibroblasts. Additionally, they compared some of their analytic findings with human database, and identified several groups of ECM genes with varying roles in mice.

      Weaknesses:

      This study is majorly based on sequencing data analysis. At the bench, they used very strident technique to study fibroblast functions by ablating one of the major cell population of heart. Also, experimental validation of their analyzed downstream pathways will be required eventually.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Most of my comments have been adequately addressed. Additional comments on new data in the revised manuscript are below.

      (1) In the new figure S11, it is not really possible to draw major conclusions on mitral valve morphology and maturation since the planes of sections to not seem comparable. Observations regarding attachment to the papillary muscle might be dependent on the particular section being evaluated. However, it is useful to see that the valves are not severely affected in the ablated animals.

      We appreciate the reviewer’s comment and agree with the reviewer’s observation. Accordingly, we have updated the manuscript by removing the original conclusion-related statement and instead highlighting that the valves were not severely affected in the ablated animals (page 6).

      (2) In the last supplemental figure S19, it is not possible to determine if results are or are not statistically significant for n=2 as shown for FS and EF for the ablated animals and controls. The text says that there is a trend of improved heart function, but evaluation of additional animals is needed to support this conclusion.

      We thank the reviewer for the comment and agree that a sample size of n = 2 is too small to draw meaningful conclusions. As previously suggested by the reviewer, we have removed this result from the manuscript (page 10).

      Reviewer #2 (Recommendations for the authors):

      The manuscript has greatly improved following the revision, and I have no additional comments to offer.

      Thanks!

      Reviewer #3 (Recommendations for the authors):

      Authors did a good job addressing questions asked at first review. However, I have some minor concerns.

      (1) The paper notes that collagen signaling is observed in FB-VasEC in humans, but not in FB-VenCM, unlike mice. Did authors analyze predictive ligand receptor interaction as they did with control and ablated mice heart? This could add valuable new insights that how FB regulate ventricular CM in human heart.

      Thank you. We have analyzed the predicted ligand-receptor interactions between Fb and Ven_CM, as well as between Fb and Vas_EC, using human scRNA-seq data. The results are provided as a supplemental figure (Fig. S8C).

      (2) The authors provided data on Defect in CD31 expression in several models. Did they observed any other phenotypes associated with defective endothelial or vascular system? Such as, blood accumulation in pericardium, larger/smaller capillaries? Did they also examined percentage of Cdh5+ cells?

      We thank the reviewer for the questions. We did not observe clear evidence of blood accumulation in the pericardium of the ablated hearts, as shown in figure 3B, 3E, 6B, and 6F. Additionally, we did not perform Cdh5 staining in either the control or ablated hearts.

      (3) Please mention the sample age of Figure 2A-C.

      These are single-cell mRNA sequencing data from CD1 mice across 18 developmental stages, ranging from E9.5 to P9. We have added this information to the manuscript (page 4).

      (4) Please follow the same style to describe X axis in graphs in Figure 3D (and all similar graphs in manuscript) as followed in 3G.

      Thank you. We assume the reviewer was referring to the descriptions in the relevant figure legends. We have updated the legend for Figure 3D to ensure consistency with the description provided for Figure 3G (page 15).

      (5) It is important to provide echocardiographic M mode images with a comparable number of cardiac cycles in control and ablated (Fig. 6H).

      We thank the reviewer for the comment. As explained in our previous response, the echocardiographic data for both control and mutant mice were collected in conscious animals. The differences in their cardiac cycles reflect variations in heart rate, which represent a disease phenotype and cannot be altered. Therefore, we are unable to provide M-mode images with a similar number of cardiac cycles for control and ablated mice.

      (6) In the long-term neonatal ablation experiments, collagen expressions return to normal. The manuscript attributes this to possible "compensatory expression," Do they have any thoughts how this is regulated? Are other cell types stepping in, or are surviving FBs proliferating?

      We thank the reviewer for the question. As suggested, the compensatory collagen expression could be driven by surviving fibroblasts or other cell types. Since we currently lack evidence to exclude either possibility, we believe both could be contributing factors.

      (7) While collagen is shown to be a dominant signaling molecule, its centrality is inferred primarily from scRNAseq and ligand-receptor predictions. Did authors try any functional rescue experiment (e.g., exogenous collagen supplementation or receptor blockade) to directly validate this pathway's role in vivo?

      We thank the reviewer for the comment. As noted in our previous revision in response to similar questions from the other two reviewers, we agree that these rescue experiments are of interest but are beyond the scope of the current study. We plan to pursue these investigations in future work and share our findings when available.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript "Rho-ROCK liberates sequestered claudin for rapid de novo tight junction formation" by Cho and colleagues investigates de novo tight junction formation during the differentiation of immortalized human HaCaT keratinocytes to granular-like cells, as well as during epithelial remodeling that occurs upon the apoptotic of individual cells in confluent monolayers of the representative epithelial cell line EpH4. The authors demonstrate the involvement of Rho-ROCK with well-conducted experiments and convincing images. Moreover, they unravel the underlying molecular mechanism, with Rho-ROCK activity activating the transmembrane serine protease Matriptase, which in turn leads to the cleavage of EpCAM and TROP2, respectively, releasing Claudins from EpCAM/TROP2/Claudin complexes at the cell membrane to become available for polymerization and de novo tight junction formation. These functional studies in the two different cell culture systems are complemented by localization studies of the according proteins in the stratified mouse epidermis in vivo.

      In total, these are new and very intriguing and interesting findings that add important new insights into the molecular mechanisms of tight junction formation, identifying Matriptase as the "missing link" in the cascade of formerly described regulators. The involvement of TROP2/EpCAM/Claudin has been reported recently (Szabo et al., Biol. Open 2022; Bugge lab), and Matriptase had been formerly described to be required for in tight junction formation as well, again from the Bugge lab. Yet, the functional correlation/epistasis between them, and their relation to Rho signaling, had not been known thus far.

      However, experiments addressing the role of Matriptase require a little more work.

      Strengths:

      Convincing functional studies in two different cell culture systems, complemented by supporting protein localization studies in vivo. The manuscript is clearly written and most data are convincingly demonstrated, with beautiful images and movies.

      Weaknesses:

      The central finding that Rho signaling leads to increased Matriptase activity needs to be more rigorously demonstrated (e.g. western blot specifically detecting the activated version or distinguishing between the full-length/inactive and processed/active version).

      First, we thank the reviewer for their fair evaluation of our manuscript and for providing constructive feedback. Regarding the detection of matriptase activation—which Reviewer 1 identified as a weakness—we fully agree that direct validation is crucial. Therefore, in this revision we have carried out additional experiments using the M69 antibody, which specifically recognizes the activated form of matriptase. Details of these new experiments are provided in our point-by-point responses below.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, the authors investigate how epithelia maintain intercellular barrier function despite and during cellular rearrangements upon e.g. apoptotic extrusion in simple epithelia or regenerative turnover in stratified epithelia like this epidermis. A fundamental question in epithelial biology. Previous literature has shown that Rho-mediated local regulation of actomyosin is essential not only for cellular rearrangement itself but also for directly controlling tight junction barrier function. The molecular mechanics however remained unclear. Here the authors use extensive fluorescent imaging of fixed and live cells together with genetic and drug-mediated interference to show that Rho activation is required and sufficient to form novo tight junctional strands at intercellular contacts in epidermal keratinocytes (HaCat) and mammary epithelial cells. After having confirmed previous literature they then show that Rho activation activates the transmembrane protease Matriptase which cleaves EpCAM and TROP2, two claudin-binding transmembrane proteins, to release claudins and enable claudin strand formation and therefore tight junction barrier function.

      Strengths:

      The presented mechanism is shown to be relevant for epithelial barriers being conserved in simple and stratifying epithelial cells and mainly differs due to tissue-specific expression of EpCAM and TROP2. The authors present careful state-of-the-art imaging and logical experiments that convincingly support the statements and conclusion. The manuscript is well-written and easy to follow.

      Weaknesses:

      Whereas the in vitro evidence of the presented mechanism is strongly supported by the data, the in vivo confirmation is mostly based on the predicted distribution of TROP2. Whereas the causality of Rho-mediated Matriptase activation has been nicely demonstrated it remains unclear how Rho activates Matriptase.

      Thank you for your valuable feedback on our manuscript. As Reviewer 2 points out, the precise mechanism by which the Rho/ROCK pathway activates matriptase remains unclear. We have discussed the possible molecular mechanisms in the Discussion section. Elucidating the detailed mechanism of matriptase activation will be the focus of our future work.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Comment 1-1 - Matriptase activation by Rho: The authors show activation of Matriptase in western blots by the simple reduction of (full-length?) protein level in Figures 5 and 7. Most publications however show activated Matriptase either by antibodies detecting specifically the active form (including the publication referenced in this manuscript), or the appearance of the activated form next to the inactive form (based on different molecular weights). Therefore, it is not completely clear whether the treatment with Rho activators (Figure 5) results in an overall decrease of Matriptase, or really in an increase in the activated form. Therefore, the authors should show the actual increase of the active form. As a control, the impact of camostat treatment and overexpression of Hai1 on the active form of Matriptase could be included. It also should be indicated in the figure legend how long cells had been treated with the drugs before being subjected to lysis. Moreover, the western blots need to be quantified.

      We performed a more rigorous analysis using the M69 antibody, which specifically recognizes the activated form of matriptase and has been widely used in previous studies(e.g. Benaud et al., 2001; Hung et al., 2004; Wang et al., 2009). We likewise confirmed a significant increase in M69 signals by both western blotting and immunostaining from samples in which matriptase was activated by acid medium treatment (Figure 5A). Crucially, we also observed matriptase activation with the M69 antibody both in Rho/ROCK activator-treated cells (Figure 5A) and in differentiated granular-layer-like cells (Figures 7A and 7D). These findings strongly support the conclusion that matriptase is activated downstream of the Rho/ROCK pathway.

      Comment 1-2 - Based on their results, the authors conclude that Matriptase cleaves TROP2 in the SG2 layer of the epidermis, which is a little contradictory to former studies, which have shown Matriptase to be most prominently expressed and active in the basal layer and only little in the spinous layer (e.g Chen et al., Matriptase regulates proliferation and early, but not terminal, differentiation of human keratinocytes. J Invest Dermatol.2013). In this light, one could also argue that inhibiting Matriptase "simply" reduces epidermal differentiation. Can other differentiation markers be tested to rule that the effects on tight junctions are secondary consequences of interferences with earlier / more global steps of keratinocyte differentiation?

      As the reviewer noted, previous studies have demonstrated that matriptase is essential for keratinocyte differentiation, and that it cleaves substrates beyond EpCAM and TROP2—any of which could potentially influence the differentiation process. To test this possibility, we chose to monitor maturation of adherens junction (AJ) as an indicator of keratinocyte differentiation into granular-layer cells. Prior work has shown that during differentiation into granular-layer cells, AJs develop and experience increased intercellular mechanical tension, and that this rise in mechanical tension at AJs is critical for subsequent TJ formation (Rübsam et al., 2017). To assess AJ tension, we stained with the α-18 monoclonal antibody, which specifically recognizes the tension-dependent conformational change of α-catenin, a core AJ component. In control cells, differentiation into granular-layer like cells led to a marked increase in α-18 signal at cell–cell adhesion sites. Importantly, when HaCaT cells were treated with Camostat to inhibit matriptase and then induced to differentiate, we observed an equivalent increase in α-18 signal at AJs (Figure 7F). However, we did not detect claudin enrichment at cell-cell contacts under these conditions (Figures 7F and 7H). These results suggest that matriptase inhibition does not impair AJ maturation during granular-layer differentiation, but does profoundly disrupt TJ formation. While we cannot rule out the possibility that matriptase acts more broadly from these results, we judged that a comprehensive substrate survey lies outside the scope of the present manuscript.

      Comment 1-3 - In addition, as in Figure 5, full-length levels of Matriptase in Figure 7A need to be complemented by the active version to demonstrate more convincingly that TROP2 processing coincides with (and is most likely caused by) increased Matriptase activation. In the quantification in 7B, levels actually go up again after 2 and 4 hours. How is that explained, and what would this mean with respect to tight junction formation seen at 24 h of differentiation? The TROP2 cleavage shown in Figure 7A should be quantified.

      This comment is related to Comment 1-1. Using the M69 antibody, which specifically recognizes the activated matriptase, we directly demonstrated that matriptase activation occurs during the differentiation of granular layer-like cells (Figures 7A and 7D). Furthermore, we performed quantitative analysis of TROP2 cleavage and found that, compared with undifferentiated cells, differentiation into granular-layer like cells was accompanied by an increase in the cleaved TROP2 fragments (Figures 7A and 7B).

      Minor points:

      Comment 1-4 - Figure 1B and C: Including orthogonal views would be a nice add-on to appreciate the findings.

      In the revised version, we have added the corresponding orthogonal views to Figure 1B and Figure 1C.

      Comment 1-5 - Figure 2D: last row: indication of orthogonal view.

      We stated that the bottom panels are orthogonal views in the figure legend of Figure 2D.

      Comment 1-6 - Figure 3A: quantification is missing. GST-Rhotekin assay is missing in methods.

      In the revised manuscript, we have added quantitative analysis for Figure 3A. We have also supplemented the Materials and Methods section with detailed information on the GST–Rhotekin assay used to quantify levels of active RhoA.

      Comment 1-7 - Figure 4H: quantification of the Western blot is missing.

      In the revised manuscript, we have added quantitative analysis for Figure 4H as Figure 4I.

      Comment 1-8 - Figure 5 and 6: Quantifications of Western blots are missing.

      In the revised manuscript, we have added quantitative analyses for Figure 5D as Figure 5F and for Figure 6A as Figure 6B.

      Comment 1-9 - Figure 7C: quantification of the Western blot is missing.

      Figure 7C does not present western blotting data. For the other western blotting results, we have added quantitative analyses as suggested by Reviewer 1.

      Comment 1-10 - Figure 8I: Including Hai1 overexpression would be good for a complete picture.

      Following Reviewer 1’s suggestion, we have added staining data for Hai1-overexpressing cells to Figure 8J.

      Comment 1-11 - Line 377: The authors say they found Matriptase always present in lateral membranes. I did not find evidence for this in the manuscript.

      Previous studies have demonstrated that in polarized epithelial cells, matriptase is localized to the basolateral membrane below TJs (Buzza et al., 2010; Wang et al., 2009). We also found that matriptase consistently localizes to the basolateral membrane but more crucially that it becomes activated there during differentiation into granular layer cells. We added these new data as Figures 7C-7E in the revised manuscript. These findings suggest that matriptase activation occurs without a change in its subcellular localization.

      Comment 1-12 - Line 381: should most likely say: and ADAM17 but it is not known whether...

      We corrected the sentence in the revised manuscript.

      Reviewer #2 (Recommendations for the authors):

      The authors have added a significant number of quantifications verifying their observations, which was a major comment in a previous version of the manuscript and thus I have only a few minor comments which should be addressed.

      Comment 2-1 - It is not required to have scale bars in every image of a panel if the same scale is used.

      Unnecessary scale bars were removed. Specifically, scale bars were removed from Figure 1B, 1C, 1F, 8F, 8G, and 8H.

      Comment 2-2 - Throughout all figures: Please state for non-quantified images whether this is a representative example and for how many technical or biological repeats this is representative. Also for "N" number, state what the N stands for and if this is what the dots in the graph represent. Are these the number of junctions or technical, experimental or biological repeats?

      In the revised manuscript, we have added the number of independent experiments and corresponding “N” values to the Quantification and Statistical Analysis subsection of the Materials and Methods.

      Comment 2-3 - Some Zooms have a scale bar (6d), and some do not (e.g. 5b).

      The scale bar was removed from the magnified image in Figure 6D.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      The study by Wu et al presents interesting data on bacterial cell organization, a field that is progressing now, mainly due to the advances in microscopy. Based mainly on fluorescence microscopy images, the authors aim to demonstrate that the two structures that account for bacterial motility, the chemotaxis complex and the flagella, colocalize to the same pole in Pseudomonas aeruginosa cells and to expose the regulation underlying their spatial organization and functioning.

      Strengths:

      The subject is of importance.

      Weaknesses:

      The conclusions are too strong for the presented data. The lack of statistical analysis makes this paper incomplete. The novelty of the findings is not clear.

      We have strengthened the data analysis by including appropriate statistical tests to support our conclusions more convincingly. Additionally, we have refined the description of the research background to better emphasize the novelty and significance of our findings. Please see the detailed responses below for further information.

      Major issues:

      (1) The novelty is in question since in the Abstract the authors highlight their main finding, which is that both the chemotaxis complex and the flagella localize to the same pole, as surprising. However, in the Introduction they state that "pathway-related receptors that mediate chemotaxis, as well as the flagellum are localized at the same cell pole17,18". I am not a pseudomonas researcher and from my short glance at these references, I could not tell whether they report colocalization of the two structures to the same pole. However, I trust the authors that they know the literature on the localization of the chemotaxis complex and flagella in their organism. See also major issue number 5 on the novelty regarding the involvement of c-di-GMP.

      We thank the reviewer for this valuable comment and appreciate the opportunity to clarify our statements.

      Kazunobu et al. (ref. 18) used scanning electron microscopy to preliminarily characterize the flagellation pattern of Pseudomonas aeruginosa during cell division, showing that existing flagella are located at the old pole. Zehra et al. (ref. 17), through fluorescence microscopy, observed that CheA and CheY proteins in dividing cells are typically also present at the old pole. Based on these observations, we inferred in the Introduction that the chemotaxis complex and flagellum may localize to the same cell pole.

      However, this inference is indirect and lacks direct live-cell evidence of colocalization, leaving its validity to be confirmed. This uncertainty was indeed the starting point and motivation for our study.

      In our work, we simultaneously visualized flagellar filaments and core chemoreceptor proteins at the single-cell level in P. aeruginosa. We characterized the assembly and spatial coordination of the chemotaxis network and flagellar motor throughout the cell cycle, providing direct evidence of their colocalization and coordinated assembly. This represents a significant advance beyond prior indirect observations and supports the novelty of our study.

      Accordingly, we have revised the relevant statements in lines 71-75 of the manuscript to better reflect the current state of the literature and emphasize the novelty of our direct observations.

      (2) Statistics for the microscopy images, on which most conclusions in this manuscript are based, are completely missing. Given that most micrographs present one or very few cells, together with the fact that almost all conclusions depend on whether certain macromolecules are at one or two poles and whether different complexes are in the same pole, proper statistics, based on hundreds of cells in several fields, are absolutely required. Without this information, the results are anecdotal and do not support the conclusions. Due to the importance of statistics for this manuscript, strict statistical tests should be used and reported. Moreover, representative large fields with many cells should be added as supportive information.

      We thank the reviewer for this important comment, which significantly improves the rigor and persuasiveness of our manuscript.

      For the colocalization analyses presented in Fig. 1D and Fig. 2B, we quantified 145 and 101 cells with fluorescently labeled flagella, respectively, and observed consistent colocalization of the chemoreceptor complexes and flagella in all examined cells (now added in the figure legends). Regarding the distribution patterns of chemoreceptors shown in Fig. 3A, we have now included comprehensive statistical analyses for both wild-type and mutant strains. For each strain, more than 300 cells were analyzed across at least three independent microscopic fields, providing robust statistical power (detailed data are presented in Fig. 3C).

      To further strengthen the evidence, statistical tests were applied to confirm the significance and reproducibility of our findings (Fig. 3C). In addition, representative large-field fluorescence images containing numerous cells have been added to the supplementary materials (Fig. S1 and Fig. S3).

      The problem is more pronounced when the authors make strong statements, as in lines 157-158: "The results revealed that the chemoreceptor arrays no longer grow robustly at the cell pole (Figure 2A)". Looking at the seven cells shown in Figure 2A, five of them show polar localization of the chemoreceptors. The question is then: what is the percentage of cells that show precise polar, near-polar, or mid cell localization (the three patterns shown here) in the mutant and in the wild type? Since I know that these three patterns can also be observed in WT cells, what counts is the difference, and whether it is statistically significant.

      We thank the reviewer for raising this important point. Following the reviewer's suggestion, we have now analyzed and categorized the distribution of the chemotaxis complex in both wild-type and flhF mutant strains into three patterns: precise-polar, near-polar, and mid-cell localization. For each strain, more than 200 cells across three independent fields of view were quantified.

      Our statistical analysis shows that in the wild-type strain, approximately 98% of cells exhibit precise polar localization of the chemotaxis complex. In contrast, the ΔflhF mutant displays a clear shift in distribution, with about 5% of cells showing mid-cell localization and 9.5% showing near-polar localization. These differences demonstrate a significant alteration in the spatial pattern upon flhF deletion.

      We have revised the relevant text in lines 166-170 accordingly and included the detailed statistical data in the newly added Fig. S4.

      Even for the graphs shown in Figures 3C and 3D, where the proportion of cells with obvious chemoreceptor arrays and absolute fluorescence brightness of the chemosensory array are shown, respectively, the questions that arise are: for how many individual cells these values hold and what is the significance of the difference between each two strains?

      The number of cells analyzed for each strain is indicated in the original manuscript: 372 wild-type cells (line 123), 221 ΔflhF cells (line 172), 234 ΔfliG cells (line 197), 323 ΔfliF cells (line 200), 672 ΔflhFΔfliF cells (line 202), and 242 ΔmotAΔmotCD cells (line 207). For each strain, data were collected from three independent fields of view. We have now also provided the number of cells in Fig. 3 legend.

      We have now performed statistical comparisons using t-tests between strains. Notably, the measured values in Fig. 3C exhibit a clear, monotonic decrease with successive gene knockouts, supporting the robustness of the observed trend.

      Regarding the absolute fluorescence intensity shown in the original Fig. 3D, the mutants did not display consistent directional changes compared to the wild type. Reliable comparison of absolute fluorescence intensity requires consistent fluorescent protein maturation levels across strains. Given the likely variability in maturation levels between strains, we concluded that this data may not accurately reflect true differences in protein concentrations. Therefore, we have removed the fluorescence intensity graph from the revised manuscript to avoid potential misinterpretation.

      (3) The authors conclude that "Motor structural integrity is a prerequisite for chemoreceptor self-assembly" based on the reduction in cells with chemoreceptor clusters in mutants deleted for flagellar genes, despite the proper polar localization of the chemotaxis protein CheY. They show that the level of CheY in the WT and the mutant strains is similar, based on Western blot, which in my opinion is over-exposed. "To ascertain whether it is motor integrity rather than functionality that influences the efficiency of chemosensory array assembly", they constructed a mutant deleted for the flagella stator and found that the motor is stalled while CheY behaves like in WT cells. The authors further "quantified the proportion of cells with receptor clusters and the absolute fluorescence intensity of individual clusters (Figures 3C-D)". While Figure 3DC suggests that, indeed, the flagella mutants show fewer cells with a chemotaxis complex, Figure 3D suggests that the differences in fluorescence intensity are not statistically significant. Since it is obvious that the regulation of both structures' production and localization is codependent, I think that it takes more than a Western blot to make such a decision.

      We thank the reviewer for the suggestions. To further clarify that the assembly of flagellar motors and chemoreceptor clusters occurs in an orderly manner rather than being merely codependent, we performed additional experiments. Specifically, we constructed a ΔcheA mutant strain, in which chemoreceptor clusters fail to assemble. Using in vivo fluorescent labeling of flagellar filaments, we observed that the proportion of cells with flagellar filaments in the ΔcheA strain was comparable to that of the wild type (Fig. S5).

      In contrast, mutants lacking complete motor structures, such as ΔfliF and ΔfliG, showed a significant reduction in the proportion of cells with obvious receptor clusters (Fig. 3C). Based on these results, we conclude that the structural integrity of the flagellar motor is, to a certain extent, a prerequisite for the self-assembly of chemoreceptor clusters.

      Accordingly, we have revised the relevant statement in lines 213-217 of the manuscript to reflect this clarification.

      (4) I wonder why the authors chose to label CheY, which is the only component of the chemotaxis complex that shuttles back and forth to the base of the flagella. In any case, I think that they should strengthen their results by repeating some key experiments with labeled CheW or CheA.

      We thank the reviewer for this valuable suggestion. In our study, we initially focused on the positional relationship between chemoreceptor clusters and flagella, then investigated factors influencing cluster distribution and assembly efficiency. The physiological significance of motor and cluster co-localization was ultimately proposed with CheY as the starting point.

      Previous work by Harwood's group demonstrated that both CheY-YFP and CheA-GFP localize to the old poles of dividing Pseudomonas aeruginosa cells. Since our physiological hypothesis centers on CheY, we chose to label CheY-EYFP in our experiments.

      To further strengthen our conclusions, we constructed a plasmid expressing CheA-CFP and introduced it into the cheY-eyfp strain via electroporation. Fluorescence imaging revealed a high degree of spatial overlap between CheA-CFP and CheY-EYFP (Fig. S2), confirming that CheY-EYFP accurately marks the location of the chemoreceptor complex.

      We have revised the manuscript accordingly (lines 119-123) and added these data as Fig. S2.

      (5) The last section of the results is very problematic, regarding the rationale, the conclusions, and the novelty. As far as the rationale is concerned, I do not understand why the authors assume that "a spatial separation between the chemoreceptors and flagellar motors should not significantly impact the temporal comparison in bacterial chemotaxis". Is there any proof for that?

      We apologize for the lack of clarity in our original explanation. The rationale behind the statement was initially supported by comparing the timescales of CheY-P diffusion and temporal comparison in chemotaxis. Specifically, the diffusion time for CheY-P to traverse the entire length of a bacterial cell is approximately 100 ms (refs 39&40), whereas the timescale for bacterial chemotaxis temporal comparison is on the order of seconds (ref 41).

      To clarify and strengthen this argument, we have expanded the discussion as follows:

      The diffusion coefficient of CheY in bacterial cells is about 10 µm2/s, which corresponds to an estimated end-to-end diffusion time on the order of 100 ms (refs 40&41). If the chemotaxis complexes were randomly distributed rather than localized, diffusion times would be even shorter. In contrast, the timescale for the chemotaxis temporal comparison is on the order of seconds (ref. 42). Additionally, a study by Fukuoka and colleagues reported that intracellular chemotaxis signal transduction requires approximately 240 ms beyond CheY or CheY-P diffusion time (ref. 41). Moreover, the intervals of counterclockwise (CCW) and clockwise (CW) rotation of the P. aeruginosa flagellar motor under normal conditions are 1-2 seconds, as determined by tethered cell or bead assays (refs. 30&43).

      Taken together, these indicate that for P. aeruginosa, which moves via a run-reverse mode, the potential 100 ms reduction in response time due to co-localization of the chemotaxis complex and motor has a limited effect on overall chemotaxis timing.

      We have revised the corresponding text accordingly (lines 238-245) to better explain this rationale.

      More surprising for me was to read that "The signal transduction pathways in E. coli are relatively simple, and the chemotaxis response regulator CheY-P affects only the regulation of motor switching". There are degrees of complexity among signal transduction pathways in E. coli, but the chemotaxis seems to be ranked at the top. CheY is part of the adaptation. Perfect adaptation, as many other issues related to the chemotaxis pathway, which include the wide dynamic range, the robustness, the sensitivity, and the signal amplification (gain), are still largely unexplained. Hence, such assumptions are not justified.

      We apologize for the confusion and imprecision in our original statements. Our intention was to convey that the chemotaxis pathway in E. coli is relatively simple compared to the more complex chemosensory systems in P. aeruginosa. We did not mean to generalize this simplicity to all signal transduction pathways in E. coli.

      We acknowledge that E. coli chemotaxis is a highly sophisticated system, involving processes such as perfect adaptation, wide dynamic range, robustness, sensitivity, and signal amplification, many aspects of which remain incompletely understood. CheY indeed plays a crucial role in adaptation and motor switching regulation.

      Accordingly, we have revised the original text (lines 249-255) to avoid any misunderstanding.

      More perplexing is the novelty of the authors' documentation of the effect of the chemotaxis proteins on the c-di-GMP level. In 2013, Kulasekara et al. published a paper in eLife entitled "c-di-GMP heterogeneity is generated by the chemotaxis machinery to regulate flagellar motility". In the same year, Kulasekara published a paper entitled "Insight into a Mechanism Generating Cyclic di-GMP Heterogeneity in Pseudomonas aeruginosa". The authors did not cite these works and I wonder why.

      We apologize for having been unaware of these important references and thank the reviewer for bringing them to our attention. We have now cited the eLife paper and the PhD thesis titled "Insight into a Mechanism Generating Cyclic di-GMP Heterogeneity in Pseudomonas aeruginosa" by Kulasekara et al.

      Regarding novelty, there are key differences between our findings and those reported by Kulasekara et al. While they proposed that CheA influences c-di-GMP heterogeneity through interaction with a specific phosphodiesterase (PDE), our results demonstrate that overexpression of CheY leads to an increase in intracellular c-di-GMP levels.

      We have revised the original text accordingly (lines 358-362) to clarify these distinctions.

      (6) Throughout the manuscript, the authors refer to foci of fluorescent CheY as "chemoreceptor arrays". If anything, these foci signify the chemotaxis complex, not the membrane-traversing chemoreceptors.

      We thank the reviewer for this clarification. We have revised the manuscript accordingly to refer to the fluorescent CheY foci as representing the chemotaxis complex rather than the chemoreceptor arrays.

      Conclusions:

      The manuscript addresses an interesting subject and contains interesting, but incomplete, data.

      Reviewer #2 (Public Review):

      Summary:

      Here, the authors studied the molecular mechanisms by which the chemoreceptor cluster and flagella motor of Pseudomonas aeruginosa (PA) are spatially organized in the cell. They argue that FlhF is involved in localizing the receptors-motor to the cell pole, and even without FlhF, the two are colocalized. FlhF is known to cause the motor to localize to the pole in a different bacterial species, Vibrio cholera, but it is not involved in receptor localization in that bacterium. Finally, the authors argue that the functional reason for this colocalization is to insulate chemotactic signaling from other signaling pathways, such as cyclic-di-GMP signaling.

      Strengths:

      The experiments and data look to be high-quality.

      Weaknesses:

      However, the interpretations and conclusions drawn from the experimental observations are not fully justified in my opinion.

      I see two main issues with the evidence provided for the authors' claims.

      (1) Assumptions about receptor localization:

      The authors rely on YFP-tagged CheY to identify the location of the receptor cluster, but CheY is a diffusible cytoplasmic protein. In E. coli, CheY has been shown to localize at the receptor cluster, but the evidence for this in PA is less strong. The authors refer to a paper by Guvener et al 2006, which showed that CheY localizes to a cell pole, and CheA (a receptor cluster protein) also localizes to a pole, but my understanding is that colocalization of CheY and CheA was not shown. My concern is that CheY could instead localize to the motor in PA, say by binding FliM. This "null model" would explain the authors' observations, without colocalization of the receptors and motor. Verifying that CheY and CheA are colocalized in PA would be a very helpful experiment to address this weakness.

      We thank the reviewer for this valuable suggestion. We agree that verifying the colocalization of CheY and CheA would strengthen our conclusions. To address this, we constructed a plasmid expressing CheA-CFP and introduced it into the CheY-EYFP strain by electroporation. Fluorescence imaging revealed a high degree of spatial overlap between CheA-CFP and CheY-EYFP signals, indicating that CheY-EYFP indeed marks the location of the chemoreceptor complex rather than the flagellar motor.

      We have revised the manuscript accordingly (lines 118-123) and included these results in the new Fig. S2.

      (2) Argument for the functional importance of receptor-motor colocalization at the pole:

      The authors argue that colocalization of the receptors and motors at the pole is important because it could keep phosphorylated CheY, CheY-p, restricted to a small region of the cell, preventing crosstalk with other signaling pathways. Their evidence for this is that overexpressing CheY leads to higher intracellular cdG levels and cell aggregation. Say that the receptors and motors are colocalized at the pole. In E. coli, CheY-p rapidly diffuses through the cell. What would prevent this from occurring in PA, even with colocalization?

      We appreciate the reviewer's insightful question. The colocalization of both the signaling source (the kinase) and sink (the phosphatase) at the chemoreceptor complex at the cell pole results in a rapid decay of CheY-P concentration within approximately 0.2 µm from the cell pole, leading to a nearly uniform distribution elsewhere in the cell, as demonstrated by Vaknin and Berg (ref. 46). This spatial arrangement effectively confines high CheY-P levels to the pole region. When the motor is also localized at the cell pole, this reduces the need for elevated CheY-P concentrations throughout the cytoplasm, thereby minimizing potential crosstalk with other signaling pathways.

      We have revised the manuscript accordingly (lines 280-286) to clarify this point.

      Elevating CheY concentration may increase the concentration of CheY-p in the cell, but might also stress the cells in other unexpected ways. It is not so clear from this experiment that elevated CheY-p throughout the cell is the reason that they aggregate, or that this outcome is avoided by colocalizing the receptors and motor at the same pole. If localization of the receptor array and motor at one pole were important for keeping CheY-p levels low at the opposite pole, then we should expect cells in which the receptors and motor are not at the pole to have higher CheY-p at the opposite pole. According to the authors' argument, it seems like this should cause elevated cdG levels and aggregation in the delta flhF mutants with wild-type levels of CheY. But it does not look like this happened. Instead of varying CheY expression, the authors could test their hypothesis that receptor-motor colocalization at the pole is important for preventing crosstalk by measuring cdG levels in the flhF mutant, in which the motor (and maybe the receptor cluster) are no longer localized in the cell pole.

      We thank the reviewer for raising the important point regarding potential cellular stress caused by elevated CheY concentrations, as well as for the suggestion to test the hypothesis using ΔflhF mutants.

      First, as noted above, CheY-P concentration rapidly decreases away from the receptor complex. While deletion of flhF alters the position of the receptor complex, thereby shifting the region of high CheY-P concentration, it does not increase CheY-P levels elsewhere in the cell. Importantly, in the ΔflhF strain, the receptor complex and the motor still colocalize, so this mutant may not effectively test the role of receptor-motor colocalization in preventing crosstalk as suggested.

      Regarding the possibility that elevated CheY levels stress the cells independently of CheY-P signaling, prior work in <i.E. coli by Cluzel et al. (ref. 11) showed that overexpressing CheY several-fold did not cause phenotypic changes, indicating that simple CheY overexpression alone may not be generally stressful. Furthermore, our data indicate that the increase in c-di-GMP levels and subsequent cell aggregation upon CheY overexpression is not an all-or-none switch but occurs progressively as CheY concentration rises.

      To further confirm that CheY overexpression promotes aggregation through increased c-di-GMP levels, we performed additional experiments co-overexpressing CheY and a phosphodiesterase (PDE) from E. coli to reduce intracellular c-di-GMP. These experiments showed that PDE expression mitigates cell aggregation caused by CheY overexpression (Fig. S8).

      We have revised the manuscript accordingly (lines 290-294) and added these new results in Fig. S8.

      Reviewer #3 (Public Review):

      Summary:

      The authors investigated the assembly and polar localization of the chemosensory cluster in P. aeruginosa. They discovered that a certain protein (FlhF) is required for the polar localization of the chemosensory cluster while a fully-assembled motor is necessary for the assembly of the cluster. They found that flagella and chemosensory clusters always co-localize in the cell; either at the cell pole in wild-type cells or randomly-located in the cell in FlhF mutant cells. They hypothesize that this co-localization is required to keep the level of another protein (CheY-P), which controls motor switching, at low levels as the presence of high levels of this protein (if the flagella and chemosensory clusters were not co-localized) is associated with high-levels of c-di-GMP and cell aggregations.

      Strengths:

      The manuscript is clearly written and straightforward. The authors applied multiple techniques to study the bacterial motility system including fluorescence light microscopy and gene editing. In general, the work enhances our understanding of the subtlety of interaction between the chemosensory cluster and the flagellar motor to regulate cell motility.

      Weaknesses:

      The major weakness in this paper is that the authors never discussed how the flagellar gene expression is controlled in P. aeruginosa. For example, in E. coli there is a transcriptional hierarchy for the flagellar genes (early, middle, and late genes, see Chilcott and Hughes, 2000). Similarly, Campylobacter and Helicobacter have a different regulatory cascade for their flagellar genes (See Lertsethtakarn, Ottemann, and Hendrixson, 2011). How does the expression of flagellar genes in P. aeruginosa compare to other species? How many classes are there for these genes? Is there a hierarchy in their expression and how does this affect the results of the FliF and FliG mutants? In other words, if FliF and FliG are in class I (as in E. coli) then their absence might affect the expression of other later flagellar genes in subsequent classes (i.e., chemosensory genes). Also, in both FliF and FliG mutants no assembly intermediates of the flagellar motor are present in the cell as FliG is required for the assembly of FliF (see Hiroyuki Terashima et al. 2020, Kaplan et al. 2019, Kaplan et al. 2022). It could be argued that when the motor is not assembled then this will affect the expression of the other genes (e.g., those of the chemosensory cluster) which might play a role in the decreased level of chemosensory clusters the authors find in these mutants.

      We thank the reviewer for the insightful comments. P. aeruginosa possesses a four-tiered transcriptional regulatory hierarchy controlling flagellar biogenesis. Within this system, fliF and fliG belong to class II genes and are regulated by the master regulator FleQ. In contrast, chemotaxis-related genes such as cheA and cheW are regulated by intracellular free FliA, and currently, there is no evidence that FliA activity is influenced by proteins like FliG.

      To verify that the expression of core chemotaxis proteins was not affected by deletion of fliG, we performed Western blot analyses to compare CheY levels in wild-type, ΔfliF, and ΔfliG strains. We observed no significant differences, indicating that the reduced presence of receptor clusters in these mutants is not due to altered expression of chemotaxis proteins.

      Accordingly, we have revised the manuscript (lines 341-348) and updated Fig. 3B to reflect these findings.

      Recommendations for the authors:

      Reviewing Editor (Recommendations For The Authors):

      The reviewers comment on several important aspects that should be addressed, namely: the lack of statistical analysis; the need for clarifications regarding assumptions made regarding receptor localization; the functional importance of receptor-motor colocalization; and the need for an elaborate discussion of flagellar gene expression. Also, two reviewers pointed out the need to prove the co-localization of CheY and CheA; This is important since CheY is dynamic, shuttling back and forth from the chemotaxis complex to the base of the flagella, whereas CheA (or cheW or, even better, the receptors) is considered less dynamic and an integral part of the chemotaxis complex.

      Reviewer #1 (Recommendations For The Authors):

      Minor points:

      Line 43: "ubiquitous" - I would choose another word.

      We changed "ubiquitous" to "widespread".

      Line 49: "order" - change to organize.

      We changed "order" to "organize".

      Line 52: "To grow and colonize within the host, bacteria have evolved a mechanism for migrating...". Motility "towards more favorable environments" is an important survival strategy of bacteria in various ecological niches, not only within the host.

      We revised it to "grow and colonize in various ecological niches".

      Line 72: Define F6 in "F6 pathway-related receptors".

      The proteins encoded by chemotaxis-related genes collectively constitute the F6 pathway, which we have now explained in the manuscript text.

      Line 72-73: Do references 17 &18 really report colocalization of the chemotaxis receptor and flagella to the same pole? If these or other reports document such colocalization, then the sentence in the Abstract "Surprisingly, we found that both are located at the same cell pole..." is not correct.

      Kazunobu et al. (ref. 18) used scanning electron microscopy to preliminarily characterize the flagellation pattern of Pseudomonas aeruginosa during cell division, showing that existing flagella are located at the old pole. Zehra et al. (ref. 17), through fluorescence microscopy, observed that CheA and CheY proteins in dividing cells are typically also present at the old pole. Based on these observations, we inferred in the Introduction that the chemotaxis complex and flagellum may localize to the same cell pole.

      However, this inference is indirect and lacks direct live-cell evidence of colocalization, leaving its validity to be confirmed. This uncertainty was indeed the starting point and motivation for our study.

      In our work, we simultaneously visualized flagellar filaments and core chemoreceptor proteins at the single-cell level in P. aeruginosa. We characterized the assembly and spatial coordination of the chemotaxis network and flagellar motor throughout the cell cycle, providing direct evidence of their colocalization and coordinated assembly. This represents a significant advance beyond prior indirect observations and supports the novelty of our study.

      Accordingly, we have revised the relevant statements in lines 71-75 of the manuscript to better reflect the current state of the literature and emphasize the novelty of our direct observations.

      Line 108: "CheY has been shown to colocalize with chemoreceptors". The authors rely here (reference 29) and in other places on findings in E. coli. However, in the Introduction, they describe the many differences between the motility systems of P. aeruginosa and E. coli, e.g., the number of chemosensory systems and their spatial distribution (E. coli is a peritrichous bacterium, as opposed to the monotrichous bacterium P. aeruginosa). There seem to be proofs for colocalization of the Che and MCP proteins in P. aeruginosa, which should be cited here.

      Thank you for pointing this out. Harwood's group reported that a cheY-YFP fusion strain exhibited bright fluorescent spots at the cell pole, which disappeared upon knockout of cheA or cheW-genes encoding structural proteins of the chemotaxis complex. This strongly suggests colocalization of CheY with MCP proteins in P. aeruginosa. We have now cited this study as reference 17 in the manuscript.

      Figure 1B: Please replace the order of the schematic presentations, so that the cheY-egfp fusion, which is described first in the text, is at the top.

      We have modified the order of related images in Fig. 1B.

      Line 127: "by introducing cysteine mutations". Replace either by "by introducing cysteines" or by "by substituting several residues with cysteines".

      We changed the relevant statement to "by introducing cysteines".

      Line 144-145: "Given that the physiological and physical environments of both cell poles are nearly identical.". I think that also the physical, but certainly the physiological environment of the two poles is not identical. First, one is an old pole, and the other a new pole. Second, many proteins and RNAs were detected mainly or only in one of the poles of rod-shaped Gram-negative bacteria that are regarded as symmetrically dividing. Although my intuition is that the authors are correct in assuming that "it is unlikely that the unipolar distribution of the chemoreceptor array can be attributed to passive regulatory factors", relating it to the (false) identity between the poles is incorrect.

      We thank the reviewer for this important correction. We agree that the physiological environments of the two poles are not identical, given that one is the old pole and the other the new pole, and that many proteins and RNAs show polar localization in rod-shaped Gram-negative bacteria. Accordingly, we have revised the original text (lines 150-152) to read:

      “Despite potential differences in the physical and especially physiological environments at the two cell poles, it is unlikely that the unipolar distribution of the chemotaxis complex can be attributed to passive regulatory factors.”

      Lines 151-154: "Considering the consistent colocalization pattern between chemosensory arrays and flagellar motors in P. aeruginosa". Does the word consistent relate to different reports on such colocalization or to the results in Figure 1D? In case it is the latter, then what is the word consistent based on? All together only 7 cells are presented in the 5 micrographs that compose Figure 1D (back to statistics...).

      We thank the reviewer for raising this point. To clarify, the word "consistent" refers to the observation of colocalization shown in Figure 1D & Figure S3. As noted in the revised figure legend for Figure 1D, a total of 145 cells with labeled flagella were analyzed, all exhibiting consistent colocalization between flagella and chemosensory arrays. Additionally, we have included a new image showing a large field of co-localization in the wild-type strain as Figure S3 to better illustrate this consistency.

      Figure 2A: Omit "Subcellular localization of" from the beginning of the caption.

      We removed the relevant expression from the caption.

      Reviewer #2 (Recommendations For The Authors):

      I strongly recommend checking that CheY localizes to the receptor cluster in PA. This could be done by tagging cheA with a different fluorophore and demonstrating their colocalization. It would also be helpful to check that they are colocalized in the delta flhF mutant.

      We thank the reviewer for this valuable suggestion. We constructed a plasmid expressing CheA-CFP and introduced it into the CheY-EYFP strain by electroporation. Fluorescence imaging revealed a high degree of spatial overlap between CheA-CFP and CheY-EYFP signals, indicating that CheY-EYFP indeed marks the location of the chemoreceptor complex.

      We have revised the manuscript accordingly (lines 118-123) and included these results in the new Fig. S2.

      The experiments under- and over-expressing CheY part seemed too unrelated to receptor-motor colocalization. I think the authors should think about a more direct way of testing whether colocalization of the motor and receptors is important for preventing signaling crosstalk. One way would be to measure cdG levels in WT and in delta flhF mutants and see if there is a significant difference.

      We thank the reviewer for raising the important point regarding potential cellular stress caused by elevated CheY concentrations, as well as for the suggestion to test the hypothesis using flhF mutants.

      First, as noted in the response to your 2nd comment in Public Review, CheY-P concentration rapidly decreases away from the receptor complex. While deletion of flhF alters the position of the receptor complex, thereby shifting the region of high CheY-P concentration, it does not increase CheY-P levels elsewhere in the cell. Importantly, in the ΔflhF strain, the receptor complex and the motor still colocalize, so this mutant may not effectively test the role of receptor-motor colocalization in preventing crosstalk as suggested.

      Regarding the possibility that elevated CheY levels stress the cells independently of CheY-P signaling, prior work in E. coli by Cluzel et al. (ref. 11) showed that overexpressing CheY several-fold did not cause phenotypic changes, indicating that simple CheY overexpression alone may not be generally stressful. Furthermore, our data indicate that the increase in c-di-GMP levels and subsequent cell aggregation upon CheY overexpression is not an all-or-none switch but occurs progressively as CheY concentration rises.

      To further confirm that CheY overexpression promotes aggregation through increased c-di-GMP levels, we performed additional experiments co-overexpressing CheY and a phosphodiesterase (PDE) from E. coli to reduce intracellular c-di-GMP. These experiments showed that PDE expression mitigates cell aggregation caused by CheY overexpression (Fig. S8).

      We have revised the manuscript accordingly (lines 290-294) and added these new results in Fig. S8.

      Reviewer #3 (Recommendations For The Authors):

      (1) Can the authors elaborate more on the hierarchy of flagellar gene expression in P. aeruginosa and how this relates to their work?

      We thank the reviewer for the suggestion. We have now described the hierarchy of flagellar gene expression in P. aeruginosa in lines 341-348.

      (2) I would suggest that the authors check other flagellar mutants (than FliF and FliG) where the motor is partially assembled (e.g., any of the rod proteins or the P-ring protein), together with FlhF mutant, to see how a partially assembled motor affects the assembly of the chemosensory cluster.

      We thank the reviewer for this valuable suggestion. The P ring, primarily composed of FlgI, acts as a bushing for the peptidoglycan layer, and its absence leads to partial motor assembly. We constructed a ΔflgI mutant and observed that the proportion of cells exhibiting distinct chemotactic complexes was similar to that of the wild-type strain, suggesting that the assembly of the receptor complex is likely influenced mainly by the C-ring and MS-ring structures rather than by the P ring. We have revised the original text accordingly (lines 217-220) and added the corresponding data as Figure S6.

      (3) I would suggest that the authors check the levels of CheY in cells induced with different concentrations of arabinose (i.e., using western blotting just like they did in Figure 3B).

      We have assessed the levels of CheY in cells induced with different concentrations of arabinose using western blotting, as suggested. The results have been incorporated into the manuscript (lines 274-275) and are presented in Figure S7.

      (4) To my eyes, most of the foci in FliF-FlhF mutant in Figure 3A are located at the pole (which is unlike the FlhF mutant in Figure 2). Is this correct? I would suggest that the authors also investigate this to see where the chemosensory cluster is located.

      We thank the reviewer for pointing this out. The distribution of the chemotaxis complex in the ΔflhFΔfliF strain was investigated and showed in Fig. S4. Indeed, most of the chemoreceptor foci in this mutant are located at the pole. This probably suggests that, in the absence of both FlhF and an assembled motor, the position of the receptor complex may be largely influenced by passive factors such as membrane curvature. This interesting possibility warrants further investigation in future studies.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary

      In this work, the authors recorded the dynamics of the 5-HT with fiber photometry from CA1 in one hemisphere and LFP from CA1 in the other hemisphere. They observed an ultra-slow oscillation in the 5-HT signal during both wake fulness and NREM sleep. The authors have studied different phases of the ultra-slow oscillation to examine the potential difference in the occurrence of some behavioral state-related physiological phenomena hippocampal ripples, EMG, and inter-area coherence).

      Strengths

      The relation between the falling/rising phase of the ultra-slow oscillation and the ripples is sufficiently shown. There are some minor concerns about the observed relations that should be addressed with some further analysis.

      Systematic observations have started to establish a strong relation between the dynamics of neural activity across the brain and measures of behavioral arousal. Such relations span a wide range of temporal scales that are heavily inter-related. Ultra-slow time-scales are specifically under-studied due to technical limitations and neuromodulatory systems are the strongest mechanistic candidates for controlling/modulating the neural dynamics at these time-scales. The hypothesis of the relation between a specific time-scale and one certain neuromodulator (5-HT in this manuscript) could have a significant impact on the understanding of the hierarchy in the temporal scales of neural activity.

      Weaknesses:

      One major caveat of the study is that different neuromodulators are strongly correlated across all time scales and related to this, the authors need to discuss this point further and provide more evidence from the literature (if any) that suggests similar ultra-slow oscillations are weaker or lack from similar signals recorded for other neuromodulators such as Ach and NA.

      The reviewer is correct to point out that the levels of different neuromodulators are often correlated. For example, most monoaminergic neurons, including serotonergic neurons of the raphe nuclei, show similar firing rates across behavioral states, firing most during wake behavior, less during NREM, and ceasing firing during ‘paradoxical sleep’ or REM (Eban-Rothschild et al 2018). Notably, other neuromodulators, such as acetylcholine (ACh), show the opposite pattern across states, with highest levels observed during REM, an intermediate level during wake behavior, and the lowest level during NREM (Vazquez et al. 2001). Despite these differences, ultraslow oscillations of both monoaminergic and non-monoaminergic neuromodulators, have been described, albeit only during NREM sleep (Zhang et al. 2021, Zhang et al. 2024, Osorio-Ferero et al. 2021, Kjaerby et al. 2022). How ultraslow oscillations of different neuromodulators are related has been only recently explored (Zhang et al. 2024). In this study, dual recording of oxytocin (Oxt) and ACh with GRAB sensors showed that the levels of the two neuromodulators were indeed correlated at ultraslow frequencies with a 2 s temporal shift. Furthermore, this shift could be explained by a hippocampal-to-lateral septum intermediate pathway, in which the level of ACh causally impacts hippocampal activity, which then in turn controls Oxt levels. Given the known temporal relationship between ripples, ACh and Oxt, and now with our work, between ripples and 5-HT, one could infer the relative timing of ultraslow oscillations of ACh, Oxt and 5-HT. While dual recordings of norepinephrine (NE) and 5-HT have not been performed, a similar correlation with temporal shift could be hypothesized given the parallel relationships between NE and spindles (OsorioFerero et al. 2021), and 5-HT and ripples, with the known temporal delay between ripples and spindles (Staresina et al. 2023). The fact that the locus coerulus receives particularly dense projections from the dorsal raphe nucleus (Kim et al. 2004) further suggests that 5-HT ultraslow oscillations could drive NE oscillations. How exactly ultraslow oscillations of serotonin are related to ultraslow oscillations of different neuromodulators in different brain regions remains to be studied.

      We have further addressed this question and how it relates to the issue of causality in the Discussion section of the manuscript (p. 13):

      “In addition to the difficulties involved with typical causal interventions already mentioned, the fact that the levels of different neuromodulators are interrelated and affected by ongoing brain activity makes it very hard to pinpoint ultraslow oscillations of one specific neuromodulator as controlling specific activity patterns, such as ripple timing. While a recent paper purported to show a causative effect of norepinephrine levels on ultraslow oscillations of sigma band power, the fact that optogenetic inhibition of locus coerulus (LC) cells, but also excitation, only caused a minor reduction of the ultraslow sigma power oscillation suggests that other factors also contribute (Osorio-Forero et al., 2021). Generally, it is thought that many neuromodulators together determine brain states in a combinatorial manner, and it is probable that the 5-HT oscillations we measure, like the similar oscillations in NE, are one factor among many.

      Nevertheless, given the known effects of 5-HT on neurons, it is not unlikely that the 5-HT fluctuations we describe have some impact on the timing of ripples, MAs, hippocampal-cortical coherence, or EMG signals that correlate with either the rising or descending phase. In fact, causal effects of 5-HT on ripple incidence (Wang et al. 2015, ul Haq et al. 2016 and Shiozaki et al. 2023), MA frequency (Thomas et al. 2022), sensory gating (Lee et al. 2020), which is subserved by inter-areal coherence (Fisher et al. 2020), and movement (Takahashi et al. 2000, Alvarez et al. 2022, Jacobs et al. 1991 and Luchetti et al. 2020) have all been shown. Our added findings that serotonin affects ripple incidence in hippocampal slices in a dose-dependent manner (Figure S1) further suggests that the relationship between ultraslow 5-HT oscillations and ripples we report may indeed result, at least in part, from a direct effect of serotonin on the hippocampal network.

      Whether these ‘causal’ relationships between 5-HT and the different activity measures we describe can be used to support a causal link between ultraslow 5-HT oscillations and the correlated activity we report remains an open question. To that point, some studies have described changes in ultraslow oscillations due to manipulation of serotonin signaling. Specifically, reduction of 5-HT1a receptors in the dentate gyrus was recently shown to reduce the power of ultraslow oscillations of calcium activity in the same region (Turi et al. 2024). Furthermore, psilocin, which largely acts on the 5-HT2a receptor, decreased NREM episode length from around 100 s to around 60 s, and increased the frequency of brief awakenings (Thomas et al. 2022). While ultraslow oscillations were not explicitly measured in this study, the change in the rhythmic pattern of NREM sleep episodes and brief awakenings, or microarousals, suggests an effect of psilocin on ultraslow oscillations during NREM. Although these studies do not necessarily point to an exclusive role for 5-HT in controlling ultraslow oscillations of different brain activity patterns, they show that changes in 5-HT can contribute to changes in brain activity at ultraslow frequencies.”

      A major question that has been left out from the study and discussion is how the same level of serotonin before and after the peak could be differentially related to the opposite observed phenomenon. What are the possible parallel mechanisms for distinguishing between the rising and falling phases? Any neurophysiological evidence for sensing the direction of change in serotonin concentration (or any other neuromodulator), and is there any physiological functionality for such mechanisms?

      We have added a paragraph in the discussion to address how this differentiation of the 5-HT signal may be carried out (Discussion, paragraph #3, p. 10):

      “In order for the ultraslow oscillation phase to segregate brain activity, as we have observed, the hippocampal network must somehow be able to sense the direction of change of serotonin levels. While single-cell mechanisms related to membrane potential dynamics are typically too fast to explain this calculation, a theoretical work has suggested that feedback circuits can enable such temporal differentiation, also on the slower timescales we observe (Tripp and Eliasmith, 2010). Beyond the direction of change in serotonin levels, temporal differentiation could also enable the hippocampal network to discern the steeper rising slope versus the flatter descending slope that we observe in the ultraslow 5-HT oscillations (Figure S2), which may also be functionally relevant (Cole and Voytek, 2017). The distinction between the rising and falling phase of ultraslow oscillations is furthermore clearly discernible at the level of unit responses, with many units showing preferences for either half of the ultraslow period (Figure S6). Another factor that could help distinguish the rising from the falling phase is the level of other neuromodulators, as it is likely the combination of many neuromodulators at any given time that defines a behavioral substate. Given the finding that ACh and Oxt exhibit ultraslow oscillations with a temporal shift (Zhang et al. 2024), one could posit that distinct combinations of different levels of neuromodulators could segregate the rising from the falling phase via differential effects of the combination of neuromodulators on the hippocampal network.”

      Functionally, the ability to distinguish between the rising and falling phases of an oscillatory cycle is a form of phase coding. A well-known example of this can be seen in hippocampal place cells, which fire relative to the ongoing theta oscillations. The key advantage of phase coding is that it introduces an additional dimension, i.e. phase of firing, beyond the simple rate of neural firing. This allows for the multiplexing of information (Panzeri et al., 2010), enabling the brain to encode more complex patterns of activity. Moreover, phase coding is metabolically more efficient than traditional spike-rate coding (Fries et al., 2007).

      Reviewer #2 (Public review):

      Summary:

      In their study, Cooper et al. investigated the spontaneous fluctuations in extracellular 5-HT release in the CA1 region of the hippocampus using GRAB5-HT3.0. Their findings revealed the presence of ultralow frequency (less than 0.05 Hz) oscillations in 5-HT levels during both NREM sleep and wakefulness. The phase of these 5-HT oscillations was found to be related to the timing of hippocampal ripples, microarousals, electromyogram (EMG) activity, and hippocampal-cortical coherence. In particular, ripples were observed to occur with greater frequency during the descending phase of 5-HT oscillations, and stronger ripples were noted to occur in proximity to the 5-HT peak during NREM. Microarousal and EMG peaks occurred with greater frequency during the ascending phase of 5-HT oscillations. Additionally, the strongest coherence between the hippocampus and cortex was observed during the ascending phase of 5-HT oscillations. These patterns were observed in both NREM sleep and the awake state, with a greater prevalence in NREM. The authors posit that 5-HT oscillations may temporally segregate internal processing (e.g., memory consolidation) and responsiveness to external stimuli in the brain.

      Strengths:

      The findings of this research are novel and intriguing. Slow brain oscillations lasting tens of seconds have been suggested to exist, but to my knowledge they have never been analyzed in such a clear way. Furthermore, although it is likely that ultra-slow neuromodulator oscillations exist, this is the first report of such oscillations, and the greatest strength of this study is that it has clarified this phenomenon both statistically and phenomenologically.

      Weaknesses:

      As with any paper, this one has some limitations. While there is no particular need to pursue them, I will describe ten of them below, including future directions:

      (1) Contralateral recordings: 5-HT levels and electrophysiological recordings were obtained from opposite hemispheres due to technical limitations. Ipsilateral simultaneous recordings may show more direct relationships.

      Although we argue that bilateral symmetry defines both the serotonin system and many hippocampal activity patterns (Methods: Dual fiber photometry and silicon probe recordings), we agree that ipsilateral recordings would be superior to describe the link between serotonin and electrophysiology in the hippocampus. In addition to noting that a recent study has adopted the same contralateral design (Zhang et al. 2024), we add a reference further supporting bilateral hippocampal synchrony, specifically of dentate spikes (Farrell et al. 2024). However, as functional lateralization has been recently proposed to underlie certain hippocampal functions in the rodent (Jordan 2020), future studies should ideally include both imaging and electrophysiology in a single hemisphere to guarantee local correlations rather than assuming inter-hemispheric synchrony. This could be accomplished using an integrated probe with attached optical fibers, as described in Markowitz et al. 2018, which is however technically more challenging and has, to our knowledge, not yet been implemented with fiber photometry recordings with GRAB sensors. Given the required separation of a few hundred micrometers between the probe shanks and the optical fiber cannula, it is important to consider whether the recordings are capturing the same neuronal populations. For example, there is a risk of recording electrical activity from dorsal hippocampal neurons while simultaneously measuring light signals from neurons in the intermediate hippocampus, which are functionally distinct populations (Fanselow and Dong 2009).

      (2) Sample size: The number of mice used in the experiments is relatively small (n=6). Validation with a larger sample size would be desirable.

      While larger sample sizes generally reduce the influence of random variability and minimize the impact of outliers on conclusions, our use of mixed-effects models mitigates these concerns by accounting for both inter-session and inter-mouse variability. With this approach, we explicitly model random effects, such as the variability between individual mice and sessions, alongside fixed effects (such as treatment), which ensures that our results are not driven by random fluctuations in a few individual mice or sessions. Furthermore, the inclusion of random intercepts and slopes in the models allows for the possibility that different animals and/or sessions have different baseline characteristics and respond to different degrees of magnitude to the treatment. In summary, while validating these findings with a larger sample size would certainly help detect more subtle effects, we are confident in the robustness of the conclusions presented.

      (3) Lack of causality: The observed associations show correlations, not direct causal relationships, between 5-HT oscillations and neural activity patterns.

      We agree that the data we present in this study is largely correlational and generally avoid claims of causality in the manuscript. In the Discussion section, we discuss barriers to interpreting typical causal interventions in vivo, such as optogenetic activation of raphe nuclei: “The two previously mentioned in vivo studies showing reduced ripple incidence…”(paragraph #10, pg. 12), as well as an added section on further causality considerations in the Discussion section of the manuscript (paragraph #12, pg. 13): “In addition to the difficulties involved with…”

      Due to these barriers, as a first step, we wanted to describe how physiological changes in serotonin levels are correlated to changes in the hippocampal activity. Equipped with a deeper understanding of physiological serotonin dynamics, future studies could explore interventions that modulate serotonin in keeping with the natural range of serotonin fluctuations for a given state. On that point, another challenge which we have not mentioned in the manuscript is that modulating serotonin, or any neuromodulator’s levels, has the potential, depending on the degree of modulation, to transition the brain to an entirely different behavioral state. This then complicates interpretation, as one is not sure whether effects observed are due to the changes in the neuromodulator itself, or secondary to changes in state. At the same time, 5-HT activity drives networks which in return can change the release of other neurotransmitters, leading to indirect effects.

      The results of our in vitro experiments suggest that a causal relationship between serotonin and ripples is possible (Figure S1). Though the hippocampal slice preparation is clearly an artificial model, it provides a controlled environment to isolate the effects of serotonin manipulation on the hippocampal formation, without the confounding influence of systemic 5-HT fluctuations in other brain regions. Notably, the dose-dependent effects of serotonin (5-HT) wash-in on ripple incidence observed in vitro closely mirror the inverted-U dose-response curve seen in our in vivo experiments across states, where small increases in serotonin lead to the highest ripple incidence, and both lower and higher levels correspond to reduced ripple activity. This parallel suggests that the gradual washing of serotonin in our in vitro system may mimic the tonic firing changes in serotonergic neurons that occur during state transitions in vivo. These findings underscore the importance of studying how different dynamics of serotonin modulation can differentially affect hippocampal network activity.

      (4) Limited behavioral states: The study focuses primarily on sleep and quiet wakefulness. Investigation of 5-HT oscillations during a wider range of behavioral states (e.g., exploratory behavior, learning tasks) may provide a more complete understanding.

      We agree that future studies should investigate a broader range of behavioral states. For this study, as we were focused on general sleep and wake patterns, our recordings were done in the home cage, and we limited ourselves to the basic behavioral states described in the paper. Future studies should be designed to investigate ultraslow 5-HT oscillations during different behaviors, such as continuous treadmill running. Specifically, a finer segregation of extended wake behaviors by level of arousal could greatly add to our understanding of the role of ultraslow serotonin oscillations.

      (5) Generalizability to other brain regions: The study focuses on the CA1 region of the hippocampus. It's unclear whether similar 5-HT oscillation patterns exist in other brain regions.

      Given the reported ultraslow oscillations of population activity in serotonergic neurons of the dorsal raphe nucleus (Kato et al. 2022) as well as the widespread projections of the serotonergic nuclei, we would expect a broad expression of ultraslow 5-HT oscillations throughout the brain. So far, ultraslow 5-HT oscillations have been described in the basal forebrain, as well as in the dentate gyrus, in addition to what we have shown in CA1 (Deng et al. 2024 and Turi et al. 2024). Furthermore, our results showing that hippocampal-cortical coherence changes according to the phase of hippocampal ultraslow 5-HT oscillations suggests that 5-HT can affect oscillatory activity either indirectly by modulating hippocampal cells projecting to the cortical network or directly by modulating the cortical postsynaptic targets. Given the heterogeneity in projection strength, as well as in pre- and postsynaptic serotonin receptor densities across brain regions (de Filippo & Schmitz, 2024), it would be interesting to see whether local ultraslow 5-HT oscillations are differentially modulated, e.g. in terms of oscillation power. Future studies investigating different brain regions via implantation of multiple optic fibers in different brain areas or using the mesoscopic imaging approach adopted in Deng et al. 2024, will be needed to examine the extent of spatial heterogeneity in this ultraslow oscillation.

      (6) Long-term effects not assessed: Long-term effects of ultra-low 5-HT oscillations (e.g., on memory consolidation or learning) were not assessed.

      While beyond the scope of our current study, we agree that an important next step would involve modulating the ultraslow serotonin oscillation after learning, and then examining potential effects on memory consolidation, presumably via changes in ripple dynamics, though many possibilities could explain potential effects. There, our results suggest it would be important to isolate effects due to the change in ultraslow oscillation features, rather than simply overall levels of 5-HT. To that end, it would be important to test different modulation dynamics, specifically modulating the oscillation strength, around a constant mean 5-HT level by carefully timed optogenetic stimulation/inhibition. Afterwards, showing a clear correlation between the strength of the 5-HT modulation and memory performance would be important to establishing the relationship, as done in Lecci et al 2017, where more prominent ultraslow oscillations of sigma power in the cortex during sleep, alongside a higher density of spindles, were correlated with better memory consolidation. Given the tight coupling of spindles and ripples during sleep, it is possible that a similar effect on memory consolidation would be observed following changes in ultraslow 5-HT oscillation power.

      (7) Possible species differences: It's uncertain whether the findings in mice apply to other mammals, including humans.

      We agree that the experiments should ultimately be replicated in humans. In the 2017 study by Lecci et al., the authors highlighted the shared functional requirements for sleep across species, despite apparent differences, such as variations in sleep volume. To explore these commonalities, the researchers conducted parallel experiments in both mice and humans, aiming to identify a universal organizing structure. They discovered that the ultraslow oscillation of sigma power serves this role, enabling both species to balance the competing demands of arousability and sleep imperviousness. Based on this finding, it is plausible that ultraslow oscillations of serotonin, which similarly modulate activity according to arousal levels, would serve a comparable function in humans.

      (8) Technical limitations: The temporal resolution and sensitivity of the GRAB5-HT3.0 sensor may not capture faster 5-HT dynamics.

      The kinetics of the GRAB5-HT3.0 sensor used in this study limit the range of serotonin dynamics we can observe. However, the ultraslow oscillations we measure reflect temporal changes on the scale of 20 s and greater, whereas the GRAB sensor we use has sub-second on kinetics and below 2 s off kinetics (Deng et al. 2024). Therefore, the sensor is capable of reporting much faster activity than the ultraslow oscillations we observe, indicating that the ultraslow 5-HT signal accurately reflects the dynamics on this time scale. Furthermore, the presence of ultraslow oscillations in spiking activity—observed in the hippocampal formation (Gonzalo Cogno et al., 2024; Aghajan et al., 2023; Penttonen et al., 1999) and in the dorsal raphe (Mlinar et al., 2016), which are not affected by the same temporal smoothing, suggests that the oscillations we record are not likely due to signal aliasing, but instead reflect genuine oscillatory activity. Of course, this does not preclude that other, faster serotonin dynamics are also present in our signal, some of which may be too fast to be observed. For instance, rapid serotonin signaling via the ionotropic 5-HT3a receptors could be missed in our recordings. Additionally, with the fiber photometry approach we adopted, we are limited to capturing spatially broad trends in serotonin levels, potentially overlooking more localized dynamics.

      (9) Interactions with other neuromodulators: The study does not explore interactions with other neuromodulators (e.g., norepinephrine, acetylcholine) or their potential ultraslow oscillations.

      We agree that the interaction between neuromodulators in the context of ultraslow oscillations is an important issue, which we have addressed in our response to reviewer #1 under ‘Weaknesses.’

      (10) Limited exploration of functional significance: While the study suggests a potential role for 5-HT oscillations in memory consolidation and arousal, direct tests of these functional implications are not included.

      We agree and reference our answer to (6) regarding memory consolidation. Regarding arousal, direct tests of arousability to different sensory stimuli during different phases of the ultraslow 5-HT oscillation during sleep would be beneficial, in addition to the indirect measures of arousal we examine in the current study, e.g. degree of movement (icEMG) and long range coherence. In line with what we have shown, Cazettes et al. (2021) has demonstrated a direct relationship between 5-HT levels and pupil size, an indicator of arousal level, which like our findings, is consistent across behavioral states.

      Reviewer #3 (Public review):

      Summary:

      The activity of serotonin (5-HT) releasing neurons as well as 5-HT levels in brain structures targeted by serotonergic axons are known to fluctuate substantially across the animal's sleep/wake cycle, with high 5-HT levels during wakefulness (WAKE), intermediate levels during non-REM sleep (NREM) and very low levels during REM sleep. Recent studies have shown that during NREM, the activity of 5HT neurons in raphe nuclei oscillates at very low frequencies (0.01 - 0.05 Hz) and this ultraslow oscillation is negatively coupled to broadband EEG power. However, how exactly this 5-HT oscillation affects neural activity in downstream structures is unclear.

      The present study addresses this gap by replicating the observation of the ultraslow oscillation in the 5-HT system, and further observing that hippocampal sharp wave-ripples (SWRs), biomarkers of offline memory processing, occur preferentially in barrages on the falling phase of the 5-HT oscillation during both wakefulness and NREM sleep. In contrast, the raising phase of the 5-HT oscillation is associated with microarousals during NREM and increased muscular activity during WAKE. Finally, the raising 5-HT phase was also found to be associated with increased synchrony between the hippocampus and neocortex. Overall, the study constitutes a valuable contribution to the field by reporting a close association between raising 5-HT and arousal, as well as between falling 5-HT and offline memory processes.

      Strengths:

      The study makes compelling use of the state-of-the-art methodology to address its aims: the genetically encoded 5-HT sensor used in the study is ideal for capturing the ultraslow 5-HT dynamics and the novel detection method for SWRs outperforms current state-of-the-art algorithms and will be useful to many scientists in the field. Explicit validation of both of these methods is a particular strength of this study.

      The analytical methods used in the article are appropriate and are convincingly applied, the use of a general linear mixed model for statistical analysis is a particularly welcome choice as it guards against pseudoreplication while preserving statistical power.

      Overall, the manuscript makes a strong case for distinct sub-states across WAKE and NREM, associated with different phases of the 5-HT oscillation.

      Weaknesses:

      All of the evidence presented in the study is correlational. While the study mostly avoids claims of causality, it would still benefit from establishing whether the 5-HT oscillation has a direct role in the modulation of SWR rate via e.g. optogenetic activation/inactivation of 5-HT axons. As it stands, the possibility that 5-HT levels and SWRs are modulated by the same upstream mechanism cannot be excluded.

      We agree that causality claims cannot be made with our data, and acknowledge the interest in exploring causal interactions between ultraslow serotonin oscillations and the correlated activity we measure. We address this point in depth in our answer to Reviewer #2, Weaknesses #3.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      One major question in the presented data is the nature of the asymmetrical shape of the targeted slow events. How much does it reflect the 5-HT concentration and how much is this shape affected by the dynamics of the designed 5-HT sensor? This needs to be addressed in more detail referencing the original paper for the used sensor.

      We have added a paragraph in the Results section of the manuscript to address the asymmetric waveform of the ultraslow 5-HT oscillations and whether it could be affected by the asymmetric kinetics of the GRAB sensor we use: “The waveform of these ultraslow 5-HT oscillations…” (Results, paragraph #4, pg. 5). We include an extended answer to the question here:

      Indeed, the GRAB5-HT3.0 sensor we use in the study shows activation response kinetics which are faster than their deactivation time, with time constants at 0.25 s and 1.39 s, respectively (Deng et al. 2024). Likewise, the slope of the rising phase of the ultraslow serotonin oscillation we measure is faster than the slope of the falling phase, and the ratio of time spent in the rising phase versus the falling phase is less than 1, indicating longer falling phases (Figure S2). Although we cannot completely rule out that the asymmetric shape of the ultraslow serotonin oscillations we record is affected by this asymmetry in the 5-HT sensor kinetics, we believe this is unlikely, as the 5-HT signal clearly contains reductions in 5-HT levels that are much faster than the descending phase of the ultraslow oscillation. Although it is difficult to directly compare the different-sized signals, the reported timescales of off kinetics, on the order of a few seconds (Deng et al. 2024), are far below the tens of seconds timescale of the ultraslow oscillation. Furthermore, the finding that some dorsal raphe neurons modulate their firing rate at ultraslow frequencies, and moreover that all examples of such ultraslow oscillations shown display clear asymmetry in rising time versus decay, suggests that the asymmetry we observe in our data could be due to neural activity rather than temporal smoothing by the sensor (Mlinar et al. 2016). In this same direction, another study found similar asymmetry in extracellular 5-HT levels measured with fast scan cyclic voltammetry (FSCV), a technique with greater temporal resolution (sampling rate of 10 Hz) than GRAB sensors, after single pulse stimulation (Bunin and Wightman 1998). In this study, 5-HT was shown to be released extrasynaptically, making the longer clearing time compared to the release time intuitive. Finally, the observation that the onsets and offsets of ripple clusters, recorded with a sampling rate of 20 kHz, are precisely aligned with the peaks and troughs of ultraslow serotonin oscillations (Figure 1, H1-2, columns 2-3) suggests that the duration of the falling phase is not artificially distorted by the temporal smoothing of the sensor dynamics.

      Regardless of the dynamics of the serotonin concentration, it should be noted that the elicited neuronal effect might have different dynamics compared to the 5-HT concentration that need to be more studied: to address this one can either examine the average of the broadband LFP (not high passfiltered by the amplifier) or the distribution of simultaneously recorded spiking activity around the peak of ultra-slow oscillations.

      We have added Figure S6, showing unit activity relative to the phase of ultraslow serotonin oscillations.

      From this analysis, we uncover three groups of units which are largely preserved across states (Figure S6, E vs. F), albeit with a slight temporal shift rightward from NREM to WAKE (Figure S6, C vs. D). Namely, some units spike preferentially during the rising phase, some during the falling phase, and a third group have no clear phase preference. Unit activity during the falling phase is unsurprising, as it is where ripples largely occur, which themselves are associated with spike bursts. During the rising phase, the unit activity we observe could correspond to firing of the hippocampal subpopulation known to be active during NREM interruption states (Jarosiewicz et al. 2002, Miyawaki et al. 2017). While the units’ phase preference was tested based on the category of rising vs. falling phase, as this division described most variation in the data, a few units in the ‘No preference’ group showed heightened activity near the oscillation peak. However, given the very small number of units with this preference, more unit data is needed to describe this group, ideally with high-density recordings. Overall, most units showed a falling vs. rising phase preference, indicating a phase coding of hippocampal activity by 5-HT ultraslow oscillations.

      Related to the previous point, it would be helpful to show the average cycle shape of these oscillations (relative to the phase 0 extracted in Figure 3) and do the shape comparison across sessions and also wake/NREM

      We agree, and to this end we have added Figure S2. From this waveform analysis, we show that the ultraslow serotonin oscillation is asymmetric, with the rising phase having a greater slope, but shorter length, than the falling phase. While this asymmetry is observed both in NREM and WAKE, the slope difference and length ratio difference in rising vs. falling phase is greater in NREM (Figure S2. B).

      In Figure 3D, there seem to be oscillatory rhythms with faster cycles on top of the targeted oscillations. That would make the phase estimation less accurate, e.g. in the left panel, in the second cycle, it is not clear if there are two faster cycles or it is one slow cycle as targeted, and if noted in the rising phase of the second fast cycle there are no ripples. This might suggest that regardless of specific oscillation frequency whenever 5-HT is started to get released, the ripples are suppressed and once the 5-HT is not synaptically effective anymore the ripples start to get generated while the photometry signal starts to wane with the serotonin being cleared. Still, if there is any rhythmicity between bouts of no ripple, it would suggest an ultra-slow regularity in the 5-HT release.

      The reviewer is correct to point out that some faster increases in serotonin, which occur on top of the ultraslow oscillations we measure, seem to be associated with decreased ripple incidence, as in the example referenced. The dominance of ultraslow frequencies in the power spectrum of the 5-HT signal suggests, however, that oscillations faster than the ultraslow oscillations we describe are far less prevalent in the data. While there may be some coupling of ripples and other measures to serotonin oscillations of different frequencies, this may be hard or impossible to detect with phase analysis based on their infrequent occurrence and nonstationary nature. In fact, we show in Figure S3 that the strongest phase modulation of ripples by ultraslow serotonin oscillations is observed in the frequencies we use (0.01-0.06 Hz). Methodologically, phase analysis indeed assumes stationary signals, which are rare if not absent in physiological data (Lo et al. 2009), however generally the narrower the frequency band, the better the phase estimation. The narrow frequency band we use provides phase estimates that are largely robust and unaffected by the presence of faster oscillations, as can be seen in the example phase traces shown in Figure 4.

      The hypothesis that the rising phase burst of synaptic serotonin is what silences ripples, and that with the clearing of serotonin from the synapses, ripples recover, is a possible explanation of our findings. However, if this were the case, one could expect the ripple rate to increase over the course of the falling phase of ultraslow 5-HT oscillations, as 5-HT decreases, and peak at the trough. This is at odds with what we observe, namely a fairly uniform distribution of ripples along the falling phase (Figure 3F2,F4). Furthermore, the Mlinar et al. 2016 study describes a subpopulation of raphe neurons whose firing rates themselves oscillate at ultraslow frequencies, rather than on-off bursting at ultraslow frequencies, which would argue against this hypothesis. However, as this study looks at a small number of neurons in slices, further in vivo experiments examining firing rates of median raphe neurons are required to understand how the ultraslow oscillation of extracellular serotonin that we measure is generated as well as how it is related to ripple rates.

      In Figure 3B, it is not clear why IRI is z-scored. It would be informative to have the actual value of IRI. What is the z relative to? Is it the mean value of IRI in each recording session? Is this to reduce the variability across sessions?

      We have now included in Figure 3D a box plot displaying the IRI distributions across different states and sessions. To minimize inter-session variability, data were z-scored within each session for visualization purposes. However, all general linear models were based on raw data, and as a result, the raw differences in IRI are shown in Figure 3C.

      Figure 3E, panel labels don't match with the caption

      We are grateful to the reviewer for pointing out this mistake, which we have corrected in the updated version of the manuscript.

      In the text related to Figure 3E, the related analysis can be more clearly described. "phase preference of individual ripples" does not immediately suggest that the occurring phase of each ripple relative to the targeted oscillation is extracted. I suggest performing this analysis individually for each session and summarizing the results across the sessions.

      We have reworded the sentence in Results: 5-HT and ripples to better reflect the analysis performed: “Next, we calculated the ultraslow 5-HT phases at which individual ripples occurred during both NREM and WAKE (3E-F) ...”. Regarding session-level data, we have added Figure S3, which shows session level mean phase vectors, as well as the grand mean across sessions for both NREM and WAKE. Included in this figure are session level means for frequency bands outside of the ultraslow band we used in our study, intended to show that ripples are most strongly timed by the ultraslow band (0.01-0.06 Hz), reflected by the greater amplitude of the mean phase vector for this band.

      Figure 3E2, based on the result of ripple-triggered 5-HT in left panels of 2H1-2, one would expect to see a preferred phase closer to 180 (toward the end of the falling phase), it would be helpful to compare and discuss the results of these two analyses.

      The reviewer is correct to point out the apparent discrepancy in where the mean ripple falls with respect to the ongoing serotonin oscillation between the two figures mentioned. We have addressed this point in Results: 5-HT and ripples, paragraph #4: “This result appear to be at odds with…”.

      Regarding the analysis in 3F, please also compare the power distribution of ripples between NREM and wake. This will help to better understand the potential difference behind the observed difference: how much the strong ripples are comparable between wake and NREM. It is also necessary to report the ripple detection failure rate across ripples with different strengths.

      We have added a figure showing analysis done on a subset of the data in which ripples were manually curated in order to evaluate the performance of the ripple detection model (Figure S7) and explanatory text in Methods: Model performance: ‘To ensure that our model …’. In summary, while missed ripples did tend to have lower power than correctly detected ripples, including them did not change the distribution of ripples by the phase of the ultraslow serotonin oscillation (Figure S7C). We would also note that while the phase preference is noisier than what is presented in Figure 3F because this analysis was done with a small subset of all recorded ripples, the fact that ripples occur more clearly on the falling phase is visible for both detected ripples and detected + false negative ripples.

      The mixed-effects model examining the influence of 5-HT ultraslow oscillation phase on ripple power revealed no significant effect of state (p = 0.088). This indicates that whether the data were collected during NREM or wake periods did not significantly impact ripple power and that the lack of a significant effect (in Figure 3G,H) in WAKE is probably not due to a difference in the distribution of ripple power between states.

      4D, y label is z?

      We are grateful for the reviewer to point that out, yes, the y label should be ‘z-score’, as the two traces represent z-scored 5-HT (blue) and z-scored shuffled data (orange). Figure 4D2 and Figure 2H1-2, which show similar data, have been corrected to address this oversight.

      Relating to Figure 4, EMG comparison across phases of the oscillations is insightful. Two related and complementary analyses are to compare the theta and gamma power between the falling and rising phases.

      We have addressed this suggestion in Figure S5 A-C. While low gamma, high gamma and theta power are modulated identically in NREM, with higher power observed during the falling phase than the rising phase, during WAKE, different patterns can be seen. Specifically, low gamma power shows no phase preference, while high gamma shows a peak near the center of the ultraslow 5-HT oscillation. Theta power, as in NREM, is higher during the falling phase of ultraslow 5-HT oscillations. Increased power across many frequency bands was shown to coincide with decreases in DRN population activity during NREM, which matches with what we report here (Kato et al. 2022). In summary, while NREM patterns are consistent in all frequency bands tested, aligning with the pattern of ripple incidence, in WAKE low and high gamma power show different relationships to ultraslow 5-HT phase.

      In the manuscript, we have used the data in both Figure S5 and S6 (unit activity relative to ultraslow 5-HT oscillations), to argue against the idea that our coherence findings result from a lack of activity in the rising phase (see next question), which would have the effect of ‘artificially’ reducing coherence in the falling phase relative the rising phase. The text can be found in Results: 5-HT and hippocampal cortical coherence, paragraph #2.

      The results presented in Figure 5 could be puzzling and need to be further discussed: if the ripple band activity is weak during the rising phase, in what circumstances the coherence between cortex and CA1 is specifically very strong in this band?

      As mentioned in the previous answer, we have addressed this concern in Results: 5-HT and hippocampal-cortical coherence, paragraph #2. In summary, it is true that the higher coherence in rising phase than in the falling phase for the highest frequency band (termed ‘high frequency oscillation’ (HFO), 100-150 Hz) could be unexpected, given that ripples occur largely during the falling phase. A few points could help explain this finding. Firstly, it should be noted that power in the 100-150 Hz band can arise from physiological activity outside of ripples, such as filtered non-rhythmic spike bursts (Liu et al. 2022), whose coherent occurrence in the rising phase could explain the coherence findings. Secondly, coherence is a compound measure which is affected by both phase consistency and amplitude covariation (Srinath and Ray 2014), thus from only amplitude one cannot predict coherence. Furthermore, HFO power in the cortex is highest near the peak of ultraslow 5-HT oscillations (Figure S5D), as opposed to the falling phase peak in the hippocampus. This shows a lack of covariation in amplitude by phase between the hippocampus and cortex at this frequency band. An alternative explanation of our findings regarding coherence could be that in the rising phase, there is simply little to no activity, which is easier to ‘synchronize’ than bouts of high activity. Hippocampal unit activity in the rising phase (Figure S6) suggests however, that it is not likely to be the absence of activity supporting higher coherence in the rising phase across frequencies. Additional experiments using high density recordings should be conducted to examine 5-HT ultraslow oscillations and their role in gating activity across brain regions, though these results strongly suggest some role exists.

      Reviewer #2 (Recommendations for the authors):

      I would like to offer two comments. I believe that these are not unusual requests, and thus I would like the authors to respond.

      (1) It would be prudent to investigate the possibility that the observed correlation between ultraslow and hippocampal ripples/microarousals is merely superficial and that there are unidentified confounding factors at play. For example, it would be beneficial to provide evidence that administering a serotonin receptor inhibitor result in the disappearance of the slow oscillation of ripples and microarousals, or that the correlation with ultraslow is no longer present. Please note that the former experiments do not require GRAB5-HT3.0 imaging.

      We agree that causality claims cannot be made with our data and acknowledge the interest in exploring causal interactions between ultraslow serotonin oscillations and the correlated activity we measure. We address this point in depth in our answer to Reviewer #2, Weaknesses #3. We would further like to note that given the large number of serotonin receptors and the lack of selectivity of many serotonin receptor antagonists, a pharmacological approach would be difficult, though the results certainly useful. Finally, we highlight the psilocin study, which reported changes in the rhythmic occurrence of microarousals, and therefore likely ultraslow oscillations, after administering a 5-HT2a receptor agonist, suggesting a potential causal effect of 5-HT (via 5-HT2a receptor) on MA occurrence (Thomas et al. 2022).

      (2) The slow frequency appears to be associated with the default mode network as observed in fMRI signals. The neural basis of the default mode network remains unclear; therefore, a more detailed examination of this possibility would be beneficial.

      We agree that it would be interesting to investigate the role of 5-HT in the neural basis of the DMN.

      The DMN as described in humans (Raichle et al. 2001) and rodents (Lu et al. 2012) may indeed include some parts of the hippocampus and perhaps some of our neocortical recordings could also be considered part of the DMN. The fact that the activity across the inter-connected brain structures of the DMN is correlated at ultraslow time scales (Gutierrez-Barragan et al. 2019, Mantini et al. 2007), as well as serotonin’s ability to modulate the DMN is intriguing (Helmbold et al. 2016). Further studies simultaneously recording DMN activity via fMRI and electrical activity via silicon probes, as done in Logothetis et al. 2001, could elucidate further a potential link between ultraslow oscillations and the DMN, with serotonergic modulation as a means to understand any potential contribution of serotonin.

      Reviewer #3 (Recommendations for the authors):

      (1) The impact of the study would benefit from an experiment causally testing the effect of hippocampal 5-HT levels on hippocampal physiology, e.g. using optogenetic manipulations.

      We agree that causality claims cannot be made with our data and acknowledge the interest in exploring causal interactions between ultraslow serotonin oscillations and the correlated activity we measure. We address this point in depth in our answer to Reviewer #2, Weaknesses #3.

      (2) Data presentation: the figures are of poor resolution, making some diagram details and, more importantly, some example traces (e.g. Figure 1A, right) impossible to see. This should be corrected by either increasing figure resolution or making important figure elements large enough to be readable.

      We apologize for the poor resolution and have corrected it in the updated version of the manuscript.

      (3) Differences in some figure panels are not statistically assessed: Figure 1H (differences in spectrum peak power), Figure 3E1 & Figure 3E3 (directional bias of the circular distributions), Figure 4C (difference from 0 mean).

      We acknowledge this oversight and have added statistical tests for all three figures, as well as further information regarding the models used in Methods: Statistics.

      (4) Lines 279-280: the claim that the study shows "organization of activity by ultraslow oscillations of 5-HT" implies a causal role of 5-HT in organizing hippocampal activity. I suggest that this statement be toned down to reflect the correlational nature of the presented evidence.

      We have rephrased the sentence in question to the following: “In our study, including both NREM and WAKE periods allowed us to additionally show that the temporal organization of activity relative to ultraslow 5-HT oscillations operates according to the same principles in both states...”, which we believe better reflects the temporal correlation we describe.

      (5) While the study claims to use the EMG (i.e. electromyograph) signal, it does not describe any electrodes placed inside the muscle in the methods section. The SleepScoreMaster toolbox used in the study estimates the EMG using high-frequency activity correlated across recording channels, so I assume this is how this signal was obtained. While such activity may well reflect muscular noise to some degree, it is an indirect measure as the electrodes are not in the muscle. Since the EMG signal is central to the message of the manuscript, the method for calculating it should be described in the methods section and it should be explicitly labelled as an indirect measure in the main text, e.g. by referring to this signal as pseudo-EMG.

      We agree and have added explanatory text to the State Scoring subsection in Methods. Given that the EMG we refer to is derived from intracranial data, and not from traditional EMG probes, we now refer to the EMG as intracranial EMG, or icEMG for short, throughout the main text.

      (6) Is ripple frequency or ripple duration different across the rising and falling phases of the ultraslow oscillation?

      We have now investigated this suggestion in Figure S4, where we show that ripple frequency is higher in the falling phase than rising phase, while ripple duration appears to show no phase preference.

      (7) Lines 315-317: I am not sure why the manuscript refers to the coupling between EMG and 5-HT levels as 'puzzling' given that, as stated, the locomotion-inducing effects of 5-HT are well documented. While the fact that even non-locomotory motor activity may be associated with 5-HT rise is certainly interesting (although not sure if 'puzzling'), the manuscript does not directly compare the association of 5-HT levels with locomotory and non-locomotory EMG spikes. Thus, I think this discussion point is not fully warranted.

      We agree and have rephrased the discussion point in question to reflect that the EMG link to serotonin oscillations is not necessarily surprising, given both the literature linking 5-HT and spontaneous movement in the hippocampus, as well as the involvement of 5-HT in repetitive movements, where the role for a regularly-occurring oscillation is perhaps more intuitive.

      (8) Line 441: Reference #67 does not describe the use of fiber photometry.

      The reviewer is to correct to point out this typo, which has been now corrected. The reference in question should be 64, where fiber photometry experiments are described. For further clarity, we have changed our referencing scheme to include authors and years in in-text references.

      (9) In Figures 3E1-3, the phase has different bounds than in the other Figures in the manuscript (0:360 vs -180:180), this should be corrected for consistency.

      We agree and have made changes so that all figures have a phase range of -180 to 180°.

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    1. Author response:

      The following is the authors’ response to the previous reviews.

      Reviewer 1:

      We would like to thank Reviewer 1 for recognising the importance of our findings on the heterogeneity in bacterial responses to tachyplesin.

      (1) A double deletion of acrA and tolC (two out of the three components of the major constitutive RND efflux pump) reduces the appearance of the low accumulator phenotype, but interestingly, the single deletions have no effect, and a well-characterised inhibitor of RND efflux pumps also has no effect. The authors identify a two-component system, qseCB, that appears necessary for the appearance of low accumulators, but this system has pleiotropic effects on many cellular systems, with only tenuous connections to efflux. The selected pharmacological agents that could prevent the appearance of low accumulators do not offer clear insight into the mechanism by which low accumulators arise, because they have diverse modes of action.

      We have added that “QseBC, was previously inferred to mediate resistance to a tachyplesin analogue by upregulating efflux genes based on transcriptomic analysis and hyper susceptibility of ΔqseBΔqseC mutants[113]”. However, we have also acknowledged that “it is conceivable that the deletion of QseBC has pleiotropic effects on other cellular mechanisms involved in tachyplesin accumulation.” and that “it is also conceivable that sertraline prevented the formation of the low accumulator phenotype via efflux independent mechanisms”

      These amendments are reported on lines 525-527, 532-534 and 539-541 of our revised manuscript.

      (2) The transcriptomics data collected for low and high accumulator sub-populations are interesting, but in my opinion, the conclusions that can be drawn from these data remain overstated. It is not possible to make any claims about the total amount of "protein synthesis, energy production, and gene expression" on the basis of RNA-Seq data. The reads from each sample are normalised, so there is no information about the total amount of transcript. Many elements of total cellular activity are post-transcriptionally regulated, so it is impossible to assess from transcriptomics alone. Finally, the transcriptomic data are analysed in aggregated clusters of genes that are enriched for biological processes, for example: "Cluster 2 included processes involved in protein synthesis, energy production, and gene expression that were downregulated to a greater extent in low accumulators than high accumulators". However, this obscures the fact that these clusters include genes that are generally inhibitory of the process named, as well as genes that facilitate the process.

      We have now acknowledged that “that our data do not take into account post-transcriptional modifications that represent a second control point to survive external stressors.”

      These amendments are reported on lines 534-535 of our revised manuscript.

      The raw transcript counts can be found in Figure 3 – Source Data, we had added these data in our previous manuscript as requested by this reviewer.

      We would also like to clarify that we have analysed our transcriptomic data via both clustering (i.e. Figure 3) and direct comparison of genes of interest (Table S1) and transcription factors (i.e. genes that are generally inhibitory of the process named, as well as genes that facilitate the process, Figure S12).

      Finally, we would like to point out that in our revised manuscript (both this and its previous version) we are stating “Cluster 2 included processes involved in protein synthesis, energy production, and gene expression that were downregulated to a greater extent in low accumulators than high accumulators”. We do not think this is an overstatement, we do not use these data to make conclusions on the total amount of "protein synthesis, energy production, and gene expression".

      (3) The authors have added an experiment to attempt to assess overall metabolic activity in the low accumulator and high accumulator populations, which is a welcome addition. They apply the redox dye resazurin and observe lower resorufin (reduced form) fluorescence in the low accumulator population, which they take to indicate a lower respiration rate. This seems possible, however, an important caveat is that they have shown the low accumulator population to retain substantially lower amounts of multiple different fluorescent molecules (tachyplesin-NBD, propidium iodide, ethidium bromide) intracellularly compared to the high accumulator population. It seems possible that the low accumulator population is also capable of removing resazurin or resorufin from the intracellular space, regardless of metabolic rate. Indeed, it has previously been shown that efflux by RND efflux pumps influences resazurin reduction to resorufin in both P. aeruginosa and E. coli. By measuring only the retained redox dye using flow cytometry, the results may be confounded by the demonstrated ability of the low accumulator population to remove various fluorescent dyes. More work is needed to strongly support broad conclusions about the physiological states of the low and high accumulator populations. The phenomenon of the emergence of low accumulators, which are phenotypically tolerant to the antimicrobial peptide tachyplesin, is interesting and important even if there is still work to be done to understand the mechanism by which it occurs.

      We have now clarified that these assays were performed in the presence of 50 μM CCCP and that “CCCP was included to minimise differences in efflux activity and preserve resorufin retention between low and high accumulators, though some variability in efflux may still persist.” We have now added this information on lines 401-406. This information was only present in the caption of Figure S16 of our previous version of this manuscript.

      We agree with the reviewers that more work needs to be done to fully understand this new phenomenon and we had already acknowledged in our previous version of this manuscript that other mechanisms could play a role in this new phenomenon, see lines 489-517 of the current manuscript.

      Reviewer 2:

      We would like to thank the reviewer for recognising that all their previous comments have now been satisfactorily addressed.

      (1) Some mechanistic questions regarding tachyplesin-accumulation and survival remain. One general shortcoming of the setup of the transcriptomics experiment is that the tachyplesin-NBD probe itself has antibiotic efficacy and induces phenotypes (and eventually cell death) in the ´high accumulator´ cells. As the authors state themselves, this makes it challenging to interpret whether any differences seen between the two groups are causative for the observed accumulation pattern of if they are a consequence of differential accumulation and downstream phenotypic effects.

      We agree with the reviewer and we had explicitly acknowledged this possibility on lines 281-285 (of the previous and current version of this manuscript).

      (2) The statement ´ Moreover, we found that the fluorescence of low accumulators decreased over time when bacteria were treated with 20 μg mL´ is, in my opinion, not supported by the data shown in Figure S4C. That figure shows that the abundance of ´low accumulator´ cells decreases over time. Following the rationale that protease K treatment may cleave surface associated/ extracellular tachyplesin-NDB, this should lead to a shift of ´low accumulator´ population to the left, indicating reduced fluorescence intensity per cell. This is not so case, but the population just disappears. However, after 120 min of treatment more cells appear in the ´high accumulator´ state. This result is somewhat puzzling.

      We agree with the reviewer that our previous discussion of this data could have been misleading. We have now reworded this part of the text as following: “We found that the fluorescence of high accumulators did not decrease over time when tachyplesin-NBD was removed from the extracellular environment and bacteria were treated with 20 μg mL<sup>-1</sup> (0.7 μM) proteinase K, a widely-occurring serine protease that can cleave the peptide bonds of AMPs [43–45] (Figure S4B and C). These data suggest that tachyplesin-NBD primarily accumulates intracellularly in high accumulators.”

      It is conceivable that extended exposure to proteinase K (i.e. we see a decrease in the abundance of low accumulators after 90 min treatment with proteinase K) increased the permeability to tachyplesin-NBD of low accumulators allowing tachyplesin-NBD to move from either the extracellular space or the membrane to the cell interior. However, we do not have data to prove this point.

      Therefore, we have now removed our claim that the data obtained using proteinase K suggest that tachyplesin-NBD accumulates primarily in the membranes of low accumulators. We believe that our two separate microscopy analyses provide more direct, stronger and less ambiguous evidence that tachyplesin-NBD accumulates primarily in the membranes of low accumulators.

      (3) The authors used the metabolic dye resazurin to measure the metabolic activity of low vs. high accumulators. I am not entirely convinced that the lower fluorescence resorufin fluorescence in tachyplesin-NBD accumulators really indicates lower metabolic activity, since a cell's fluorescence levels would also be affected by the cellular uptake and efflux. It appears plausible that the lower resorufin-fluorescence may result from reduced accumulation/increased efflux in the ‘low-tachyplesin NBD´ population.

      We have now clarified that these assays were performed in the presence of 50 μM CCCP and that “CCCP was included to minimise differences in efflux activity and preserve resorufin retention between low and high accumulators, though some variability in efflux may still persist.” We have now added this information on lines 401-406. This information was only present in the caption of Figure S16 of our previous version of this manuscript.

      (4) P8 line 343. The text should refer to Figure. 13B, instead of 14B

      We have now changed the text accordingly on line 337.

      Reviewer 3:

      We would like to thank the reviewer for recognising that we have done a very impressive job in taking care of their comments.

      (1) Despite these advances, the contribution of efflux may require more direct evidence to further dissect whether efflux is necessary, sufficient, or contributory. The facts that the key low efflux mutant still retains a small fraction of survivors and that the inhibitors used may cause other physiological changes leading to higher efflux are still unaccounted for. The lipidomic and vesicle findings, while intriguing, remain descriptive, and direct tests of their functional relevance would further solidify the mechanistic models.

      We agree with the reviewers that more work needs to be done to fully understand this new phenomenon and we had already acknowledged in our previous version of this manuscript that other mechanisms could play a role in this new phenomenon, see lines 489-517 of the current manuscript.

    1. Author response:

      Reviewer #1 (Public review):

      (1) Legionella effectors are often activated by binding to eukaryote-specific host factors, including actin. The authors should test the following: a) whether Lfat1 can fatty acylate small G-proteins in vitro; b) whether this activity is dependent on actin binding; and c) whether expression of the Y240A mutant in mammalian cells affects the fatty acylation of Rac3 (Figure 6B), or other small G-proteins.

      We were not able to express and purify the full-length recombinant Lfat1 to perform fatty acylation of small GTPases in vitro. However, in cellulo overexpression of the Y240A mutant still retained ability to fatty acylate Rac3 and another small GTPase RheB (see Author response image 1 below). We postulate that under infection conditions, actin-binding might be required to fatty acylate certain GTPases due to the small amount of effector proteins that secreted into the host cell.

      Author response image 1.

      (2) It should be demonstrated that lysine residues on small G-proteins are indeed targeted by Lfat1. Ideally, the functional consequences of these modifications should also be investigated. For example, does fatty acylation of G-proteins affect GTPase activity or binding to downstream effectors?

      We have mutated K178 on RheB and showed that this mutation abolished its fatty acylation by Lfat1 (see Author response image 2 below). We were not able to test if fatty acylation by Lfat1 affect downstream effector binding.

      Author response image 2.

      (3) Line 138: Can the authors clarify whether the Lfat1 ABD induces bundling of F-actin filaments or promotes actin oligomerization? Does the Lfat1 ABD form multimers that bring multiple filaments together? If Lfat1 induces actin oligomerization, this effect should be experimentally tested and reported. Additionally, the impact of Lfat1 binding on actin filament stability should be assessed. This is particularly important given the proposed use of the ABD as an actin probe.

      The ABD domain does not form oligomer as evidenced by gel filtration profile of the ABD domain. However, we do see F-actin bundling in our in vitro -F-actin polymerization experiment when both actin and ABD are in high concentration (data not shown). Under low concentration of ABD, there is not aggregation/bundling effect of F-actin.

      (4) Line 180: I think it's too premature to refer to the interaction as having "high specificity and affinity." We really don't know what else it's binding to.

      We have revised the text and reworded the sentence by removing "high specificity and affinity."

      (5) The authors should reconsider the color scheme used in the structural figures, particularly in Figures 2D and S4.

      Not sure the comments on the color scheme of the structure figures.

      (6) In Figure 3E, the WT curve fits the data poorly, possibly because the actin concentration exceeds the Kd of the interaction. It might fit better to a quadratic.

      We have performed quadratic fitting and replaced Figure 3E.

      (7) The authors propose that the individual helices of the Lfat1 ABD could be expressed on separate proteins and used to target multi-component biological complexes to F-actin by genetically fusing each component to a split alpha-helix. This is an intriguing idea, but it should be tested as a proof of concept to support its feasibility and potential utility.

      It is a good suggestion. We plan to thoroughly test the feasibility of this idea as one of our future directions.

      (7) The plot in Figure S2D appears cropped on the X-axis or was generated from a ~2× binned map rather than the deposited one (pixel size ~0.83 Å, plot suggests ~1.6 Å). The reported pixel size is inconsistent between the Methods and Table 1-please clarify whether 0.83 Å refers to super-resolution.

      Yes, 0.83 Å is super-resolution. We have updated in the cryoEM table

      Reviewer #2 (Public review):

      Weaknesses:

      (1) The authors should use biochemical reactions to analyze the KFAT of Llfat1 on one or two small GTPases shown to be modified by this effector in cellulo. Such reactions may allow them to determine the role of actin binding in its biochemical activity. This notion is particularly relevant in light of recent studies that actin is a co-factor for the activity of LnaB and Ceg14 (PMID: 39009586; PMID: 38776962; PMID: 40394005). In addition, the study should be discussed in the context of these recent findings on the role of actin in the activity of L. pneumophila effectors.

      We have new data showed that Actin binding does not affect Lfat1 enzymatic activity. (see figure; response to Reviewer #1). We have added this new data as Figure S7 to the paper. Accordingly, we also revised the discussion by adding the following paragraph.

      “The discovery of Lfat1 as an F-actin–binding lysine fatty acyl transferase raised the intriguing question of whether its enzymatic activity depends on F-actin binding. Recent studies have shown that other Legionella effectors, such as LnaB and Ceg14, use actin as a co-factor to regulate their activities. For instance, LnaB binds monomeric G-actin to enhance its phosphoryl-AMPylase activity toward phosphorylated residues, resulting in unique ADPylation modifications in host proteins (Fu et al, 2024; Wang et al, 2024). Similarly, Ceg14 is activated by host actin to convert ATP and dATP into adenosine and deoxyadenosine monophosphate, thereby modulating ATP levels in L. pneumophila–infected cells (He et al, 2025). However, this does not appear to be the case for Lfat1. We found that Lfat1 mutants defective in F-actin binding retained the ability to modify host small GTPases when expressed in cells (Figure S7). These findings suggest that, rather than serving as a co-factor, F-actin may serve to localize Lfat1 via its actin-binding domain (ABD), thereby confining its activity to regions enriched in F-actin and enabling spatial specificity in the modification of host targets.”

      (2) The development of the ABD domain of Llfat1 as an F-actin domain is a nice extension of the biochemical and structural experiments. The authors need to compare the new probe to those currently commonly used ones, such as Lifeact, in labeling of the actin cytoskeleton structure.

      We fully agree with the reviewer’s insightful suggestion. However, a direct comparison of the Lfat1 ABD domain with commonly used actin probes such as Lifeact, as well as evaluation of the split α-helix probe (as suggested by Reviewer #1), would require extensive and technically demanding experiments. These are important directions that we plan to pursue in future studies.

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife Assessment

      This valuable study reports the development of a novel organoid system for studying the emergence of autorhythmic gut peristaltic contractions through the interaction between interstitial cells of Cajal and smooth muscle cells. While the utility of the organoids for studying hindgut development is well illustrated by showing, for example, a previously unappreciated potential role for smooth muscle cells in regulating the firing rate of interstitial cells of Cajal, some of the functional analyses are incomplete. There are some concerns about the specificity and penetrance of perturbations and the reproducibility of the phenotypes. With these concerns properly addressed, this paper will be of interest to those studying the development and physiology of the gut.

      We greatly appreciate constructive comments raised by the Editors and all the Reviewers. We have newly conducted pharmacological experiments using Nifedipine, a L-type Ca<sup>2+</sup> blocker known to operate in smooth muscles (new Fig 7). The treatment abrogated not only the oscillation of SMCs but also that in ICCs, further corroborating our model that not only ICC-to-SMC interactions but also the reverse direction, namely SMC-to-ICC feedback signals, are operating to achieve coordinated/stable rhythm of gut contractile organoids.

      Concerning the issues of the specificity and penetrance in pharmacological experiments with gap junction inhibitors, we have carefully re-examined effects by multiple blockers (CBX and 18b-GA) at different concentrations (new Fig 5D and Fig. S3B).We have newly found that: (1) the effects observed by CBX (100 µM) that the latency of Ca<sup>2+</sup> peaks between ICCs (preceding) and SMCs (following) was abolished are not seen by 18b-GA at any concentrations including 100 µM, implying that the latency of Ca<sup>2+</sup> peaks between these cells is governed by connexin(s) that are not inhibited by18bGA. Such difference in inhibiting effects by these two drugs were previously reported in multiple model systems including guts (Daniel et al., 2007; Parsons & Huizinga, 2015; Schultz et al., 2003).

      Regarding the penetrance of the drugs, we have carried out earlier administration (Day 3) of the gap junction inhibitor, either CBX (100 µM) or 18b-GA (100 µM), in the course of organoidal formation in culture when cells are still at 2D to exclude a possible penetrance problem (new Fig. S3C). There treatments render no or little effects to the patterns of organoidal contractions in a way similar to the drug administration at Day 7. As already shown in the first version, CBX (100 µM) eliminates the latency of Ca<sup>2+</sup> peaks, we believe that this drug successfully penetrates into the organoid and exerts its specific effects.

      Unfortunately, due to very unstable condition in climate including extreme heat and sporadically occurring bird flu epidemic since the last summer in Japan, the poultry farm must have faced problems. In the course of revision experiments, we got in a serious trouble at multiple times with unhealthy eggs/embryos lasting from last summer until present. These unfortunate incidents did not allow us to engage in the revision experiments as fully as we originally planned. Nevertheless, we did our very best within a limited time fame, and we believe that the revised version is suitable as a final version of an eLife article.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      In this study, the authors developed an organoid system that contains smooth muscle cells (SMCs) and interstitial cells of Cajal (ICCs; pacemaker) but few enteric neurons, and generates rhythmic contractions as seen in the developing gut. The stereotypical arrangements of SMCs and ICCs in the organoid allowed the authors to identify these cell types in the organoid without antibody staining. The authors took advantage of this and used calcium imaging and pharmacology to study how calcium transients develop in this system through the interaction between the two types of cells. The authors first show that calcium transients are synchronized between ICC-ICC, SMC-SMC, and SMC-ICC. They then used gap junction inhibitors to suggest that gap junctions are specifically involved in ICC-to-SMC signaling. Finally, the authors used an inhibitor of myosin II to suggest that feedback from SMC contraction is crucial for the generation of rhythmic activities in ICCs. The authors also show that two organoids become synchronized as they fuse and SMCs mediate this synchronization.

      Strengths:

      The organoid system offers a useful model in which one can study the specific roles of SMCs and ICCs in live samples.

      Thank you very much for the constructive comments.

      Weaknesses:

      Since only one blocker each for gap junction and myosin II was used, the specificities of the effects were unclear.

      We appreciate these comments. We have addressed those of “weaknesses” as described in “Responses to the eLife assessment” (please see above).

      Reviewer #2 (Public Review):

      Summary:

      In this study, Yagasaki et al. describe an organoid system to study the interactions between smooth muscle cells (SMCs) and interstitial cells of Cajal (ICCs). While these interactions are essential for the control of rhythmic intestinal contractility (i.e., peristalsis), they are poorly understood, largely due to the complexity of and access to the in vivo environment and the inability to co-culture these cell types in vitro for long term under physiological conditions. The "gut contractile organoids" organoids described herein are reconstituted from stromal cells of the fetal chicken hindgut that rapidly reorganize into multilayered spheroids containing an outer layer of smooth muscle cells and an inner core of interstitial cells. The authors demonstrate that they contract cyclically and additionally use calcium imagining to show that these contractions occur concomitantly with calcium transients that initiate in the interstitial cell core and are synchronized within the organoid and between ICCs and SMCs. Furthermore, they use several pharmacological inhibitors to show that these contractions are dependent upon non-muscle myosin activity and, surprisingly, independent of gap junction activity. Finally, they develop a 3D hydrogel for the culturing of multiple organoids and found that they synchronize their contractile activities through interconnecting smooth muscle cells, suggesting that this model can be used to study the emergence of pacemaking activities. Overall, this study provides a relatively easy-to-establish organoid system that will be of use in studies examining the emergence of rhythmic peristaltic smooth muscle contractions and how these are regulated by interstitial cell interactions. However, further validation and quantification will be necessary to conclusively determine show the cellular composition of the organoids and how reproducible their behaviors are.

      Strengths:

      This work establishes a new self-organizing organoid system that can easily be generated from the muscle layers of the chick fetal hindgut to study the emergence of spontaneous smooth muscle cell contractility. A key strength of this approach is that the organoids seem to contain few cell types (though more validation is needed), namely smooth muscle cells (SMCs) and interstitial cells of Cajal (ICCs). These organoids are amenable to live imaging of calcium dynamics as well as pharmacological perturbations for functional assays, and since they are derived from developing tissues, the emergence of the interactions between cell types can be functionally studied. Thus, the gut contractile organoids represent a reductionist system to study the interactions between SMCs and ICCs in comparison to the more complex in vivo environment, which has made studying these interactions challenging.

      Thank you very much for the constructive comments.

      Weaknesses:

      The study falls short in the sense that it does not provide a rigorous amount of evidence to validate that the gut organoids are made of bona fide smooth muscle cells and ICCs. For example, only two "marker" proteins are used to support the claims of cell identity of SMCs and ICCs. At the same time, certain aspects of the data are not quantified sufficiently to appreciate the variance of organoid rhythmic contractility. For example, most contractility plots show the trace for a single organoid. This leads to a concern for how reproducible certain aspects of the organoid system (e.g. wavelength between contractions/rhythm) might be, or how these evolve uniquely over time in culture. Furthermore, while this study might be able to capture the emergence of ICC-SMC interactions as they related to muscle contraction and pacemaking, it is unclear how these interactions relate to adult gastrointestinal physiology given that the organoids are derived from fetal cells that might not be fully differentiated or might have distinct functions from the adult. Finally, despite the strength of this system, discoveries made in it will need to be validated in vivo. Thank you very much for the comments, which are helpful to improve our MS. In the revised version, we have additionally used antibody against desmin, known to be a maker for mature SMCs (new Fig 3B). The signal is seen only in the peripheral cells overlapping with the αSMA staining (line 169-170).

      Concerning the reproducibility, while contractility changes were shown for a representative organoid in the original version, experiments had been carried out multiple times, and consistent data were reproduced as already mentioned in the text of the first version of MS. However, we agree with this reviewer that it must be more convincing if we assess quantitatively. We have therefore conducted quantitative assessments of organoidal contractions and Ca<sup>2+</sup> transients (new Fig. 2B, new Fig. 4D, new Fig 5D, E, new Fig. 6B, new Fig. 7B, new Fig. 8C, new Fig. S2, S3). Details such as repeats of experiments and size of specimens are carefully described in the revised version (Figure legends)

      In particular, in place of contraction numbers/time, we have plotted “contraction intervals” between two successive peaks (Fig. 2B and others). Actually, with your suggestion, we have tried to perform a periodicity analysis of organoid contractions. Unfortunately, no clear value has been obtained, probably because the contractions/Ca<sup>2+</sup> transitions are not as “regularly periodical” as seen in conventional physics. This led us to perform the peak-interval analysis. Methods to quantify the contraction intervals are carefully explained in the revised version.

      As already mentioned in the “Our provisional responses” following the receipt of Reviewers’ comments, we agree that our organoids derived from embryonic hind gut (E15) might not necessarily recapitulate the full function of cells in adult. However, it has well been accepted in the field of developmental biology that studies with embryonic tissue/cells make a huge contribution to unveil complicated physiological cell functions. Nevertheless, we have carefully considered in the revised version so that the MS would not send misleading messages. We agree that in vivo validation of our gut contractile organoid must be wonderful, and this is a next step to go.

      Reviewer #3 (Public Review):

      Summary:

      The paper presents a novel contractile gut organoid system that allows for in vitro studying of rudimentary peristaltic motions in embryonic tissues by facilitating GCaMPlive imaging of Ca<sup>2+</sup> dynamics, while highlighting the importance and sufficiency of ICC and SMC interactions in generating consistent contractions reminiscent of peristalsis. It also argues that ENS at later embryonic stages might not be necessary for coordination of peristalsis.

      Strengths:

      The manuscript by Yagasaki, Takahashi, and colleagues represents an exciting new addition to the toolkit available for studying fundamental questions in the development and physiology of the hindgut. The authors carefully lay out the protocol for generating contractile gut organoids from chick embryonic hindgut, and perform a series of experiments that illustrate the broader utility of these organoids for studying the gut. This reviewer is highly supportive of the manuscript, with only minor requests to improve confidence in the findings and broader impact of the work. These are detailed below.

      Thank you very much for the constructive comments.

      Weaknesses:

      (1) Given that the literature is conflicting on the role GAP junctions in potentiating communication between intestinal cells of Cajal (ICCs) and smooth muscle cells (SMCs), the experiments involving CBX and 18Beta-GA are well-justified. However, because neither treatment altered contractile frequency or synchronization of Ca++ transients, it would be important to demonstrate that the treatments did indeed inhibit GAP junction function as administered. This would strengthen the conclusion that GAP junctions are not required, and eliminate the alternative explanation that the treatments themselves failed to block GAP junction activity.

      Thank you for these comments, and we agree. In the revised version, we have verified the drugs, CBX and 18b-GA, using dissociated embryonic heart cells in culture, a well-established model for the gap junction study (new Fig. S3D, line 237-239). Expectedly, both inhibitors abrogate the rhythmic beats of heart cells, and importantly, cells’ beats resume after wash-out of the drug.

      (2) Given that 5uM blebbistatin increases the frequency of contractions but 10uM completely abolishes contractions, confirming that cell viability is not compromised at the higher concentration would build confidence that the phenotype results from inhibition of myosin activity. One could either assay for cell death, or perform washout experiments to test for recovery of cyclic contractions upon removal of blebbistatin. The latter may provide access to other interesting questions as well. For example, do organoids retain memory of their prior setpoint or arrive at a new firing frequency after washout?

      We greatly appreciate these suggestions and also interesting ideas to explore! In the revised version, we have newly conducted washout experiments (new Fig. 6B) (10 µM drug is washed-out from culture medium), and found that contractions resume, showing that cell viability is not compromised at 10 µM concentration (line 257-259). Intriguingly, the resumed rhythm appears more regular than that before drug administration. Thus, the contraction rhythm of the organoid might be determined by cellcell interactions at any given time rather than by memory of their prior setpoint. This is an interesting issue we would like to further explore in the future. These issues, although potentially interesting, are not mentioned in the text of the revised version, since it is too early to interpret there observations.

      (3) Regulation of contractile activity was attributed to ICCs, with authors reasoning that Tuj1+ enteric neurons were only present in organoids in very small numbers (~1%).

      However, neuronal function is not strictly dependent on abundance, and some experimental support for the relative importance of ICCs over Tuj1+ cells would strengthen a central assumption of the work that ICCs the predominant cell type regulating organoid contraction. For example, one could envision forming organoids from embryos in which neural crest cells have been ablated via microdissection or targeted electroporation. Another approach would be ablation of Tuj1+ cells from the formed organoids via tetrodotoxin treatment. The ability of organoids to maintain rhythmic contractile activity in the total absence of Tuj1+ cells would add confidence that the ICCs are indeed the driver of contractility in these organoids.

      We agree. In the revised version, we have conducted TTX administration (new Fig. S2C). Changes in contractility by this treatment is not detected, supporting the argument that neural cells/activities are not essential for rhythmic contractions of the organoid (line 178-181).

      (4) Given the implications of a time lag between Ca++ peaks in ICCs and SMCs, it would be important to quantify this, including standard deviations, rather than showing representative plots from a single sample.

      In the revised version, we have elaborated a series of quantitative assessments as mentioned above (please see our responses to the “eLife assessments” at the beginning of these correspondences). The latency between Ca<sup>2+</sup> peaks in ICCs and SMCs is shown in new Fig. 4D, in which measured value is 700 msec-terraced since the time-lapse imaging was performed with 700 msec intervals (as already described in the first version).

      117 peaks for 14 organoids have been assessed (line 218).

      (5) To validate the organoid as a faithful recreation of in vivo conditions, it would be helpful for authors to test some of the more exciting findings on explanted hindgut tissue. One could explant hindguts and test whether blebbistatin treatment silences peristaltic contractions as it does in organoids, or following RCAS-GCAMP infection at earlier stages, one could test the effects of GAP junction inhibitors on Ca++ transients in explanted hindguts. These would potentially serve as useful validation for the gut contractile organoid, and further emphasize the utility of studying these simplified systems for understanding more complex phenomena in vivo.

      Thank you very much for insightful comments. We would love to explore these issues in near future. Just a note is that it was previously reported that Nifedipine silences peristaltic contractions in ex-vivo cultured gut (Chevalier et al., 2024; Der et al., 2000).

      (6) Organoid fusion experiments are very interesting. It appears that immediately after fusion, the contraction frequency is markedly reduced. Authors should comment on this, and how it changes over time following fusion. Further, is there a relationship between aggregate size and contractile frequency? There are many interesting points that could be discussed here, even if experimental investigation of these points is left to future work.

      It would indeed be interesting to explore how cell communications affect/determine the contraction rhythm, and our novel organoids must serve as an excellent model to address these fundamental questions. We have observed multiple times that when two organoids fuse, they undergo “pause”, and resume coordinated contractions as a whole, and we have mentioned such notice briefly in the revised version (line 282). To know what is going on during this pause time should be tempting. In addition, we have an impression that the larger in size organoids grow, the slower rhythm they count. We would love to explore this in near future.

      (7) Minor: As seen in Movie 6 and Figure 6A, 5uM blebbistatin causes a remarkable increase in the frequency of contractions. Given the regular periodicity of these contractions, it is a surprising and potentially interesting finding, but authors do not comment on it. It would be helpful to note this disparity between 5 and 10 uM treatments, if not to speculate on what it means, even if it is beyond the scope of the present study to understand this further.

      We assume that the increase in the frequency of contractions at 5 µM might be due to a shorter refractory period caused by a decreasing magnitude (amplitude) of contraction. We have made a short description in the revised text (line 256-257).

      (8) Minor: While ENS cells are limited in the organoid, it would be helpful to quantify the number of SMCs for comparison in Supplemental Figure S2. In several images, the number of SMCs appears quite limited as well, and the comparison would lend context and a point of reference for the data presented in Figure S2B.

      In the revised version, the number of SMCs has been counted and added in Fig. S2B. Contrary to that SMCs are more abundant than ICCs in an intact gut, the proportion is reversed in our organoid (line 181-183). It might due to treatments during cell dissociation/plating.

      (9) Minor: additional details in the Figure 8 legend would improve interpretation of these results. For example, what is indicated in orange signal present in panels C, G and H? Is this GCAMP?

      We apologize for this confusion. In the revised version, we have added labeling directly in the photos of new Fig. 9 (old Fig. 8). For C, G and H, the left photo is mRuby3+GCaMP6s, and the right one is GCaMP6s only.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      I have a few comments for the authors to consider:

      (1) Figure 4C: The authors propose that calcium signals propagate from ICC to SMC based on the results presented in this figure. While it is observed that the peak of the calcium signal in ICC precedes that in SMC, it's worth noting that the onset of the rise in calcium signals occurs simultaneously in ICC and SMC. Doesn't this suggest that they are activated simultaneously? The latency observed for the peaks of calcium signals could reflect different kinetics of the rise in calcium concentration in the two types of cells rather than the order of calcium signal propagation.

      We greatly appreciate these comments. We have re-examined kinetics of GCaMP signals in ICC and SMC, but we did not succeed in validating rise points precisely. We agree that the possibility that the rise in calcium signals could be occurring simultaneously. To clarify these issues, analyses with higher resolution is required, such as using GCaMP6f or GCaMP7/8. Nevertheless, the disappearance of the latency of Ca<sup>2+</sup> peak by CBX implies a role of gap junction in ICC to SMC signaling. In the revised version, we replaced the wording “rise” by “peak” when the latency is discussed.

      (2) Figure 5C: The specific elimination of the latency in the calcium signal peaks between ICC and SMC is interesting. However, I am curious about how gap junction inhibitors specifically eliminate the latency between ICC and SMC without affecting other aspects of calcium transients in these cells, such as amplitude and synchronization among ICCs and/or SMCs. Readers of the manuscript would expect some discussion on possible mechanisms underlying this specificity. Additionally, I wonder if the elimination of the latency was observed consistently across all samples examined. The authors should provide information on the frequency and number of samples examined, and whether the elimination occurs when 18-beta-GA is used.

      In the revised version, we have elaborated quantitative demonstration. For the effects by CBX on latency or Ca<sup>2+</sup> peaks, a new graph has been added to new Fig 5, in which 100 µM eliminated the latency. Intriguingly, the latency appears to be attributed to a gap junction that is not inhibited by18-beta-GA (please see new Fig. S3E). As already mentioned above, inhibiting activity of both CBX and 18-beta-GA has been verified using dissociated cells of embryonic heart, a popular model for gap junction studies.

      At present, we do not know how gap junction(s) contribute to the latency of Ca<sup>2+</sup> peaks without affecting synchronization among ICCs and/or SMCs (we have not addressed amplitude of the oscillation in this study). Actually, it was surprising to us to find that GJ’s contribution is very limited. We do not exclude the importance of GJs, and currently speculate that GJs might be important for the initiation of contraction/oscillation signals, whereas the requirement of GJs diminishes once the ICC-SMC interacting rhythm is established. What we observed in this study might be the synchronization signals AFTER these interactions are established (Day 7 of organoidal culture). Upon the establishment, it is possible that mechanical signaling elicited by smooth muscles’ contraction might become prominent as a mediator for the (stable) synchronization, as implicated by experiments with blebbistatin and Nifedipin, the latter being newly added to the revised version (new Fig. 7). We have added such speculation, although briefly in Discussion (line 374-377)

      (3) Figure 6: The significant effects of blebbistatin on calcium dynamics in both ICC and SMC are intriguing. However, since only one blocker is utilized, the specificity of the effects is unclear. If other blockers for muscle contraction are available, they should be employed. Considering that a rise in calcium concentration precedes contraction, calcium transients should persist even if muscle contraction is inhibited. One concern is whether blebbistatin inadvertently rendered the cells unhealthy. The authors should demonstrate at least that contraction and calcium transients recover after removal of the drug. The frequency and number of samples examined should be shown, as requested for Figure 5C above.

      Thank you for these critical comments. A possible harmfulness of the drugs was also raised by other reviewers, and we have therefore conducted wash-out experiments in the revised version (new Fig. 6B). Contractions resume after wash-out showing that cell viability is not compromised at 10 µM concentration. The number of samples examined has been described more explicitly in the revised version. Regarding the blocker of SMC, we have newly carried out pharmacological assays using nifedipine, a blocker of a L-type Ca<sup>2+</sup> channel known to operate in smooth muscle cells (new Fig 7) (Chevalier et al., 2024; Der et al., 2000). As already explained in the “Responses to eLife assessment”, the treatment abrogated ICCs’ rhythm and synchronous Ca<sup>2+</sup> transients between ICCs and SMCs, further corroborating our model that not only ICC-to-SMC interactions but also SMC-to-ICC feedback signals are operating to achieve coordinated/stable rhythm of gut contractile organoids of Day 7 culture (please also see our responses shown above for Comment (2)).

      Reviewer #2 (Recommendations For The Authors):

      Major:

      (1) The claim that organoids contain functional SMCs and ICCs is insufficient as it currently relies on only c-Kit and aSMA antibodies. This conclusion could be additionally supported by staining with other markers of contractile smooth muscle (e.g. TAGLN and MYH14) and an additional accepted marker of ICCs (e.g. ANO1/TMEM16). Moreover, it should be demonstrated whether these cells are PDGFRA+, as PDGFRA is a known marker of other mesenchymal fibroblast cell types. These experiments would additionally rule out whether these cells were simply less differentiated myofibroblasts. Given that there might not be available antibodies that react with chicken protein versions, the authors could support their conclusions using alternative approaches, such as fluorescent in situ hybridization. A more thorough approach, such as single-cell RNA sequencing to compare the cell composition of the in vitro organoids to the in vivo colon, would fully justify the use of these organoids as a system for studying in vivo cell physiology.

      With these suggestions provided, we have newly stained contractile organoids with anti-desmin antibody, known to be a marker for differentiated SMCs. As shown in new Fig. 3B, desmin-positive cells perfectly overlapped with aSMA-staining, indicating that the peripherally enclosing cells are SMCs. Regarding the interior cells, as this Reviewer concerned, there are no antibodies against ANO1/TMEM16 which are available for avian specimens. The anti- c-Kit antibody used in this study is what we raised in our hands by spending years (Yagasaki et al., 2021)), in which the antibody was carefully validated in intact guts of chicken embryos by multiple methods including Western Blot analyses, immunostaining, and in situ hybridization. We have attempted several times to perform organoidal whole-mount in situ hybridization for expression of PDGFRα, but we have not succeeded so far. In addition, as explained to the Editor, the very unhealthy condition of purchased eggs these past 7 months did not allow us to continue any further. We are planning to interrogate cell types residing in the central area of the organoid, results of which will be reported in a separate paper in near future.

      (2) The key ICC-SMC relationship and physiological interaction seems to arise developmentally, but the mechanisms of this transition are not well defined (Chevalier 2020). To further support the claim that ICC-SMC interactions can be interrogated in this system, this study would benefit from establishing organoids at distinct developmental stages to (a) show that they have unique contractile profiles, and (b) demonstrate that they evolve over time in vitro toward an ICC-driven mechanism.

      We agree with these comments. We tried to prepare gut contractile organoids derived from different stages of development, and we had an impression that slightly younger hindguts are available for the organoid preparations. In addition, not only the hindgut, but also midgut and caecum also yield organoids. However, since formed organoids derived from these “non-E15 hindgut” vary substantially in shapes, contraction frequencies/amplitudes etc., we are currently not ready to report these preliminary observations. Instead, we decided to optimize and elaborate in vitro culture conditions by focusing on the E15 hindgut, which turned out to be most stable in our hands. Nevertheless, it is tempting to see how organoid evolves over time during gut development.

      (3) This manuscript would be greatly enhanced by a functional examination of the prospective organoid ICCs. For example, the authors could test whether the c-Kit inhibitor Imatinib, which has previously been used to impair ICC differentiation and function in the developing chick gut (Chevalier 2020), has an effect on contractility at different stages.

      Following the paper of (Chevalier 2020), we had already conducted similar experiments with Imatinib in the culture with our organoids, but we did not see detectable effects. In that paper, the midgut of younger embryos was used, whereas we used E15 hindgut to prepare organoids. It would be interesting to see if we add Imanitib earlier during organoidal formation, and this is a next step to go.

      (4) It is claimed that there is a 690s msec delay in SMC spike relative to ICC spike, however, it is unclear where this average is derived from and whether the organoid calcium trace shown in Figure 4C is representative of the data. The latency quantification should be shown across multiple organoids, and again in the case of carbenoxolone treatment, to better understand the variations in treatment.

      We apologize that the first version failed to clearly demonstrate quantitative assessments. In the revised version, we have elaborated quantitative assessments (117 peaks for 14 organoids) (line 216-218). In new Fig. 4D, measured value is 700 msecterraced since as already mentioned in the first version, the time-lapse imaging was performed with 700 msec intervals.

      (5) As above, a larger issue is that only single traces are shown for each organoid. This makes it challenging to understand the variance in contractile properties across multiple organoids. While contraction frequencies are shown several times, the manuscript would benefit from additional quantifications, such as rhythm (average wavelength between events) in control and perturbed conditions.

      We have substantially elaborated quantitative assessments (please also see our responses to the “Public Review”). In particular, in place of contraction numbers/time, we have plotted “contraction intervals” between two successive peaks (Fig. 2B and others). Actually, we have tried to perform a periodicity analysis of organoid contractions. Unfortunately, no clear value has been obtained, probably because the contractions/Ca<sup>2+</sup> transitions are not as “regularly periodical” as seen in conventional physics. This led us to perform the peak-interval analysis. Methods to quantify the contraction intervals are carefully explained in the revised version.

      (6) The synchronicity observed between ICCs and SMCs within the organoid is interesting, and should be emphasized by making analyses more quantitative so as to understand how consistent and reproducible this phenomenon is across organoids. Moreover, one of the most exciting parts of the study is the synchronicity established between organoids in the hydrogel system, but it is insufficiently quantified. For example, how rapidly is pacemaking synchronization achieved?

      As we replied above to (5), and described in the responses to the “Public Review”, we have substantially elaborated quantitative assessments in the revised version. Concerning the synchronicity between ICCs and SMCs, our data explicitly show that as long as the organoid undergoes healthy contraction, they perfectly match their rhythm (Fig. 4) making it difficult to display quantitatively. Instead, to demonstrate such synchronicity more convincingly, we have carefully described the number of peaks and the number of independent organoids we analyzed in each of Figure legends. In the experiments with hydrogels, the time required for two organoids to start/resume synchronous contraction varies greatly. For example, for the experiment shown in new Fig 9F, it takes 1 day to 2 days for cells crawling out of organoids and cover the surface of the hydrogel. In the experiments shown in new Fig. 8, two organoids undergo “pause” before resuming contractions. In the revised version, we have briefly mentioned our notice and speculation that active cell communications take place during this pausing time, (line 282-283 in Result and line 437-439 in Discussion). We agree with this reviewer saying that the pausing time is potentially very interesting. However, it is currently difficult to quantify these phenomena. More elaborate experimental design might be needed.

      (7) Smooth muscle layers in vivo are well organized into circular and longitudinal layers. To establish physiological relevance, the authors should demonstrate if these organoids have multiple layers (though it looks like just a single outer layer) and if they show supracellular organization across the organoid.

      The immunostaining data suggest that peripherally lining cells are of a single layer, and we assume that they might be aligned in register with contracting direction. However, to clarify these issues, observation with higher resolution would be required.

      (8) To further examine whether the organoids contain true functional ICCs, the authors should test whether their calcium transients are impacted by inhibitors of L-type calcium channels, such as nifedipine and nicardipine. These channels have been demonstrated to be important for SMCs but not ICCs, so one might expect to see continued transients in the core ICCs but a loss of them in SMCs (Lee et al., 1999; PMID: 10444456)

      We appreciate these comments. We have accordingly conducted new experiments with Nifedipine. Contrary to the expectation, Nifedipine ceases not only organoidal contractions, but also ICC activities (and its resulting synchronization) (new Fig. 7). These findings actually corroborate our model already mentioned in the first version that ICCs receive mechanical feedback from SMC’s contraction to stably maintain their oscillatory rhythm. We believe that the additional findings with Nifedipine have improved the quality of our paper. Concerning the central cells in the organoid, we have additionally used anti-desmin antibody known to mark differentiated SMCs. Desmin signals perfectly overlap with those of aSMA in the peripheral single layer, supporting that the peripheral cells are SMCs and central cells are ICCs. The anti c-Kit antibody used in this study is what we raised in our hands by spending years (Yagasaki et al., 2021)), in which the antibody was carefully validated in intact guts of chicken embryos by multiple methods including Western Blot analyses, immunostaining, and in situ hybridization.

      ANO1/TMEM16 are known to stain ICCs in mice. Antibodies against ANO1/TMEM16 available for avian specimens are awaited.

      (9) Despite Tuj1+ enteric neurons only making up a small fraction of the organoids, the authors should still functionally test whether they regulate any aspect of contractility by treating organoids with an inhibitor such as tetrodotoxin to rule out a role for them.

      Thank you for these advices, which are also raised by other reviewers. We have conducted TTX administration (new Fig. S2C). Changes in contractility by this treatment is not detected, supporting the argument that neural cells/activities are not essential for rhythmic contractions of the organoid (line 178-181).

      (10) Finally, the manuscript is written to suggest that the focus of the study is to establish a system to interrogate ICC-SMC interactions in gut physiology and peristalsis. However, the organoids designed in this study are derived from the fetal precursors to the adult cell types. Thus, they might not accurately portray the adult cell physiology. I don't believe that this is a downfall, but rather a strength of the study that should be emphasized. That is, the focus could be shifted toward stressing the power of this new system as a reductionist, self-organizing model to examine the developmental emergence of contractile synchronization in the intestine - in particular that arising through ICC-SMC interactions.

      We appreciate these advices. In the revised MS, we are careful so that our findings do not necessarily portray the physiological functions in adult gut.

      Minor:

      More technical information could be used in the methods:

      (1) What concentration of Matrigel is used for coating, and what size were the wells that cells were deposited into?

      We have added, “14-mm diameter glass-bottom dishes (Matsunami, D11130H)” and “undiluted Matrigel (Corning, 354248) at 38.5°C for 20 min” (line 471473).

      (2) How were organoids transferred to the hydrogels? And were the hydrogels coated?

      We have added “Organoids were transferred to the hydrogel using a glass capillary” (line 560-561).

      (3) Tests for significance and p values should be added where appropriate (e.g. Figure S3B).

      We have added these in Figure legend of new Fig. S3.

      Reviewer #3 (Recommendations For The Authors):

      This is an exciting study, and while the majority of our comments are minor suggestions to improve the clarity and impact of findings, it would be important to verify the effective disruption of GAP junction function with CBX or 18Beta-GA treatments before concluding they are not required for coordination of contractility and initiation by ICCs. It is possible that sufficient contextual support exists in the literature for the nature of treatments used, but this may need to be conveyed within the manuscript to allay concerns that the results could be explained by ineffective inhibition of GAP junctions.

      Thank you very much for these advices. In the revised version, we have newly carried out experiments with dissociated embryonic heart cells cultured in vitro, a model widely used for gap junction studies (Fig. S3D). Both CBX or 18b-GA exert efficient inhibiting activity on contractions of heart cells. We have added the following sentence, “The inhibiting activity of the drugs used here was verified using embryonic heart culture (line 237-239)”.

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Reviewer #1 (Public Review):

      Comments on revisions)

      The authors have done a good job at revising the manuscript to put this work into the context of earlier work on brainstem central pattern generators.

      Thank you.

      I still believe the case for the method is not as convincing as it would have been if the method had been validated first on oscillations produced by a known CPG model. Why would the inference of synaptic types from the model CPG voltage oscillations be predetermined? Such inverse problems are quite complicated and their solution is often not unique or sufficiently constrained. Recovering synaptic weights (or CPG parameters) from limited observations of a highly nonlinear system is not warranted (Gutenkunst et al., Universally sloppy parameter sensitivities in systems biology models, PLoS Comp. Biol. 2007; www.doi.org/10.1371/journal.pcbi.0030189) especially when using surrogate biological models like Hodgkin-Huxley models.

      The model of the CPG is irrelevant for such a test of validity because what we reconstruct are postsynaptic conductances of an individual neuron. The network creates a periodic input to this neuron and thus forms a periodic pattern of excitatory and inhibitory conductances. The nature of this input, whether autonomously generated or created artificially (say by periodic optogenetic stimulation), is generally not important. To illustrate this, we used a one-compartment conductance-based (Hodgkin-Huxley style) model neuron incorporating a certain common set of channels (fast sodium (I<sub>NaF</sub>), potassium delayed rectifier (I<sub>Kdr</sub>), persistent sodium (I<sub>NaP</sub>), calcium-dependent potassium (I<sub>KCa</sub>), and cationic non-specific current (I<sub>CAN</sub>)), as well as excitatory and inhibitory synaptic channels whose conductances were implemented as predefined periodic functions. The test suggested by the reviewer would be to implement a current-step protocol similar to the experiments and apply our technique to see if the reconstructed conductance profiles match those predefined functions. Below we show the reconstruction steps for the following arbitrarily chosen pattern:

      𝑔<sub>𝐸𝑋𝐶</sub>(𝑡) /𝑔<sub>𝐿𝐸𝐴𝐾</sub> = 0.1(1 + sin(π𝑡)) and 𝑔<sub>𝐼𝑁𝐻</sub>(𝑡)/𝑔<sub>𝐿𝐸𝐴𝐾</sub> = 0.1 (1 + cos(π𝑡)). Author response image 1 below shows the baseline activity of this model neuron in the absence of the injected current.

      Author response image 1.

      Then we applied a current-step protocol with four steps producing different levels of hyperpolarization and applied our method by calculating the total conductance using linear regression (see the current-voltage plots below) and then decomposing it into the excitatory and inhibitory components.

      Author response image 2.

      As one can see, the reconstructed conductances in Author response image 3 below are nearly identical to their theoretical profiles. This is not surprising because all voltage-dependent currents in the model neuron were inactive in the range of voltages matching our experimental conditions. Therefore, the model could be reduced to just the leak current, synaptic currents and the injected current, which matches precisely the model we used in our manuscript.

      Author response image 3.

      In p.2, the edited section refers to the interspike interval being much smaller than the period of the network. More important is to mention the relationship between the decay time of inhibitory synapses and the period of the network.

      This interpretation misunderstands the focus of our method. The edited sections (including in the theory section of Results) highlight the conditions under which the capacitive current becomes negligible, emphasizing that the membrane time constant must be much smaller than the network oscillation period. This separation of time scales ensures that the membrane potential adjusts quickly to changes in postsynaptic conductance, rendering the capacitive current insignificant over the network’s rhythm. In contrast, the synaptic decay time governs how presynaptic inputs are transduced into postsynaptic conductances—a process relevant to understanding synaptic dynamics but not directly tied to our method’s core objective. Our approach reconstructs postsynaptic conductances from intracellular recordings, not presynaptic spike trains. While interpreting these conductance profiles in terms of specific synaptic connections would indeed involve synaptic decay dynamics, such an analysis exceeds the scope of our paper. Thus, the condition emphasized in the edited sections—concerning the membrane time constant and network period—is the critical one for our method’s applicability, and the synaptic decay time, while relevant to broader synaptic modeling, does not undermine our conclusions.

      We have added the requirement for a much smaller membrane time constant in the Introduction on page 2. The Results theory section already incorporates an extensive discussion of this requirement.

      Comments from the editors:

      We apologize for the delay in coming to this decision, but there was quite a bit of post-review discussion that needed to be resolved. There are two issues that the reviewers agree should be addressed. They remain unconvinced that the simplifying assumptions of the approach are valid. 1) The main issue with the phase argument is that the biological synaptic conductance depends on time and not on the phase of the respiratory cycle as mentioned in the first round of reviews. The approximation g(t)=g(phase) seems to be far too simple to be biologically realistic.

      As we elaborate below, time and phase are fundamentally and mathematically equivalent representations of the same underlying dynamics in a periodic system, and thus, a phase-based representation—where conductances are expressed as functions of the cycle’s phase—is a justified and effective approach for capturing their behavior. We have added this explanation to the theory section of Results. Below are the bases for our assertion.

      In a periodic system, such as the respiratory CPG, the system’s behavior repeats at regular intervals, defined by a period T. For the respiratory cycle in our experimental preparation, this period is approximately 3–4 seconds, encompassing phases like inspiration, post-inspiration, and expiration. In such systems:

      Time (t) is a continuous variable that progresses linearly.

      Phase (φ) represents the position within one cycle, typically normalized between 0 and 1 (or 0 to 2π in some contexts). It can be mathematically related to time via: φ(t) = (t mod T)/T, where (t mod T) is the time elapsed within the current cycle.

      Because the system is periodic, any variable that repeats with period T—such as synaptic conductance in a rhythmically active network—can be expressed as a function of either time or phase. Specifically, if g(t) is periodic with period T, then g(t) = g(t+T). This periodicity allows us to redefine g(t) in terms of phase: g(t) = g(φ(t)), where φ(t) maps time onto a repeating cycle. Thus, in a periodic system, time and phase are fundamentally equivalent representations of the same underlying dynamics. Saying that synaptic conductance depends on phase is mathematically equivalent to saying it depends on time in a periodic manner.

      In a rhythmically active network like the respiratory central pattern generator (CPG), the synaptic conductances, regardless of the specific mechanisms by which they are formed, exhibit periodicity that matches the network’s oscillatory cycle. This occurs because the conductances are driven by the repetitive activity of presynaptic neurons, which are synchronized to the network’s overall rhythm. As a result, the synaptic conductances vary with the same period as the network, making a phase-based representation—where conductances are expressed as functions of the cycle’s phase—a justified and effective approach for capturing their behavior. In our study, we utilized the in situ arterially perfused brainstem-spinal cord preparation from mature rats, which is known to produce a highly periodic respiratory rhythm. To ensure the consistency of this periodicity, we carefully selected recordings where the coefficient of variation of the respiratory cycle period was less than 10%, as outlined in our methods. This strict selection criterion confirms the stability and regularity of the rhythm, supporting the validity of using a phase representation to analyze the synaptic conductances.

      (2) Figure S1 is problematic. First, the currents injected appear to be infinitesimally small.

      There was a typo in the current units, which should be nA and not pA, as evident from the injected current–membrane potential plots in Figure 1B. Figure S1 has been corrected.

      Second, the input resistance is completely independent of voltage, as though there was little or no contribution from hyperpolarization activated currents, which would be surprising.

      While hyperpolarization-activated currents are indeed present in many neuronal types and could theoretically affect input resistance, our data consistently show linear I-V relationships across the voltage range tested (-60 to -100 mV) for the neurons analyzed (see Figure S1 and Author response image 4-9 below). This linearity suggests that, under our experimental conditions, the contribution of voltage-dependent currents, such as h-currents, is negligible within this range.

      Additionally, we now indicate in the manuscript in the theory section of Results how the presence of significant hyperpolarization-activated h-currents would impact our synaptic conductance reconstruction method. In current-clamp recordings, non-linearity from h-currents could introduce voltage-dependent changes in total conductance unrelated to synaptic inputs, potentially skewing the reconstruction. However, this concern does not apply to voltage-clamp recordings, where the membrane potential is held constant, eliminating contributions from voltage-dependent intrinsic currents. As strong evidence of the minimal influence of h-currents, we directly compared synaptic conductance reconstructions using both current-clamp and voltage-clamp protocols in a subset of neurons. The results from these two approaches were highly consistent, indicating that h-currents do not significantly affect our findings. This robustness across experimental methods reinforces the reliability of our conclusions.

      Together, the linear I-V relationships and the agreement between current- and voltage-clamp reconstructions provide compelling evidence that our method accurately captures synaptic conductances without interference from h-currents.

      Typical examples of I-V relationships for each respiratory neuron firing phenotype:

      Author response image 4.

      ramp-I

      Author response image 5.

      pre-I/I

      Author response image 6.

      post-I

      Author response image 7.

      aug-E

      Author response image 8.

      early-I

      Author response image 9.

      late-I

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The study aims to create a comprehensive repository about the changes in protein abundance and their modification during oocyte maturation in Xenopus laevis.

      Strengths:

      The results contribute meaningfully to the field.

      Weaknesses:

      The manuscript could have benefitted from more comprehensive analyses and clearer writing. Nonetheless, the key findings are robust and offer a valuable resource for the scientific community.

      We would like to thank the reviewer for his/her positive feedback on our article. The public review points out that "The manuscript could have benefitted from more comprehensive analyses and clearer writing." We have rewritten several sections and provided more detailed explanations of the analysis and interpretation of some data (see below for details). We have also followed all of the reviewer's recommendations, some of which specifically highlighted areas lacking clarity. We would also like to thank the reviewer for pointing out some errors, for which we apologize, and which have now been corrected. We sincerely appreciate the reviewer's thorough work, as it has greatly enhanced the clarity and precision of the manuscript.

      Reviewer #2 (Public review):

      Summary:

      The authors analyzed Xenopus oocytes at different stages of meiosis using quantitative phosphoproteomics. Their advanced methods and analyses revealed changes in protein abundances and phosphorylation states to an unprecedented depth and quantitative detail. In the manuscript they provide an excellent interpretation of these findings putting them in the context of past literature in Xenopus as well as in other model systems.

      Strengths:

      High quality data, careful and detailed analysis, outstanding interpretation in the context of the large body of the literature.

      Weaknesses:

      Merely a resource, none of the findings are tested in functional experiments.

      I am very impressed by the quality of the data and the careful and detailed interpretation of the findings. In this form the manuscript will be an excellent resource to the cell division community in general, and it presents a very large number of hypotheses that can be tested in future experiments. Xenopus has been and still is a popular and powerful model system that led to critical discoveries around countless cellular processes, including the spindle, nuclear envelope, translational regulation, just to name a few. This also includes a huge body of literature on the cell cycle describing its phosphoregulation. It is indeed somewhat frustrating to see that these earlier studies using phosphomutants and phospho-antibodies were just scratching the surface. The phosphoproteomics analysis presented here reveals much more extensive and much more dynamic changes in phosphorylation states. Thereby, in my opinion, this manuscript opens a completely new chapter in this line of research, setting the stage for more systematic future studies.

      We thank the reviewer for his/her extremely positive comments. The public review points out that "none of the findings are tested in functional experiments." This is entirely accurate. We focused our work on obtaining the highest quality proteomic and phosphoproteomic data possible, and then sought to highlight these data by connecting them with existing functional data from the literature. This approach has opened up research avenues with enormous, previously unforeseen potential, in a wide range of biological fields (cell cycle, meiosis, oogenesis, embryonic development, cell biology, cellular physiology, signaling, evolution, etc.). We chose not to delay publication by experimentally investigating the narrow area in which we are specialists (meiotic maturation), while our data offer a vast array of research opportunities across various fields. Our goal was, therefore, to present this extensive dataset as a resource for different scientific communities, who can explore their specific biological questions using our data. This is why we submitted our article to the "Repository" section of eLife. Nevertheless, in the context of the comparative analysis of the mouse and Xenopus phosphoproteomes performed at the reviewer’s request, we felt it was important to complement this new section with functional experiments that not only validate the proteomic data but also provide new insights into certain proteins and their regulation by Cdk1 (new paragraph lines 824-860 and new Figure 9).

      We are also grateful to the reviewer for the recommendation to improve the manuscript by including more comparisons between our Xenopus data and those from other systems. We have followed this suggestion (see below), which has significantly enriched the article (new paragraph lines 824-860 and new Figure 9).

      Reviewer #3 (Public review):

      Summary:

      The authors performed time-resolved proteomics and phospho-proteomics in Xenopus oocytes from prophase I through the MII arrest of the unfertilized egg. The data contains protein abundance and phosphorylation sites of a large number set of proteins at different stages of oocyte maturation. The large sets of the data are of high quality. In addition, the authors discussed several key pathways critical for the maturation. The data is very useful for the researchers not only researchers in Xenopus oocytes but also those in oocyte biology in other organisms.

      Strengths:

      The data of proteomics and phospho-proteomics in Xenopus oocyte maturation is very useful for future studies to understand molecular networks in oocyte maturation.

      Weaknesses:

      Although the authors offered molecular pathways of the phosphorylation in the translation, protein degradation, cell cycle regulation, and chromosome segregation. The author did not check the validity of the molecular pathways based on their proteomic data by the experimentation.

      We thank the reviewer for his/her positive comments. The public review points out that "The author did not check the validity of the molecular pathways based on their proteomic data by the experimentation." This is entirely accurate. We focused our work on obtaining the highest quality proteomic and phosphoproteomic data possible, and then sought to highlight these data by connecting them with existing functional data from the literature. This approach has opened up research avenues with enormous, previously unforeseen potential, in a wide range of biological fields (cell cycle, meiosis, oogenesis, embryonic development, cell biology, cellular physiology, signaling, evolution, etc.). We chose not to delay publication by experimentally investigating the very narrow area in which we are specialists (meiotic maturation), while our data offer a vast array of research opportunities across various fields. Our goal was, therefore, to present this extensive dataset as a resource for different scientific communities, who can explore their specific biological questions using our data. This is why we submitted our article to the "Repository" section of eLife. Nevertheless, in the context of the comparative analysis of the mouse and Xenopus phosphoproteomes performed at the reviewer’s request, we felt it was important to complement this new section with functional experiments that not only validate the proteomic data but also provide new insights into certain proteins and their regulation by Cdk1 (new paragraph lines 824-860 and new Figure 9).

      We have also followed all of the reviewer's recommendations and thank him/her, as the suggestions have significantly enhanced the manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Fig. 1 -> In the Figure legend "mPRβ" is called "mPRb". In the Figure, it is indicated that PKA substrates are always activated by the phosphorylation. As the relevant substrates and the mode-of-action of the Arpp19 phosphorylation are not clear at the moment, this seems to be preliminary. It could for example also be conceivable that PKA phosphorylation inhibits a translation activator. In addition, the PG-dependent translation of RINGO/Speedy should be included in the model.

      We fully agree with the reviewer. PKA substrates can either be activators of the Cdk1 activation pathway, which are inhibited by phosphorylation by PKA, or repressors of the same pathway, which are activated by phosphorylation by PKA. This is now illustrated in the new Fig. 1. In addition, we have also included RINGO/Speedy in the model and in the text (lines 78-79) and corrected "mPRb" in the legend.

      (2) Lane 51-52 -> it is questionable if the meiotic divisions can be called "embryonic processes"

      We agree with the reviewer comment, and we have removed the word “embryonic”.

      (3) Lane 53 and lane 106-107 -> recent data have indicated that transcription already starts during cell cycle 12 and 13 in most cells (e.g. Blitz and Cho: Control of zygotic genome activation in Xenopus (2021))

      We apologize for this mistake. The text has been corrected and the reference added (lines 53 and 107).

      (4) Lane 61-62 -> "MI" and "MII" are given as abbreviation for "first and second meiotic spindle"

      The text has been clarified to explain that MI is referred to metaphase I and MII stands for metaphase II (lines 61-64).

      (%) Lane 131-132 -> "single-cell" is mentioned redundantly in this sentence.

      The sentence has been corrected (lines 131-132).

      (6) Fig. 2B -> it is not explained what is plotted as "Average levels" on the x-Axis. Is it the average of expression over all samples or at a given time point? Are the values given as a concentration or are the values normalized? If so, how were they normalized?

      We agree with the reviewer comment that “Average levels” may have been unclear. In the new Fig. 2B, we have re-plotted the graph using the average protein concentration during meiosis, measured as described in the Methods section.

      (7) In Fig. 2-supplement 3E -> from the descriptions it is not entirely clear to me what the difference to the data in Fig. 2B is?

      We thank the reviewer for his/her question regarding the relationship between the data in Fig. 2B and Fig. 2-supplement 3E. We confirm that the raw data visualized in Fig. 2-supplement 3E are the same as those in Fig. 2B. However, in Fig. 2-supplement 3E, the data are color-coded differently to highlight the number of proteins whose concentrations change during meiotic divisions, based on the threshold adopted. The legend of Fig. 2-supplement 3E has been modified to clarify this point.

      (8) Lane 225-226 -> Kifc1 is a minus-end directed motor

      This mistake has been corrected (lines 232-233).

      (9) Lane 271 -> Serbp1, here mentioned to be involved in stabilization of mRNAs, has also been implicated in the regulation of ribosomes (e.g. Leesch et al. 2023). Regarding the overall topic of this manuscript, this could be mentioned as well.

      We agree with the referee that the important role of Serbp1 in the control of ribosome hibernation needs to be mentioned. We have included this point in the revised manuscript together with the reference (lines 277-279).

      (10) Lane 360-363 -> it is mentioned that APPL1 and Akt2 act "to induce meiosis". Furthermore, in the Nader et al. 2020 paper, Akt2 phosphorylation is reported to happen within 30min after PG treatment. In the present work, they only seem to get phosphorylated when Cdk1 is activated. Is there an explanation for this discrepancy?

      Indeed, Nader et al. (2020) indicate that Akt2 is phosphorylated on Ser473 (actually, they should have mentioned Ser474, which is the phosphorylated residue on Akt2; Ser473 corresponds to the numbering of Akt1) between 5 and 30 minutes post-Pg, which supports their hypothesis of an early role for this kinase. However, these conclusions should be taken with caution, considering that their functional experiment using antisense against Akt2 depletes only 25% of the protein, the antibody used to visualize Akt2 phosphorylation also recognizes phosphorylated Akt1 and Akt3, and they did not analyze phosphorylation of the protein after 30 minutes. Therefore, we cannot determine whether the level observed at 30 minutes represents a maximum or if it is just the onset of the phosphorylation that peaks later, possibly after activation of Cdk1, for example.

      Regarding our measurements: we clearly observe phosphorylation of Akt2 following Cdk1 activation on Ser131. We did not detect Akt2 phosphorylation on Ser474, but since our measurements started 1 hour post-Pg, this protein may have returned to a dephosphorylated state on Ser474.

      Therefore, the observations of Nader et al. and ours involve different residues and different phosphorylation kinetics, Nader et al. limiting their analysis to the first 30 minutes, whereas we started at 1 hour.

      We have revised the manuscript text to make these aspects clearer (lines 387-392).

      (11) Fig. 3B -> it could be made clearer in the Figure that all these sites belong to class I

      A title “Class I proteins” has been added in Fig. 3B to clarify it.

      (12) Lane 433-434 -> the authors write that the proteomic data of this study confirm that PATL1 is accumulating during meiotic maturation. However, in Fig. 2B PATL1 is not among the significantly enriched proteins.

      We apologize for this error. Indeed, PATL1 protein is not significantly enriched. The text has been corrected (lines 461-465).

      (13) Fig. 4B -> Zar2 is color-coded to increase in abundance. This is clearly different to published results and what is shown in Fig. 2B of this manuscript.

      Indeed, our dataset shows that the quantity of Zar2 decreases. This does not appear anymore in Figure 2B since Zar2 average concentration cannot be estimated. We made an error in the color coding, which has now been corrected in Figure 4B.

      (14) Lane 442-444 -> it might be worth mentioning that the interaction between CPEB1 and Maskin, and thus probably its role in regulation of translation, could not be reproduced in other studies (Minshall et al.: CPEB interacts with an ovary-specific eIF4E and 4E-T in early Xenopus oocytes (2007) or Duran-Arque et al.: Comparative analyses of vertebrate CPEB proteins define two subfamilies with coordinated yet distinct functions in post-transcriptional gene regulation (2022)).

      This clarification is now mentioned in the text, supported by the two references that have been added (lines 471-477).

      (15) Lane 483-485 -> The meaning of these sentences is not entirely clear to me. What exactly is the similarity with the function of Emi1? What does "...binding of Cyclin B1..." mean (binding to which other protein?). What is the similarity between Emi1 and CPEB1/BTG4, both of which are regulators of mRNA stability/polyadenylation?

      We apologize if these sentences were unclear. Our intention was to emphasize the central role of ubiquitin ligases in regulating multiple events during meiotic divisions. We used SCF<sup>βTrCP</sup>, a wellstudied ubiquitin ligase in Xenopus and mouse oocytes during meiosis, as an example. SCF<sup>βTrCP</sup> regulates the degradation of several substrates, including Emi1, Emi2, CPEB1, and Btg4, whose degradation or stabilization is essential for the proper progression of meiosis. Lastly, we highlighted that these regulatory processes, mediated by protein degradation, may be conserved in mitosis, as for example the destruction of Emi1. We have rewritten this paragraph for clarity (lines 513-518).

      (16) Lane 521-522 and 572-573 -> the authors write that Myt1 was not detected in their proteome. However, in Fig. 6A they list "pkmyt1" as a class II protein. On Xenbase, "pkmyt1" is the Cdk1 kinase, "Myt1" is a transcription factor, so the authors might have been looking for the wrong protein.

      We thank the reviewer for this accurate observation. We have modified the text to correct this error (lines 554 and 607).

      (17) Lane 564-565 -> The authors state that Cdk1 activity can be measured by analyzing Cdc27 S428 phosphorylation. However, in vivo the net phosphorylation of a site is always depending on the relevant kinase and phosphatase activities. As S428 is a Cdk1 site, it is not unlikely that it is dephosphorylated by PP2A-B55, which by itself is under the control of Cdk1. Do the authors have direct evidence that the change in phosphorylation of S428 can only be attributed to the changes in Cdk1 activity?

      There is evidence in the literature that Cdc27 is dephosphorylated by PP2A (Torres et al., 2010). In Xenopus oocytes, PP2A activity is high during prophase (Lemonnier et al., 2021) and decreases at the time of Cdk1 activation, mediated by the Greatwall-ENSA/Arpp19 system, remaining low until MII (Labbé et al., 2021). Therefore, the period where fluctuations in Cdk1 activity are difficult to assess, from NEBD to MII, corresponds to a phase of inhibited PP2A activity. As a result, the phosphorylation level of Cdc27 reflects primarily the activity of Cdk1. We have added this clarification in the text (lines 597-600).

      (18) Fig. 7C and 7D -> in 7C, for Nup35/Nup53 there is a phospho-peptide GIMEVRS(60)PPLHSGG. In Fig. 7D phosphorylation of GVMEMRS(59)PLFSGG is analyzed. Is this the same phosphosite/region of Nup35/Nup53? How can there be a slightly different version of the same peptide in one protein? Are these the L- and S-version of Nup35/Nup53? It is also very surprising that the two phosphosites belong to different classes, class III and class II, respectively.

      We thank the reviewer for this observation. The peptides GIMEVRS(60)PPLHSGG and GVMEMRS(59)PLFSGG correspond to the same phosphorylation site in the L and S versions of Xenopus laevis Nup35, respectively. The L version peptide was classified as Class III, while the S version was not assigned to any class due to its high phosphorylation level in prophase, which prevented it from meeting the log<sub>2</sub> fold-change threshold of 1 required by our analysis to detect significant differences.

      (19) Table 1 -> second last column is headed "Whur, 2014"

      The typo has been corrected.

      (20) Fig. 8 -> Why are all the traces starting at t=1h after PG?

      The labeling of the graphs in Fig. 8 has been corrected, and the traces now begin at t0.

      (21) Lane 754 -> Although a minority, there are also some minus-end directed kinesins, e.g. Kifc1

      We agree with the reviewer. We should have mentioned that, in addition to dyneins, some kinesins are minus-end directed motors, especially since one of them, Kifc1, is regulated at the level of its accumulation. We have rephrased the relevant sentences to incorporate this observation (lines 790-793).

      (22) Section "Assembly of microtubule spindles and microtubule dynamics" -> Although this section clearly has a strong focus on phosphorylation, it might be worth mentioning again that many regulators of the microtubule spindle, e.g. TXP2, are among the upregulated proteins in Fig. 2B/C

      We have already discussed that the protein levels of certain key regulators of the mitotic spindle (Tpx2, PRC1, SSX2IP, Kif11/Eg5 among others) are subject to control during meiotic maturation in a previous chapter “Protein accumulation: the machinery of cell division and DNA replication” (lines 230-239). We agree with the reviewer that this important observation can be mentioned again at the beginning of this chapter on phosphorylation control. We have added a sentence regarding this at the start of the paragraph (lines 774-775).

      Reviewer #2 (Recommendations for the authors):

      While I find the manuscript excellent and detailed already in its current form, I would appreciate including even more comparisons to other systems. In particular, a similar phosphoproteomics experiment has been performed in starfish oocytes undergoing meiosis (Swartz et al, eLife, 2021), and there are several studies on mitosis of diverse mammalian cells. It would be very exciting to see to what extent changes are conserved.

      We thank the reviewer for this recommendation, which we have attempted to follow. We have matched our dataset of mass spectrometry using the the phosphor-occupancy_matlab package, available as part of our code repository (https://github.com/elizabeth-van-itallie) previously described in (Van Itallie et al, 2025). Unfortunately, we were unable to match our dataset with the data from Swartz et al. (2021) on starfish oocyte due to the low sequence conservation. However, we have compared our dataset with the dataset from Sun et al. (2024) on mouse oocyte maturation. We identified a total of 408 conserved phosphorylation sites, which mapped to 320 proteins in Xenopus and 277 in mice (refer to a new paragraph: lines 824-860, new Figure 9, Methods: lines 1011-1032 and 1060-1065, and Appendix 7). The phosphorylation patterns during meiosis showed a significant crossspecies correlation (Pearson r = 0.39, p < 0.0001; see new Figure 9A), demonstrating the evolutionary conservation of phosphoproteomic regulation. Important phosphorylation events, including Plk1 at T201, Gwl at S467, and Erk2 at T188, were upregulated in both species, in line with the activation of the Cdk1 and MAPK signaling cascades (Figure 6B, new Figure 9A-B). We validated several of these phosphorylation sites by western blotting and demonstrated their dependency on Cdk1 activation (new Figure 9C). Together, these findings reinforce the notion that fundamental phospho-regulatory pathways are conserved during oocyte maturation in vertebrates.

      Reviewer #3 (Recommendations for the authors):

      (1) Page 6, the first paragraph of Results section: Please describe the method on how the authors measured and quantified the proteomes in different stages of Xenopus oocyte maturation briefly. Without the experimental design, it is very hard to evaluate the results in the following paragraphs.

      As requested by the reviewer, we added a few sentences describing the method of proteomics and phosphoproteomics measurements in oocytes resuming meiosis (lines 151-158).

      (2) In the phospho-proteome, it is better to classify the amino acids for the phosphorylation such as Ser, Thr, and Tyr. Particularly how many tyrosine phosphorylations are in the list.

      Our phosphosites dataset contains 80% Ser, 19.9% Thr, and 0.01% Tyr. Phospho-Tyr are slightly less abundant than what has been described in the literature (in most cells “roughly 85-90% of protein phosphorylation happens on Ser, ~10% on Thr, and less than 0.05% on Tyr" after Sharma et al., 2014. The same observation was made regarding the distribution of phosphorylated amino acids in mouse oocytes, where phospho-Tyr abundance is relatively diminished in oocytes compared to mouse organs (Sun et al., 2024). These observations are now reported in the manuscript (lines 309-313).

      (3) In class II (Figure 3), when Cdk1 (line 326) is a major kinase, how many phosphorylation sites are a target of Cdk1 (with the Cdk1-motif)? Moreover, do the authors find any other consensus sequences for the phosphorylation? Those are either known or unknown. This information would be useful for the readers.

      We thank the reviewer for this valuable comment. To address it, we used the kinase prediction server (https://kinase-library.phosphosite.org/kinase-library/score-site) to analyze Class II phosphosites. These new results are mentioned in lines 340-349 and illustrated in a new Figure (Figure 3—figure supplement 1A). We identified 303 sites predicted to be phosphorylated by Cdk1. Of these, 166 were also predicted as Erk1/2 targets, reflecting the similarity between Cdk1 and Erk1/2 consensus motifs.

      Cdk1 substrate phosphorylation is governed by more than just the presence of a consensus sequence. In addition to its preference for the (S/T)P×(K/R) motif, Cdk1/cyclin complexes achieve specificity through docking interactions with short linear motifs (SLiMs) recognized by the cyclin subunit (as LxF motifs)(Loog & Morgan, 2005), and via the Cdk-binding subunits Cks1 or Cks2, which interact with phosphorylated threonine residues in primed substrates (Örd et al, 2019). These mechanisms promote processive multisite phosphorylation and allow Cdk1 to target substrates even at non-canonical sites. Our motif-based analysis captures only part of this complexity and may underestimate the number of true Cdk1 targets.

      To further explore kinase involvement across phosphosite classes, we extended the analysis to all clusters and identified the most enriched kinase predictions for each (lines 360-365, new Figure 3— figure supplement 1B). In Class II, the most enriched kinases included Cdk1, Erk2, and Plk1, supporting the conclusions derived from the identification of the phosphosites of this Class. But others such as Cdk2, Cdk3, Cdk5, Cdk16, KIS, JNK1, and JNK3 were also identified.

      (4) Figure 3B: Why do the authors show this kind of Table only for Class I, not Classes II-V? It would be informative to show candidate proteins in other classes.

      We chose to present the candidate proteins from Class I in a table format because the number of phosphosites (136) was too small to allow a meaningful Gene Ontology (GO) enrichment analysis. Therefore, we manually curated the data and highlighted proteins whose Class I phosphosites are associated with specific biological processes. For Classes II–V, the higher number of phosphosites allowed us to perform GO enrichment analyses. Since several of the enriched processes were shared across different classes, and some proteins have phosphosites in multiple classes, we opted to organize the results by biological processes rather than by class. We agree with the reviewer that it is indeed valuable to highlight interesting proteins with Class II–V phosphosites. We have done so in Figures 4 through 8, using graphical representations instead of tables, in order to make the data more accessible and avoid long tables. Additionally, the Supplementary Figures provide detailed phosphorylation trends for many of the proteins discussed in the main figures.

      (5) It would be nice if the authors compare this phospho-proteome in Xenopus oocyte maturation with that in mouse oocyte maturation (Sun et al. 2024) in terms of evolutional conservation of the phospho-proteomes.

      We thank the reviewer for this suggestion. As now detailed in the manuscript, we compared our Xenopus phosphoproteome with the dataset from Sun et al. (2024) on mouse oocyte maturation using the the phospho_occupancy_matlab package, available as part of our code repository (https://github.com/elizabeth-van-itallie) previously described in (Van Itallie et al, 2025). We identified 408 conserved phosphorylation sites corresponding to 320 Xenopus and 277 mouse proteins (see new paragraph: lines 824-860, new Figure 9, Methods: lines 1011-1032 and 1060-1065, and Appendix 7). Phosphorylation dynamics across meiosis were significantly correlated between the species (Pearson r = 0.39, p < 0.0001; new Figure 9A), highlighting evolutionary conservation of the phosphoproteomes. Key phosphorylation events such as Plk1 at T201, Gwl at S467, and Erk2 at T188 increased in both species, consistent with activation of the Cdk1 and MAPK pathways (Figure 6B, new Figure 9A–B). We validated experimentally several of these phosphorylation sites by western blot (Erk2, Plk1, Fak1 and Akts1) and demonstrated their dependency on Cdk1 activation (new Figure 9C). Together, these new findings support the conservation of key phospho-regulatory mechanisms across vertebrate oocyte maturation.

      Minor points:

      (1) Reference lists: Please add Sun et al (2024) shown in line 115.

      This important reference has been added (lines 115, 134, 313 and 826).

      (2) Figure 1, red arrows for the inhibition: This should be "T" shape for a better understanding of these complicated pathways.

      We agree with the reviewer’s remark, and we have modified Figure 1.

      (3) Line 236-238: The authors referred to the absence of Cdc6 in oocyte maturation in Xenopus. However, Figure 2C shows that Cdc6 belongs to a list of accumulating proteins with Orc1 and Ocr2 etc. and the authors did not discuss this discrepancy in the text. Please clarity the claim.

      We apologize for the unclear wording in our text. The section of the manuscript regarding the pre-RC components may have been misleading. The text has been revised to clarify that Cdc6 was not detected in prophase-arrested oocytes by western blot and that it accumulates during meiotic maturation after MI, enabling oocytes to replicate DNA (lines 243-250).

      (4) Line 306: Please add the link to phosphosite.org.

      The link has been added (line 319).

    1. Author response:

      Reviewer #1 (Public review):

      Summary:

      The authors use the theory of planned behavior to understand whether or not intentions to use sex as a biological variable (SABV), as well as attitude (value), subjective norm (social pressure), and behavioral control (ability to conduct behavior), across scientists at a pharmacological conference. They also used an intervention (workshop) to determine the value of this workshop in changing perceptions and misconceptions. Attempts to understand the knowledge gaps were made.

      Strengths:

      The use of SABV is limited in terms of researchers using sex in the analysis as a variable of interest in the models (and not a variable to control). To understand how we can improve on the number of researchers examining the data with sex in the analyses, it is vital we understand the pressure points that researchers consider in their work. The authors identify likely culprits in their analyses. The authors also test an intervention (workshop) to address the main bias or impediments for researchers' use of sex in their analyses.

      Weaknesses:

      There are a number of assumptions the authors make that could be revisited:

      (1) that all studies should contain across sex analyses or investigations. It is important to acknowledge that part of the impetus for SABV is to gain more scientific knowledge on females. This will require within sex analyses and dedicated research to uncover how unique characteristics for females can influence physiology and health outcomes. This will only be achieved with the use of female-only studies. The overemphasis on investigations of sex influences limits the work done for women's health, for example, as within-sex analyses are equally important.

      The Sex and Gender Equity in Research (SAGER) guidelines (1) provide guidance that “Where the subjects of research comprise organisms capable of differentiation by sex, the research should be designed and conducted in a way that can reveal sex-related differences in the results, even if these were not initially expected.”. This is a default position of inclusion where the sex can be determined and analysis assessing for sex related variability in response. This position underpins many of the funding bodies new policies on inclusion.

      However, we need to place this in the context of the driver of inclusion. The most common reason for including male and female samples is for those studies that are exploring the effect of a treatment and then the goal of inclusion is to assess the generalisability of the treatment effect (exploratory sex inclusion)(2). The second scenario is where sex is included because sex is one of the variables of interest and this situation will arise because there is a hypothesized sex difference of interest (confirmatory sex inclusion).

      We would argue that the SABV concept was introduced to address the systematic bias of only studying one sex when assessing treatment effect to improve the generalisability of the research. Therefore, it isn’t directly to gain more scientific knowledge on females. However, this strategy will highlight when the effect is very different between male and female subjects which will potentially generate sex specific hypotheses.

      Where research has a hypothesis that is specific to a sex (e.g. it is related to oestrogen levels) it would be appropriate to study only the sex of interest, in this case females. The recently published Sex Inclusive Research Framework gives some guidance here and allows an exemption for such a scenario classifying such proposals “Single sex study justified” (3).

      We plan to add an additional paragraph to the introduction to clarify the objectives behind inclusion and how this assists the research process.

      (2) It should be acknowledged that although the variability within each sex is not different on a number of characteristics (as indicated by meta-analyses in rats and mice), this was not done on all variables, and behavioral variables were not included. In addition, across-sex variability may very well be different, which, in turn, would result in statistical sex significance. In addition, on some measures, there are sex differences in variability, as human males have more variability in grey matter volume than females. PMID: 33044802.

      The manuscript was highlighting the common argument used to exclude the use of females, which is that females are inherently more variable as an absolute truth. We agree there might be situations, where the variance is higher in one sex or another depending on the biology. We will extend the discussion here to reflect this, and we will also link to the Sex Inclusive Research Framework (3) which highlights that in these situations researchers can utlise this argument provided it is supported with data for the biology of interest.

      (3) The authors need to acknowledge that it can be important that the sample size is increased when examining more than one sex. If the sample size is too low for biological research, it will not be possible to determine whether or not a difference exists. Using statistical modelling, researchers have found that depending on the effect size, the sample size does need to increase. It is important to bare this in mind as exploratory analyses with small sample size will be extremely limiting and may also discourage further study in this area (or indeed as seen the literature - an exploratory first study with the use of males and females with limited sample size, only to show there is no "significance" and to justify this as an reason to only use males for the further studies in the work.

      The reviewer raises a common problem: where researchers have frequently argued that if they find no sex differences in a pilot then they can proceed to study only one sex. The SAGER guidelines (1), and now funder guidelines (4, 5), challenge that position. Instead, the expectation is for inclusion as the default in all experiments (exploratory inclusion strategy) to allow generalisable results to be obtained. When the results are very different between the male and female samples, then this can be determined. This perspective shift (2) requires a change in mindset and understanding that the driver behind inclusion is of generalisability not exploration of sex differences. This will be added to the introduction as an additional paragraph exploring the drivers behind inclusion.

      We agree with the reviewer that if the researcher is interested in sex differences in an effect (confirmatory inclusion strategy, aka sex as a primary variable) then the N will need to be higher. However, in this situation, one, of course, must have male and female samples in the same experiment to allow the simultaneous exploration to assess the dependency on sex.

      Reviewer #2 (Public review):

      Summary:

      The investigators tested a workshop intervention to improve knowledge and decrease misconceptions about sex inclusive research. There were important findings that demonstrate the difficulty in changing opinions and knowledge about the importance of studying both males and females. While interventions can improve knowledge and decrease perceived barriers, the impact was small.

      Strengths:

      The investigators included control groups and replicated the study in a second population of scientists. The results appear to be well substantiated. These are valuable findings that have practical implications for fields where sex is included as a biological variable to improve rigor and reproducibility.

      Thank you for assessment and highlighting these strengths. We appreciate your recognition of the value and practical implications of this work.

      Weaknesses:

      I found the figures difficult to understand and would have appreciated more explanation of what is depicted, as well as greater space between the bars representing different categories.

      We plan to review the figures and figure legends to improve clarity of the data.

      Reviewer #3 (Public review):

      Summary:

      This manuscript aims to determine cultural biases and misconceptions in inclusive sex research and evaluate the efficacy of interventions to improve knowledge and shift perceptions to decrease perceived barriers for including both sexes in basic research.

      Overall, this study demonstrates that despite the intention to include both sexes and a general belief in the importance of doing so, relatively few people routinely include both sexes. Further, the perceptions of barriers to doing so are high, including misconceptions surrounding sample size, disaggregation, and variability of females. There was also a substantial number of individuals without the statistical knowledge to appropriately analyze data in studies inclusive of sex. Interventions increased knowledge and decreased perception of barriers. Strengths:

      (1) This manuscript provides evidence for the efficacy of interventions for changing attitudes and perceptions of research.

      (2) This manuscript also provides a training manual for expanding this intervention to broader groups of researchers.

      Thank you for highlighting these strengths. We appreciate your recognition that the intervention was effect in changing attitudes and perception. We deliberately chose to share the material to provide the resources to allow a wider engagement.

      Weaknesses:

      The major weakness here is that the post-workshop assessment is a single time point, soon after the intervention. As this paper shows, intention for these individuals is already high, so does decreasing perception of barriers and increasing knowledge change behavior, and increase the number of studies that include both sexes? Similarly, does the intervention start to shift cultural factors? Do these contribute to a change in behavior?

      Measuring change in behaviour following an intervention is challenging and hence we had implemented an intention score as a proxy for behaviour. We appreciate the benefit of a long-term analysis, but it was beyond the scope of this study and would need a larger dataset size to allow for attrition. We agree that the strategy implemented has weaknesses. We plan to extend the limitation section in the discussion to include these.

      References

      (1) Heidari S, Babor TF, De Castro P, Tort S, Curno M. Sex and Gender Equity in Research: rationale for the SAGER guidelines and recommended use. Res Integr Peer Rev. 2016;1:2.

      (2) Karp NA. Navigating the paradigm shift of sex inclusive preclinical research and lessons learnt. Commun Biol. 2025;8(1):681.

      (3) Karp NA, Berdoy M, Gray K, Hunt L, Jennings M, Kerton A, et al. The Sex Inclusive Research Framework to address sex bias in preclinical research proposals. Nat Commun. 2025;16(1):3763.

      (4) MRC. Sex in experimental design - Guidance on new requirements https://www.ukri.org/councils/mrc/guidance-for-applicants/policies-and-guidance-for-researchers/sex-in-experimental-design/: UK Research and Innovation; 2022

      (5) Clayton JA, Collins FS. Policy: NIH to balance sex in cell and animal studies. Nature. 2014;509(7500):282-3.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This manuscript presents a compelling study identifying RBMX2 as a novel host factor upregulated during Mycobacterium bovis infection.

      The study demonstrates that RBMX2 plays a role in:

      (1) Facilitating M. bovis adhesion, invasion, and survival in epithelial cells.

      (2) Disrupting tight junctions and promoting EMT.

      (3) Contributing to inflammatory responses and possibly predisposing infected tissue to lung cancer development.

      By using a combination of CRISPR-Cas9 library screening, multi-omics, coculture models, and bioinformatics, the authors establish a detailed mechanistic link between M. bovis infection and cancer-related EMT through the p65/MMP-9 signaling axis. Identification of RBMX2 as a bridge between TB infection and EMT is novel.

      Strengths:

      This topic and data are both novel and significant, expanding the understanding of transcriptomic diversity beyond RBM2 in M. bovis responsive functions.

      Weaknesses:

      (1) The abstract and introduction sometimes suggest RBMX2 has protective anti-TB functions, yet results show it facilitates pathogen adhesion and survival. The authors need to rephrase claims to avoid contradiction.

      We sincerely appreciate the reviewer's valuable feedback regarding the need to clarify RBMX2's role throughout the manuscript. We have carefully revised the text to ensure consistent messaging about RBMX2's function in promoting M. bovis infection. Below we detail the specific modifications made:

      (1) Introduction Revisions:

      Changed "The objective of this study was to elucidate the correlation between host genes and the susceptibility of M.bovis infection" to "The objective of this study was to identify host factors that promote susceptibility to M.bovis infection"

      Revised "RBMX2 polyclonal and monoclonal cell lines exhibited favorable phenotypes" to "RBMX2 knockout cell lines showed reduced bacterial survival"

      Replaced "The immune regulatory mechanism of RBMX2" with "The role of RBMX2 in facilitating M.bovis immune evasion"

      (2) Results Revisions:

      Modified "RBMX2 fails to affect cell morphology and the ability to proliferate and promotes M.bovis infection" to "RBMX2 does not alter cell viability but significantly enhances M.bovis infection"

      Strengthened conclusion in Figure 4: "RBMX2 actively disrupts tight junctions to facilitate bacterial invasion"

      (3) Discussion Revisions:

      Revised screening description: "We screened host factors affecting M.bovis susceptibility and identified RBMX2 as a key promoter of infection"

      Strengthened concluding statement: "In summary, RBMX2 drives TB pathogenesis by compromising epithelial barriers and inducing EMT"

      These targeted revisions ensure that:

      All sections consistently present RBMX2 as promoting infection; the language aligns with our experimental finding; potential protective interpretations have been eliminated. We believe these modifications have successfully addressed the reviewer's concern while maintaining the manuscript's original structure and scientific content. We appreciate the opportunity to improve our manuscript and thank the reviewer for this constructive suggestion.

      (2) >While p65/MMP-9 is convincingly implicated, the role of MAPK/p38 and JNK is less clearly resolved.

      We sincerely appreciate the reviewer's insightful comment regarding the roles of MAPK/p38 and JNK in our study. Our experimental data clearly demonstrated that RBMX2 knockout significantly reduced phosphorylation levels of p65, p38, and JNK (Fig. 5A), indicating potential involvement of all three pathways in RBMX2-mediated regulation.

      Through systematic functional validation, we obtained several important findings:

      In pathway inhibition experiments, p65 activation (PMA treatment) showed the most dramatic effects on both tight junction disruption (ZO-1, OCLN reduction) and EMT marker regulation (E-cadherin downregulation, N-cadherin upregulation);

      p38 activation (ML141 treatment) exhibited moderate effects on these processes;

      JNK activation (Anisomycin treatment) displayed minimal impact.

      Most conclusively, siRNA-mediated silencing of p65 alone was sufficient to:

      Restore epithelial barrier function

      Reverse EMT marker expression

      Reduce bacterial adhesion and invasion

      These results establish a clear hierarchy in pathway importance: p65 serves as the primary mediator of RBMX2's effects, while p38 plays a secondary role and JNK appears non-essential under our experimental conditions. We have now clarified this relationship in the revised Discussion section to strengthen this conclusion.

      This refined understanding of pathway hierarchy provides important mechanistic insights while maintaining consistency with all our experimental data. We thank the reviewer for this valuable suggestion that helped improve our manuscript.

      (3) Metabolomics results are interesting but not integrated deeply into the main EMT narrative.

      Thank you for this constructive suggestion. In this article, we detected the metabolome of RBMX2 knockout and wild-type cells after Mycobacterium bovis infection, which mainly served as supporting evidence for our EMT model. However, we did not conduct an in-depth discussion of these findings. We have now added a detailed discussion of this section to further support our EMT model.

      ADD:Meanwhile, metabolic pathways enriched after RBMX2 deletion, such as nucleotide metabolism, nucleotide sugar synthesis, and pentose interconversion, primarily support cell proliferation and migration during EMT by providing energy precursors, regulating glycosylation modifications, and maintaining redox balance; cofactor synthesis and amino sugar metabolism participate in EMT regulation through influencing metabolic remodeling and extracellular matrix interactions; chemokine and cGMP-PKG signaling pathways may further mediate inflammatory responses and cytoskeletal rearrangements, collectively promoting the EMT process.

      (4) A key finding and starting point of this study is the upregulation of RBMX2 upon M. bovis infection. However, the authors have only assessed RBMX2 expression at the mRNA level following infection with M. bovis and BCG. To strengthen this conclusion, it is essential to validate RBMX2 expression at the protein level through techniques such as Western blotting or immunofluorescence. This would significantly enhance the credibility and impact of the study's foundational observation.

      Thank you for your comment. We have supplemented the experiments in this part and found that Mycobacterium bovis infection can significantly enhance the expression level of RBMX2 protein.

      (5) The manuscript would benefit from a more in-depth discussion of the relationship between tuberculosis (TB) and lung cancer. While the study provides experimental evidence suggesting a link via EMT induction, integrating current literature on the epidemiological and mechanistic connections between chronic TB infection and lung tumorigenesis would provide important context and reinforce the translational relevance of the findings.

      We sincerely appreciate the valuable comments from the reviewer. We fully agree with your suggestion to further explore the relationship between tuberculosis (TB) and lung cancer. In the revised manuscript, we will add a new paragraph in the Discussion section to systematically integrate the current literature on the epidemiological and mechanistic links between chronic tuberculosis infection and lung cancer development, including the potential bridging roles of chronic inflammation, tissue damage repair, immune microenvironment remodeling, and the epithelial-mesenchymal transition (EMT) pathway. This addition will help more comprehensively interpret the clinical implications of the observed EMT activation in the context of our study, thereby enhancing the biological plausibility and clinical translational value of our findings.

      ADD:There is growing epidemiological evidence suggesting that chronic TB infection represents a potential risk factor for the development of lung cancer. Studies have shown that individuals with a history of TB exhibit a significantly increased risk of lung cancer, particularly in areas of the lung with pre-existing fibrotic scars, indicating that chronic inflammation, tissue repair, and immune microenvironment remodeling may collectively contribute to malignant transformation 74. Moreover, EMT not only endows epithelial cells with mesenchymal features that enhance migratory and invasive capacity but is also associated with the acquisition of cancer stem cell-like properties and therapeutic resistance 75. Therefore, EMT may serve as a crucial molecular link connecting chronic TB infection with the malignant transformation of lung epithelial cells, warranting further investigation in the intersection of infection and tumorigenesis.

      Reviewer #2 (Public review):

      Summary:

      I am not familiar with cancer biology, so my review mainly focuses on the infection part of the manuscript. Wang et al identified an RNA-binding protein RBMX2 that links the Mycobacterium bovis infection to the epithelial-Mesenchymal transition and lung cancer progression. Upon mycobacterium infection, the expression of RBMX2 was moderately increased in multiple bovine and human cell lines, as well as bovine lung and liver tissues. Using global approaches, including RNA-seq and proteomics, the authors identified differential gene expression caused by the RBMX2 knockout during M. bovis infection. Knockout of RBMX2 led to significant upregulations of tight-junction related genes such as CLDN-5, OCLN, ZO-1, whereas M. bovis infection affects the integrity of epithelial cell tight junctions and inflammatory responses. This study establishes that RBMX2 is an important host factor that modulates the infection process of M. bovis.

      Strengths:

      (1) This study tested multiple types of bovine and human cells, including macrophages, epithelial cells, and clinical tissues at multiple timepoints, and firmly confirmed the induced expression of RBMX2 upon M. bovis infection.

      (2) The authors have generated the monoclonal RBMX2 knockout cell lines and comprehensively characterized the RBMX2-dependent gene expression changes using a combination of global omics approaches. The study has validated the impact of RBMX2 knockout on the tight-junction pathway and on the M. bovis infection, establishing RBMX2 as a crucial host factor.

      Weaknesses:

      (1) The RBMX2 was only moderately induced (less than 2-fold) upon M. bovis infection, arguing its contribution may be small. Its value as a therapeutic target is not justified. How RBMX2 was activated by M. bovis infection was unclear.

      Thank you for your valuable and constructive comments. In this study, we primarily utilized the CRISPR whole-genome screening approach to identify key factors involved in bovine tuberculosis infection. Through four rounds of screening using a whole-genome knockout cell line of bovine lung epithelial cells infected with Mycobacterium bovis, we identified RBMX2 as a critical factor.

      Although the transcriptional level change of RBMX2 was less than two-fold, following the suggestion of Reviewer 1, we examined its expression at the protein level, where the change was more pronounced, and we have added these results to the manuscript.

      Regarding the mechanism by which RBMX2 is activated upon M. bovis infection, we previously screened for interacting proteins using a Mycobacterium tuberculosis secreted and membrane protein library, but unfortunately, we did not identify any direct interacting proteins from M. tuberculosis (https://doi.org/10.1093/nar/gkx1173).

      (2) Although multiple time points have been included in the study, most analyses lack temporal resolution. It is difficult to appreciate the impact/consequence of M. bovis infection on the analyzed pathways and processes.

      We appreciate the valuable comments from the reviewers. Although our study included multiple time points post-infection, in our experimental design we focused on different biological processes and phenotypes at distinct time points:

      During the early phase (e.g., 2 hours post-infection), we focused on barrier phenotypes; during the intermediate phase (e.g., 24 hours post-infection), we concentrated more on pathway activation and EMT phenotypes;

      And during the later phase (e.g., 48–72 hours post-infection), we focused more on cell death phenotypes, which were validated in another FII article (https://doi.org/10.3389/fimmu.2024.1431207).

      We also examined the impact of varying infection durations on RBMX2 knockout EBL cellular lines via GO analysis. At 0 hpi, genes were primarily related to the pathways of cell junctions, extracellular regions, and cell junction organization. At 24 hpi, genes were mainly associated with pathways of the basement membrane, cell adhesion, integrin binding and cell migration By 48 hpi, genes were annotated into epithelial cell differentiation and were negatively regulated during epithelial cell proliferation. This indicated that RBMX2 can regulate cellular connectivity throughout the stages of M. bovis infection.

      For KEGG analysis, genes linked to the MAPK signaling pathway, chemical carcinogen-DNA adducts, and chemical carcinogen-receptor activation were observed at 0 hpi. At 24 hpi, significant enrichment was found in the ECM-receptor interaction, PI3K-Akt signaling pathway, and focal adhesion. Upon enrichment analysis at 48 hpi, significant enrichment was noted in the TGF-beta signaling pathway, transcriptional misregulation in cancer, microRNAs in cancer, small cell lung cancer, and p53 signaling pathway.

      Reviewer #3 (Public review):

      Summary:

      This study investigates the role of the host protein RBMX2 in regulating the response to Mycobacterium bovis infection and its connection to epithelial-mesenchymal transition (EMT), a key pathway in cancer progression. Using bovine and human cell models, the authors have wisely shown that RBMX2 expression is upregulated following M. bovis infection and promotes bacterial adhesion, invasion, and survival by disrupting epithelial tight junctions via the p65/MMP-9 signaling pathway. They also demonstrate that RBMX2 facilitates EMT and is overexpressed in human lung cancers, suggesting a potential link between chronic infection and tumor progression. The study highlights RBMX2 as a novel host factor that could serve as a therapeutic target for both TB pathogenesis and infection-related cancer risk.

      Strengths:

      The major strengths lie in its multi-omics integration (transcriptomics, proteomics, metabolomics) to map RBMX2's impact on host pathways, combined with rigorous functional assays (knockout/knockdown, adhesion/invasion, barrier tests) that establish causality through the p65/MMP-9 axis. Validation across bovine and human cell models and in clinical tissue samples enhances translational relevance. Finally, identifying RBMX2 as a novel regulator linking mycobacterial infection to EMT and cancer progression opens exciting therapeutic avenues.

      Weaknesses:

      Although it's a solid study, there are a few weaknesses noted below.

      (1) In the transcriptomics analysis, the authors performed (GO/KEGG) to explore biological functions. Did they perform the search locally or globally? If the search was performed with a global reference, then I would recommend doing a local search. That would give more relevant results. What is the logic behind highlighting some of the enriched pathways (in red), and how are they relevant to the current study?

      We appreciate the reviewer's thoughtful questions regarding our transcriptomic analysis. In this study, we employed a localized enrichment approach focusing specifically on gene expression profiles from our bovine lung epithelial cell system. This cell-type-specific analysis provides more biologically relevant results than global database searches alone.

      Regarding the highlighted pathways, these represent:

      (1) Temporally significant pathways showing strongest enrichment at each stage:

      • 0h: Cell junction organization (immediate barrier response)

      • 24h: ECM-receptor interaction (early EMT initiation)

      • 48h: TGF-β signaling (chronic remodeling)

      (2) Mechanistically linked to our core findings about RBMX2's role in:

      • Epithelial barrier disruption

      • Mesenchymal transition

      • Chronic infection outcomes

      We selected these particular pathways because they:

      (1) Showed the most statistically significant changes (FDR <0.001)

      (2) Formed a coherent biological narrative across infection stages

      (3) Were independently validated in our functional assays

      This targeted approach allows us to focus on the most infection-relevant pathways while maintaining statistical rigor.

      (2) While the authors show that RBMX2 expression correlates with EMT-related gene expression and barrier dysfunction, the evidence for direct association remains limited in this study. How does RBMX2 activate p65? Does it bind directly to p65 or modulate any upstream kinases? Could ChIP-seq or CLIP-seq provide further evidence for direct RNA or DNA targets of RBMX2 that drive EMT or NF-κB signaling?

      We sincerely appreciate the reviewer's in-depth questions regarding the mechanisms by which RBMX2 activates p65 and its association with EMT. Although the molecular mechanism remains to be fully elucidated, our study has provided experimental evidence supporting a direct regulatory relationship between RBMX2 and the p65 subunit of the NF-κB pathway. Specifically, we investigated whether the transcription factor p65 could directly bind to the promoter region of RBMX2 using CHIP experiments. The results demonstrated that the transcription factor p65 can physically bind to the RBMX2 region.

      Furthermore, dual-luciferase reporter assays were conducted, showing that p65 significantly enhances the transcriptional activity of the RBMX2 promoter, indicating a direct regulatory effect of RBMX2 on p65 expression.

      These findings support our hypothesis that RBMX2 activates the NF-κB signaling pathway through direct interaction with the p65 protein, thereby participating in the regulation of EMT progression and barrier function.

      In our subsequent work papers, we will also employ experiments such as CLIP to further investigate the specific mechanisms through which RBMX2 exerts its regulatory functions.

      (3) The manuscript suggests that RBMX2 enhances adhesion/invasion of several bacterial species (e.g., E. coli, Salmonella), not just M. bovis. This raises questions about the specificity of RBMX2's role in Mycobacterium-specific pathogenesis. Is RBMX2 a general epithelial barrier regulator or does it exhibit preferential effects in mycobacterial infection contexts? How does this generality affect its potential as a TB-specific therapeutic target?

      Thank you for your valuable comments. When we initially designed this experiment, we were interested in whether the RBMX2 knockout cell line could confer effective resistance not only against Mycobacterium bovis but also against Gram-negative and Gram-positive bacteria. Surprisingly, we indeed observed resistance to the invasion of these pathogens, albeit weaker compared to that against Mycobacterium bovis.

      Nevertheless, we believe these findings merit publication in eLife. Moreover, RBMX2 knockout does not affect the phenotype of epithelial barrier disruption under normal conditions; its significant regulatory effect on barrier function is only evident upon infection with Mycobacterium bovis.

      Importantly, during our genome-wide knockout library screening, RBMX2 was not identified in the screening models for Salmonella or Escherichia coli, but was consistently detected across multiple rounds of screening in the Mycobacterium bovis model.

      (4) The quality of the figures is very poor. High-resolution images should be provided.

      Thank you for your feedback; we provided higher-resolution images.

      (5) The methods are not very descriptive, particularly the omics section.

      Thank you for your comments; we have revised the description of the sequencing section.

      (6) The manuscript is too dense, with extensive multi-omics data (transcriptomics, proteomics, metabolomics) but relatively little mechanistic integration. The authors should have focused on the key mechanistic pathways in the figures. Improving the narratives in the Results and Discussion section could help readers follow the logic of the experimental design and conclusions.

      Thank you for your valuable comments. We have streamlined the figures and revised the description of the results section accordingly.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this interesting and original paper, the authors examine the effect that heat stress can have on the ability of bacterial cells to evade infection by lytic bacteriophages. Briefly, the authors show that heat stress increases the tolerance of Klebsiella pneumoniae to infection by the lytic phage Kp11. They also argue that this increased tolerance facilitates the evolution of genetically encoded resistance to the phage. In addition, they show that heat can reduce the efficacy of phage therapy. Moreover, they define a likely mechanistic reason for both tolerance and genetically encoded resistance. Both lead to a reorganization of the bacterial cell envelope, which reduces the likelihood that phage can successfully inject their DNA.

      Strengths:

      I found large parts of this paper well-written and clearly presented. I also found many of the experiments simple yet compelling. For example, the experiments described in Figure 3 clearly show that prior heat exposure can affect the efficacy of phage therapy. In addition, the experiments shown in Figures 4 and 6 clearly demonstrate the likely mechanistic cause of this effect. The conceptual Figure 7 is clear and illustrates the main ideas well. I think this paper would work even without its central claim, namely that tolerance facilitates the evolution of resistance. The reason is that the effect of environmental stressors on stress tolerance has to my knowledge so far only been shown for drug tolerance, not for tolerance to an antagonistic species.

      Weaknesses:

      I did not detect any weaknesses that would require a major reorganization of the paper, or that may require crucial new experiments. However, the paper needs some work in clarifying specific and central conclusions that the authors draw. More specifically, it needs to improve the connection between what is shown in some figures, how these figures are described in the caption, and how they are discussed in the main text. This is especially glaring with respect to the central claim of the paper from the title, namely that tolerance facilitates the evolution of resistance. I am sympathetic to that claim, especially because this has been shown elsewhere, not for phage resistance but for antibiotic resistance. However, in the description of the results, this is perhaps the weakest aspect of the paper, so I'm a bit mystified as to why the authors focus on this claim. As I mentioned above, the paper could stand on its own even without this claim.

      Thank you for your feedback. We understand your concern regarding the central claim that tolerance facilitates the evolution of resistance, while the paper can stand on its own without this claim, we think it provides an important layer to the interpretation of our findings. Considering your comments, we plan to revise the title and adjust to “Heat Stress Induces Phage Tolerance in Bacteria”.

      More specific examples where clarification is needed:

      (1) A key figure of the paper seems to be Figure 2D, yet it was one of the most confusing figures. This results from a mismatch between the accompanying text starting on line 92 and the figure itself. The first thing that the reader notices in the figure itself is the huge discrepancy between the number of viable colonies in the absence of phage infection at the two-hour time point. Yet this observation is not even mentioned in the main text. The exclusive focus of the main text seems to be on the right-hand side of the figure, labeled "+Phage". It is from this right-hand panel that the authors seem to conclude that heat stress facilitates the evolution of resistance. I find this confusing, because there is no difference between the heat-treated and non-treated cells in survivorship, and it is not clear from this data that survivorship is caused by resistance, not by tolerance/persistence. (The difference between tolerance and resistance has only been shown in the independent experiments of Figure 1B.)

      Thank you for your helpful comment. Figure 2d presents colony counts from a plating assay following the phage killing experiment in Figure 2c. Bacteria collected after 0 and 2 hours of phage exposure were plated on both phage-free (−phage) and phage-containing (+phage) plates. The “−phage” condition reflects total survivors, while the “+phage” condition indicates the resistant subset.

      As seen in Figure 2d (left part), heat-treated bacteria showed markedly higher survival on phage-free plates than untreated cells, which were largely eliminated by phage. However, resistant colony counts on phage-containing plates were similar between two groups (as shown in figure 2d right part), suggesting that heat stress increased survival but did not promote resistance.

      To clarify, we have revised the labels in Figure 2d as follows: “Total” will replace “-phage” to indicate the total survivors from the phage killing assay, and “Resisters” will replace “+phage” to indicate the resistant survivors, which are detected on phage-containing plates. This adjustment should eliminate any confusion and better reflect the experimental design.

      Figure 2F supports the resistance claim, but it is not one of the strongest experiments of the paper, because the author simply only used "turbidity" as an indicator of resistance. In addition, the authors performed the experiments described therein at small population sizes to avoid the presence of resistance mutations. But how do we know that the turbidity they describe does not result from persisters?

      I see three possibilities to address these issues. First, perhaps this is all a matter of explaining and motivating this particular experiment better. Second, the central claim of the paper may require additional experiments. For example, is it possible to block heat induced tolerance through specific mutations, and show that phage resistance does not evolve as rapidly if tolerance is blocked? A third possibility is to tone down the claim of the paper and make it about heat tolerance rather than the evolution of heat resistance.

      Thank you for your thoughtful comment. We appreciate the opportunity to clarify the interpretation of Figure 2f and the rationale behind the experimental design. We agree that turbidity alone cannot fully distinguish resistance from persistence. However, our earlier experiments (Figures 2d and 2e) demonstrated that heat-treated survivors remained largely susceptible to phage, indicating that heat stress does not directly induce resistance. This led us to hypothesize that heat enhances phage tolerance, which in turn increases the likelihood of resistance emergence during subsequent infection.

      To test this, we used a low initial bacterial population (~10³ CFU per well) to minimize the chance of pre-existing resistance. Bacteria were exposed to phages at MOIs of 1, 10, and 100 and incubated for 24 hours in 100 µL volumes. This setup ensured:

      (1) The low initial population minimizes the presence of pre-existing resistant mutants, ensuring that any phage-resistant bacteria observed arise during the infection process.

      (2) The high MOI (≥ 1) ensures that each bacterial cell has a high probability of infection by at least one phage.

      (3) The small volume (100 µL per well) maximizes the interaction between bacteria and phages, ensuring rapid infection of susceptible bacteria, which leads to clear wells. If resistant mutants arise, they will grow and cause turbidity.

      Thus, the turbidity observed in heat-treated samples reflects de novo emergence and outgrowth of resistant mutants from a tolerant population. This assay supports the idea that heat-induced tolerance increases the probability of resistance evolution, rather than directly causing resistance.

      We have revised the text to better explain this experimental logic and adjust the framing of our conclusions accordingly.

      A minor but general point here is that in Figure 2D and in other figures, the labels "-phage" and "+phage" do not facilitate understanding, because they suggest that cells in the "-phage" treatment have not been exposed to phage at all, but that is not the case. They have survived previous phage treatment and are then replated on media lacking phage.

      Thank you for your valuable comment. To clarify, we have revised the labels in Figure 2d as follows: “Total” will replace “-phage” to indicate the total survivors from the phage killing assay, and “Resisters” will replace “+phage” to indicate the resistant survivors, which are detected on phage-containing plates.

      (2) Another figure with a mismatch between text and visual materials is Figure 5, specifically Figures 5B-F. The figure is about two different mutants, and it is not even mentioned in the text how these mutants were identified, for example in different or the same replicate populations. What is more, the two mutants are not discussed at all in the main text. That is, the text, starting on line 221 discusses these experiments as if there was only one mutant. This is especially striking as the two mutants behave very differently, as, for example, in Figure 5C. Implicitly, the text talks about the mutant ending in "...C2", and not the one ending in "...C1". To add to the confusion, the text states that the (C2) mutant shows a change in the pspA gene, but in Figure 5f, it is the other (undiscussed) mutant that has a mutation in this gene. Only pspA is discussed further, so what about the other mutants? More generally, it is hard to believe that these were the only mutants that occurred in the genome during experimental evolution. It would be useful to give the reader a 2-3 sentence summary of the genetic diversity that experimental evolution generated.

      Thank you for your thoughtful comment. In our heat treatment evolutionary experiment, we isolated six distinct bacterial clones, of which two are highlighted in the manuscript as representative examples. One clone, BC2G11C1, acquired both heat tolerance and phage resistance, while another clone, BC3G11C2, became heat-tolerant but did not develop resistance to phage infection. This variation highlights the inherent diversity in evolutionary responses when exposed to selective pressures. It demonstrates that not all evolutionary pathways lead to the same outcome, even under similar stress conditions. This variability is a key observation in our study, illustrating that different genetic adaptations may arise depending on the specific mutations or genetic context, and not every strain will evolve phage resistance in parallel with heat tolerance. We have updated the manuscript to better reflect this diversity in the evolutionary trajectories observed.

      Reviewer #2 (Public review):

      Summary:

      An initial screening of pretreatment with different stress treatments of K. pneumoniae allowed the identification of heat stress as a protection factor against the infection of the lytic phage Kp11. Then experiments prove that this is mediated not by an increase of phage-resistant bacteria but due to an increase in phage transient tolerant population, which the authors identified as bacteriophage persistence in analogy to antibiotic persistence. Then they proved that phage persistence mediated by heat shock enhanced the evolution of bacterial resistance against the phage. The same trait was observed using other lytic phages, their combinations, and two clinical strains, as well as E. coli and two T phages, hence the phenomenon may be widespread in enterobacteria.

      Next, the elucidation of heat-induced phage persistence was done, determining that phage adsorption was not affected but phage DNA internalization was impaired by the heat pretreatment, likely due to alterations in the bacterial envelope, including the downregulation of envelope proteins and of LPS; furthermore, heat treated bacteria were less sensitive to polymyxins due to the decrease in LPS.

      Finally, cyclic exposure to heat stress allowed the isolation of a mutant that was both resistant to heat treatment, polymyxins, and lytic phage, that mutant had alterations in PspA protein that allowed a gain of function and that promoted the reduction of capsule production and loss of its structure; nevertheless this mutant was severely impaired in immune evasion as it was easily cleared from mice blood, evidencing the tradeoffs between phage/heat and antibiotic resistance and the ability to counteract the immune response.

      Strengths:

      The experimental design and the sequence in which they are presented are ideal for the understanding of their study and the conclusions are supported by the findings, also the discussion points out the relevance of their work particularly in the effectiveness of phage therapy and allows the design of strategies to improve their effectiveness.

      Weaknesses:

      In its present form, it lacks the incorporation of some relevant previous work that explored the role of heat stress in phage susceptibility, antibiotic susceptibility, tradeoffs between phage resistance and resistance against other kinds of stress, virulence, etc., and the fact that exposure to lytic phages induces antibiotic persistence.

      Thank you for your insightful comments. I appreciate your suggestion regarding the inclusion of relevant previous works. I have now incorporated additional citations to discuss these points, including studies on the relationship between heat stress and antibiotic resistance, as well as the tradeoffs between phage resistance and other stress factors.

      Reviewer #3 (Public review):

      PspA, a key regulator in the phage shock protein system, functions as part of the envelope stress response system in bacteria, preventing membrane depolarization and ensuring the envelope stability. This protein has been associated in the Quorum Sensing network and biofilm formation. (Moscoso M., Garcia E., Lopez R. 2006. Biofilm formation by Streptococcus pneumoniae: role of choline, extracellular DNA, and capsular polysaccharide in microbial accretion. J. Bacteriol. 188:7785-7795; Vidal JE, Ludewick HP, Kunkel RM, Zähner D, Klugman KP. The LuxS-dependent quorum-sensing system regulates early biofilm formation by Streptococcus pneumoniae strain D39. Infect Immun. 2011 Oct;79(10):4050-60.)

      It is interesting and very well-developed.

      (1) Could the authors develop experiments about the relationship between Quorum Sensing and this protein?

      (2) It would be interesting to analyze the link to phage infection and heat stress in relation to Quorum. The authors could study QS regulators or AI2 molecules.

      Thank you for your insightful comments and for bringing up the role of PspA in quorum sensing and biofilm formation. However, we would like to clarify a potential misunderstanding: the PspA discussed in our manuscript refers to phage-shock protein A, a key regulator in the bacterial envelope stress response system. This is distinct from the pneumococcal surface protein A, which has been associated with quorum sensing and biofilm formation in Streptococcus pneumoniae (as referenced in your comment).

      To avoid any confusion for readers, we will ensure that our manuscript explicitly states “phage-shock protein A (PspA)” at its first mention. We appreciate your feedback and hope this clarification addresses your concern.

      (3) Include the proteins or genes in a table or figure from lytic phage Kp11 (GenBank: ON148528.1).

      Thank you for your helpful suggestion. We have now included a figure, as appropriate summarizing the proteins of the lytic phage Kp11 (GenBank: ON148528.1) in supplementary Figure S1.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Issues unrelated to those discussed in the public review

      (1) Figure 4a and its caption describe an evolution experiment, but they do not mention how many cycles of high-temperature treatment and growth this experiment lasted. I assume it lasted for more than one cycle, because the methods section mentions "cycles", but the number is not provided.

      Thank you for pointing this out. The evolutionary experiment shown in Figure 5a involved 11 cycles of high-temperature treatment and growth. We have now explicitly stated this in the figure legend to ensure clarity: BC: Batch culture, G: Evolution cycle number, C: Colony. BC2G11C1 refers to the first colony from batvh culture 2 after 11 rounds of heat treatment.

      (2) It is not clear what Figure 5F is supposed to show. What are the gray boxes? The caption claims that the figure shows non-synonymous mutations, but the only information it contains is about genes that seem to be affected by mutation. Judging from the mismatch between the main text and the figure, the mutants with these mutations may actually be mislabeled.

      Thank you for your careful review. Figure 5f highlights the non-synonymous mutations identified in the evolved strains. The gray boxes represent the ancestral strain’s whole genome without mutations, serving as a control. The corresponding labels indicate the specific mutations found in each evolved strain. We have clarified this in the figure caption to improve clarity. Additionally, we have carefully reviewed the labeling to ensure accuracy and consistency between the figure, main text, and sequencing data.

      (3) I think that the acronym NC, which is used in just about every figure, is explained nowhere in the paper. Spell out all acronyms at first use.

      Thank you for pointing this out. We have rivewed ensure that NC is clearly defined at its first mention in the text and figure legends to improve clarity. Additionally, we have reviewed the manuscript to ensure that all acronyms are properly introduced when first used.

      (4) The same holds for the acronym N.D. This is an especially important oversight because N.D. could mean "not determined" or "not detectable", which would lead to very different interpretations of the same figure.

      Thank you for your careful review. We have clarified the meaning of N.D., which stands for non-detectable, at its first use to avoid ambiguity and ensure accurate interpretation in the figure legend. Additionally, we have reviewed the manuscript to ensure that all acronyms are clearly defined.

      (5) The panel labels (a,b, etc.) in all figure captions are very difficult to distinguish from the rest of the text, and should be better highlighted, for example by using a bold font. However, this is a matter of journal style and will probably be fixed during typesetting.

      Thank you for your suggestion. We have adjusted the figure captions to better distinguish panel labels, such as using bold font, to improve readability and final formatting will follow the journal’s style during typesetting.

      (6) Line 224: enhanced insusceptibility -> reduced susceptibility.

      Thank you for your suggestion. We have revised “enhanced insusceptibility” to “reduced susceptibility” for clarity and precision.

      (7) Line 259: mice -> mouse.

      Thank you for catching this. We have corrected “mice” to “mouse”.

      Reviewer #2 (Recommendations for the authors):

      I have no concerns about the experimental design and conclusions of your work; however, I strongly recommend incorporating several relevant pieces of the literature related to your work, in the discussion of your manuscript, specifically:

      (1) Previous studies about the role of heat stress in phage infections, see:

      Greenrod STE, Cazares D, Johnson S, Hector TE, Stevens EJ, MacLean RC, King KC. Warming alters life-history traits and competition in a phage community. Appl Environ Microbiol. 2024 May 21;90(5):e0028624. doi: 10.1128/aem.00286-24. Epub 2024 Apr 16. PMID: 38624196; PMCID: PMC11107170.

      Thank you for your thoughtful comment. We have ensured to incorporate the study by Greenrod et al. (2024) into the discussion to enrich the context of our findings. As this article pointed out, a temperature of 42°C can indeed limit phage infection in bacteria, acting as a barrier from the phage’s perspective. Our study builds on this by demonstrating that bacteria pre-treated with high temperatures exhibit tolerance to phage infection. These findings, together with the work you referenced, underscore the importance of heat stress or elevated temperature in host-phage interactions, with 42°C being particularly relevant in the context of fever. We will make sure to clarify this connection in our revised manuscript.

      (2) The effect of heat stress and the tolerance/resistance against other antibiotics besides polymyxins, see:

      Lv B, Huang X, Lijia C, Ma Y, Bian M, Li Z, Duan J, Zhou F, Yang B, Qie X, Song Y, Wood TK, Fu X. Heat shock potentiates aminoglycosides against gram-negative bacteria by enhancing antibiotic uptake, protein aggregation, and ROS. Proc Natl Acad Sci U S A. 2023 Mar 21;120(12):e2217254120. doi: 10.1073/pnas.2217254120. Epub 2023 Mar 14. PMID: 36917671; PMCID: PMC10041086.

      Thank you for bringing this study to our attention. We have incorporated the findings from Lv et al. (2023) into the discussion of our manuscript, highlighting how sublethal temperatures may facilitate the killing of bacteria by antibiotics like kanamycin. This is consistent with our data showing enhanced susceptibility of heat-shocked bacteria to kanamycin. The study also provides insights into the potential role of PMF, which is relevant to our work on PspA, and strengthens the broader context of heat stress influencing both antibiotic resistance and tolerance.

      (3) Perhaps the most relevant overlooked fact was that recently it was demonstrated for E. coli, Klebsiella and Pseudomonas that pretreatment with lytic phages induced antibiotic persistence! Please discuss this finding and its implications for your work, see:

      Fernández-García L, Kirigo J, Huelgas-Méndez D, Benedik MJ, Tomás M, García-Contreras R, Wood TK. Phages produce persisters. Microb Biotechnol. 2024 Aug;17(8):e14543. doi: 10.1111/1751-7915.14543. PMID: 39096350; PMCID: PMC11297538.

      Sanchez-Torres V, Kirigo J, Wood TK. Implications of lytic phage infections inducing persistence. Curr Opin Microbiol. 2024 Jun;79:102482. doi: 10.1016/j.mib.2024.102482. Epub 2024 May 6. PMID: 38714140.

      Thank you for suggesting this important reference. We agree that the phenomenon of phage-induced bacterial persistence is highly relevant to our study. While our manuscript focuses on the role of heat stress in bacterial tolerance and resistance, we acknowledge that bacterial persistence against phages is an established concept. We have incorporated this finding into our discussion, emphasizing how persistence and tolerance can overlap in their effects on bacterial survival, especially under stress conditions like heat treatment. This will provide a more comprehensive understanding of how phage interactions with bacteria can lead to both persistence and resistance.

      (4) Finally, you observed a tradeoff pf the pspA* mutant increased phage/heat/polymyxin resistance and decreased immune evasion (perhaps by being unable to counteract phagocytosis), those tradeoffs between gaining phage resistance but losing resistance to the immune system, virulence impairment and resistance against some antibiotics had been extensively documented, see:

      Majkowska-Skrobek G, Markwitz P, Sosnowska E, Lood C, Lavigne R, Drulis-Kawa Z. The evolutionary trade-offs in phage-resistant Klebsiella pneumoniae entail cross-phage sensitization and loss of multidrug resistance. Environ Microbiol. 2021 Dec;23(12):7723-7740. doi: 10.1111/1462-2920.15476. Epub 2021 Mar 27. PMID: 33754440.

      Gordillo Altamirano F, Forsyth JH, Patwa R, Kostoulias X, Trim M, Subedi D, Archer SK, Morris FC, Oliveira C, Kielty L, Korneev D, O'Bryan MK, Lithgow TJ, Peleg AY, Barr JJ. Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials. Nat Microbiol. 2021 Feb;6(2):157-161. doi: 10.1038/s41564-020-00830-7. Epub 2021 Jan 11. PMID: 33432151.

      García-Cruz JC, Rebollar-Juarez X, Limones-Martinez A, Santos-Lopez CS, Toya S, Maeda T, Ceapă CD, Blasco L, Tomás M, Díaz-Velásquez CE, Vaca-Paniagua F, Díaz-Guerrero M, Cazares D, Cazares A, Hernández-Durán M, López-Jácome LE, Franco-Cendejas R, Husain FM, Khan A, Arshad M, Morales-Espinosa R, Fernández-Presas AM, Cadet F, Wood TK, García-Contreras R. Resistance against two lytic phage variants attenuates virulence and antibiotic resistance in Pseudomonas aeruginosa. Front Cell Infect Microbiol. 2024 Jan 17;13:1280265. doi: 10.3389/fcimb.2023.1280265. Erratum in: Front Cell Infect Microbiol. 2024 Mar 06;14:1391783. doi: 10.3389/fcimb.2024.1391783. PMID: 38298921; PMCID: PMC10828002.

      Thank you for highlighting these important studies. We have incorporated the work by Majkowska-Skrobek et al. (2021), Gordillo Altamirano et al. (2021), and García-Cruz et al. (2024) into the discussion to provide further context to the evolutionary trade-offs observed in our study. The findings in these studies, which describe the cross-sensitization to antimicrobials and the loss of multidrug resistance in phage-resistant bacteria, align with our observations of trade-offs in the pspA mutant. Specifically, our results show that while the pspA mutant exhibits increased resistance to phage, heat, and polymyxins, it also experiences a decrease in immune evasion and potential virulence. These trade-offs are significant in understanding the broader consequences of developing resistance to phages and other stressors.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Structural colors (SC) are based on nanostructures reflecting and scattering light and producing optical wave interference. All kinds of living organisms exhibit SC. However, understanding the molecular mechanisms and genes involved may be complicated due to the complexity of these organisms. Hence, bacteria that exhibit SC in colonies, such as Flavobacterium IR1, can be good models.

      Based on previous genomic mining and co-occurrence with SC in flavobacterial strains, this article focuses on the role of a specific gene, moeA, in SC of Flavobacterium IR1 strain colonies on an agar plate. moeA is involved in the synthesis of the molybdenum cofactor, which is necessary for the activity of key metabolic enzymes in diverse pathways.

      The authors clearly showed that the absence of moeA shifts SC properties in a way that depends on the nutritional conditions. They further bring evidence that this effect was related to several properties of the colony, all impacted by the moeA mutant: cell-cell organization, cell motility and colony spreading, and metabolism of complex carbohydrates. Hence, by linking SC to a single gene in appearance, this work points to cellular organization (as a result of cell-cell arrangement and motility) and metabolism of polysaccharides as key factors for SC in a gliding bacterium. This may prove useful for designing molecular strategies to control SC in bacterial-based biomaterials.

      Strengths:

      The topic is very interesting from a fundamental viewpoint and has great potential in the field of biomaterials.

      Thank you for this.

      The article is easy to read. It builds on previous studies with already established tools to characterize SC at the level of the flavobacterial colony. Experiments are well described and well executed. In addition, the SIBR-Cas method for chromosome engineering in Flavobacteria is the most recent and is a leap forward for future studies in this model, even beyond SC.

      We appreciate these comments.

      Weaknesses:

      The paper appears a bit too descriptive and could be better organized. Some of the results, in particular the proteomic comparison, are not well exploited (not explored experimentally). In my opinion, the problem originates from the difficulty in explaining the link between the absence of moeA and the alterations observed at the level of colony spreading and polysaccharide utilization, and the variation in proteomic content.

      We have looked at the organisation of the manuscript carefully in this revision, as suggested. In terms of the proteomics, there are a large number of proteins affected by the moeA deletion and not all could be followed up. We chose spreading, structural colour formation and starch degradation to follow up phenotypically, as the most likely to be relevant. For example, (L615-617) we discuss the downregulation of GldL (which is known to be involved Flavobacterial gliding motility [Shrivastava et al., 2013]) in the moeA KO as a possible explanation for the reduced colony spreading of this mutant. Changes in polysaccharide (starch) utilization were seen on solid medium, as well as in the proteomic profile where we observed the upregulation of carbohydrate metabolism proteins linked to PUL (polysaccharide utilisation locus) operons (Terrapon et al., 2015), such as PAM95095-90 (Figure 8), and other carbohydrate metabolism-related proteins, including a pectate lyase (Table S7) which is involved in starch degradation (Aspeborg et al., 2012). And as noted in L555-566 and Figure 9, alterations in starch metabolism were investigated experimentally.

      First, the effect of moeA deletion on molybdenum cofactor synthesis should be addressed.

      MoeA is the last enzyme in the MoCo synthesis pathway, thus if only MoeA is absent the cell would accumulate MPT-AMP (molybdopterin-adenosine monophosphatase) (Iobbi-Nivol & Leimkühler, 2013), and the expressed molybdoenzymes would not be functional. In L582-585, we commented how the lack of molybdenum cofactor may affect the synthesis of molybdoenzymes. However, if you meant to analyse the presence of the small molecules, i.e. the cofactors involved in these pathways, that was an assay we were not able to perform. However, in L585-587, we addressed how the deletion of moeA affected the proteins encoded by the rest of genes in the operon which is relevant to the question.

      Second, as I was reading the entire manuscript, I kept asking myself if moeA (and by extension molybdenum cofactor) was really involved in SC or it was an indirect effect. For example, what if the absence of moeA alters the cell envelope because the synthesis of its building blocks is perturbed, then subsequently perturbates all related processes, including gliding motility and protein secretion? It would help to know if the effects on colony spreading and polysaccharide metabolism can be uncoupled. I don't think the authors discussed that clearly.

      The message of the paper is that the moeA gene, as predicted from a previous genomics analysis, is important in SC. This is based on the representation of the moeA gene in genomes of bacteria that display SC. This analysis does not predict the mechanism. When knocked out, a significant change in structural colour occurred, supporting this hypothesis. Whether this effect is direct or indirect is difficult to assess, as this referee rightly suggests. In order to follow up this central result, we performed proteomics (both intra- and extracellular). As we observed, the deletion of a single gene generated many changes in the proteomic profile, thus in the biological processes. Based on the known functions of molybdenum cofactor, we could only hypothesize that pterin metabolism is important for SC, not exactly how.

      We have discussed the links between gliding/spreading and polysaccharide metabolism more clearly, with reference to the literature, as quite a bit is known here including possible links to SC.

      “Polysaccharide metabolism in IR1 has been linked to changes in colony color and motility through the study of fucoidan metabolism (van de Kerkhof et al., 2022). Polysaccharide degradation and gliding motility are coupled to the same mechanism: the phylum-specific type IX secretion system, used for the secretion of enzymes and proteins involved in both functions (McKee et al., 2021).” [L622-626]

      Reviewer #2 (Public review):

      Summary:

      The authors constructed an in-frame deletion of moeA gene, which is involved in molybdopterin cofactor (MoCo) biosynthesis, and investigated its role in structural colors in Flavobacterium IR1. The deletion of moeA shifted colony color from green to blue, reduced colony spreading, and increased starch degradation, which was attributed to the upregulation of various proteins in polysaccharide utilization loci. This study lays the ground for developing new colorants by modifying genes involved in structural colors.

      Major strengths and weaknesses:

      The authors conducted well-designed experiments with appropriate controls and the results in the paper are presented in a logical manner, which supports their conclusions.

      We appreciate these comments.

      Using statistical tests to compare the differences between the wild type and moeA mutant, and adding a significance bar in Figure 4B, would strengthen their claims on differences in cell motility regarding differences in cell motility.

      Thank you. Figure 4B contains the significance bars that represent the standard deviation of the mean value of the three replicates, but we have modified it to make them more clear.

      Additionally, in the result section (Figure 6), the authors suggest that the shift in blue color is "caused by cells which are still highly ordered but narrower", which to my knowledge is not backed up by any experimental evidence.

      Thanks. We mentioned that the mutant cells are narrower than the wild type based on the estimated periodicity resulting from the goniometry analysis (L427-430). We will now say “likely to be narrower based on the estimated periodicity from the optical analysis” rather than just “narrower”.

      “This optical analysis aligns with visual observations, confirming the blue shift in ΔmoeA, and suggests that this change in SC is caused by cells which are likely to be narrower based on the estimated periodicity from the optical analysis.” [L409-411]

      Overall, this is a well-written paper in which the authors effectively address their research questions through proper experimentation. This work will help us understand the genetic basis of structural colors in Flavobacterium and open new avenues to study the roles of additional genes and proteins in structural colors.

      Much appreciated.

      Recommendations for the authors:

      Reviewing Editor Comments:

      As you will see, the reviewers were rather positive about the paper but suggested a number of points to improve it, including a discussion of the direct role of moeA as well as specific editorial comments.

      Reviewer #1 (Recommendations for the authors):

      More specific comments to the authors:

      (1( Line 300, Paragraph on bioinformatic analysis of molybdopterin operon : As written, it is not clear whether this operon is crucial for pterin cofactor synthesis or only some genes are involved. And what is the contribution of moeA?

      Based on the bioinformatic analysis done in Zomer et al., 2024, we know the score of which genes of the molybdopterin cofactor synthesis operon may be more relevant to the display of SC, in addition to moeA. We chose moeA to KO as it had the highest score, being careful to delete the coding sequence and not any upstream promoter. The other genes in the predicted operon are moaE, moaC2, and moaA. Then in the proteomic analysis (L435-442), we analysed how the encoded proteins from this operon were upregulated (MoaA, MoaC2, and MobA), indicating also the unaltered proteins (MoeZ and MoaE) and the undetected proteins (MoaD and SumT). Nevertheless, the operon is crucial for pterin cofactor synthesis because it contains all the genes involved in the pathway, and moeA encoded the enzyme for the last reaction of the pathway, being the the molecule produced in the mutated pathway the adenylated molybdopterin (MPT-AMP) instead of molybdenum cofactor (MoCo).

      (2) Paragraph line 342 on moeA mutant phenotyping :

      Is the reduction in colony spreading caused by a defect in single-cell gliding motility or is the cause more complex? This can be quantified.

      We believe the cause is more complex. As mentioned above, for example, in (L615-617) we discuss the downregulation of GldL (which is known to be involved Flavobacterial gliding motility [Shrivastava et al., 2013]) in the moeA KO as a possible explanation for the reduced colony spreading of this mutant. This cannot be explained simply by spreading, but must (from the optical analysis) indicate changes in cell organisation/dimensions.

      (3) During the description of the moeA mutant phenotype (associated with Figures 2 and 4) and throughout the article, the optical properties are « functions » of colony spreading and moeA-dependent metabolism. However it is not quite clear if these two effects are independent or if one may be a consequence of the other.

      As noted above, colony spreading alone does not explain the blue-shift in SC observed. Given the function of MoeA (molybdate insertion into MPT-AMP [adenylated molybdopterin], MoMPT [molybdenum-molybdopterin] formation) for the synthesis of MoCo (molybdenum cofactor), the primary effect seems to be on metabolism but as we are dealing with an influential enzymatic cofactor a number of secondary effects are likely, and indeed the proteomics supports this. It is likely that the effect on spreading is secondary as seen with the downregulation of GldL (see above), but we cannot be sure.

      (4) Paragraph starting line 381 and Figure 5 on gliding motility:

      Gliding motility has to be tested at the level of single cells, allowing a more thorough characterization of the spreading defects. In addition, since gliding is entangled with Type IX-dependent secretion in Flavobacteria, the authors should test if Type IXdependent was perturbed in the absence of moeA.

      Based on the intracellular and extracellular proteomic analyses, the regulated T9SS proteins in the absence of moeA are the downregulation of GldL and SprT, and the upregulation of PorU. It shows the log2 FC (moeA/WT) of each these extracellular proteins:

      Author response table 1.

      <-1: downregulated in moeA KO, -1<X<1: no significant regulation, >1: upregulated in moeA KO, -: not detected

      (5) L401: In my opinion, the section "Quantification of the optical responses of IR1 WT and ΔmoeA colonies" should be moved up, before the characterization of motility.

      We have done this, as suggested. The section was moved from L401-423 to L388-411.

      (6) L475: Proteome comparison: « Of the total known proteins in IR1, 27.5% (1,504 proteins) extracellular proteins were identified » Are some of these proteins also found in the cell fraction? Wouldn't it be more accurate to write that « 1504 proteins were found in the extracellular fraction"?

      We have done this, as suggested.

      “Of the total known proteins in IR1, 27.5% (1,504 proteins) proteins were detected in the extracellular fraction, 60.4% (909) were statistically significant (p<0.01), with 20.5% (186) considered downregulated, and 20% (182) upregulated in ΔmoeA (Figure 7B).” [L484-486]

      How can the authors exclude contamination of the extracellular fraction? This could easily explain the number of proteins lacking secretion signals: "29.6% (55) were likely secreted through a non-classical way, lacking typical secretion sequence motifs in their N-terminus."

      Based on the results from SecretomeP and SignalP, we excluded contamination, reducing the significant downregulated proteins from 186 (L476) to 69 (L486), and the upregulated ones from 182 (L477) to 111 (L500).

      (7) L490: if the protein misannotated flagellin is highly downregulated, why not push the analysis a bit further and ask what true function may be perturbed? In addition, it should not be classified as a motility protein in Table S6 and considered as a motility protein in the article.

      We reconsidered the information given by this and decided to remove it because after checking the homology of the polypeptide by Blast searching, we feel it is probably due to a missannotation.

      As is, the whole proteomic section is not that useful. Too many functions are evoked and the reader is not directed toward any particular conclusion. The most convincing hits from the proteomic analysis should be confirmed using another method. Transcriptional regulation could be easily probed by RT-qPCR. Or, since genetics is possible, proteins could be tagged and levels compared by western blot maybe? Do knock-out of the encoding genes generate any phenotype on SC? This would bring weight to the proteomic analysis.

      We have revised the proteomics section and removed functions that are not directly relevant to our conclusion.

      We feel the most important observation suggested by proteomics was the possible link between moeA and starch metabolism, because the metabolism of complex polysaccharides is important in the Flavobacteriia and known to be linked to SC (van de Kerkhof et al., 2022). It was not possible to follow up every pathway suggested by the proteomics, but the study is appropriately performed with the correct statistics.

      (8) Figure 9 : Does the absence of moeA affect the spreading of ASWS? Were colony sizes similar during the starch degradation assay? How can the authors rule out the idea that starch degradation is impacted by the difference in spreading rather than an independent function of moeA in starch metabolism? Slower spreading could lead to the accumulation of amylases, hence stronger activity. Why does starch degradation only accumulate at the center of the colony in the WT case?

      The colonies of the WT and moeA had similar size during the starch degradation assay (2 days). However, after day 3, only WT colonies kept expanding on diameter.

      Starch degradation is logically in the centre of the colony as it is where the greatest concentration of cells exists, secreting degradative enzymes, for the longest time. Presumably starch degradation at the colony edge is not yet seen as the action of extracellular enzymes is low and has not had time to degrade the starch to the point that there is no iodine staining.

      “In contrast to other media where ΔmoeA colony expansion was less than WT, the ΔmoeA showed similar colony spreading and stronger starch degradation, supporting a role of moeA in complex polysaccharides metabolism.” [L562-565]

      (9) Finally, I am not quite sure what the authors mean by « a role of moeA in complex polysaccharides metabolism ». Are they referring to enzymes secreted in the medium to degrade starch? or to the incorporation and use of starch degradation products?

      We meant that the deletion of moeA showed an increase of extracellular starch degradation as seen in the iodine assay (Figure 9), as well as the upregulation of three different PUL operons (Figure 8).

      Reviewer #2 (Recommendations for the authors):

      The paper in general is well written with proper experimentation. However, here are a few recommendations for improving the writing and presentation, including minor corrections to the text and figures.

      Thank you.

      (1) It would be helpful for the readers if you could expand on "some metabolic pathways" in line 71. Please provide examples of metabolic pathways that are linked to SC.

      We have done this.

      “A recent bioinformatic study has shown the possible link of some metabolic pathways, such as carbohydrate, pterin, and acetolactate metabolism, to bacterial SC (Zomer et al., 2024).”[L70-72]

      (2) "Line 79 : a bioinformatics analysis", please mention what kind of bioinformatics analysis was done and by whom to provide clarity for the readers: Either mention bio info analysis or give more details on what kind of bio info analysis and study done by whom"

      We have clarified this, as suggested.

      “A large-scale, genomic-based analysis of 117 bacteria strains (87 with SC and 30 without) identified genes potentially involved in SC by comparing gene presence/absence, providing a SC-score (Zomer et al., 2024). By this method, pterin pathway genes were strongly predicted to be involved in SC.” [L80-83]

      (3) Please correct "Bacteria strains used in this study" to "bacterial" strains in Line 122.

      We have done so.

      (4) Please indicate in "Lines 394-396" that there were no vortex patterns observed in the moeA mutant.

      We have done so.

      “In contrast, ΔmoeA exhibited limited motility, with a more tightly packed cell organization and a fine, slow-moving layer at the edge (Figure 6, blue arrows), and did not show a ‘vortex’ pattern. This suggests that moeA deletion significantly impairs cell motility and colony expansion.” [428-L431]

      (5) In Figure 4 it looks like with a different carbon source (ASWB with agar and Fucoidan (ASWBF)) the moeA mutant and wild type exchanges its phenotype compared to ASWBKC. Could you explain why this happens in the discussion by highlighting the differences between fucose and Kappa-Carrageenan or confirm if there are any differences in the carbohydrate utilization between the wild type and moeA mutant using biolog assays?

      We have explained the differences. Biolog would not be appropriate as we are looking for metabolic processes of bacteria on surfaces (agar) and this is not necessarily appropriate to biolog, which we understand uses liquid cultivation in microplates.

      “On different polysaccharide media, the ΔmoeA strain showed varied SC and colony expansion patterns: green/blue SC and low colony expansion on agar, intense blue SC and low colony expansion on kappa-carrageenan, dull green SC and low colony expansion on fucoidan, and blue/green SC with higher colony expansion on starch. Interestingly, the color phenotype of the WT and ΔmoeA exchanged their phenotype on kappa-carrageenan (a simple linear sulfated polysaccharide of D-galactopyranose) and fucoidan (a complex sulfated polysaccharide of fucose and other sugars as galactose, xylose, arabinose and rhamnose), showing the importance of the polysaccharide metabolism in SC. While reduced motility has been associated with dull or absent SC, and reduced polysaccharide metabolism (Kientz et al., 2012a; Johansen et al., 2018), ΔmoeA showed reduced motility, but an intense blue SC, and high polysaccharide metabolism. Based on these results, we established a link among polysaccharide metabolism, MoCo biosynthesis, and SC, showing that intense SC is not strictly dependent on motility.” [L636-648]

      (6) In the discussion "Line 632" it is unclear what loss is being limited, and it would help strengthen your discussion if you could add references for lines: 633-636. There are a lot of hypotheses in lines 637-642, it would help the readers if you could clearly mention that these are hypotheses and will need experimental evidence or provide appropriate evidence to support these claims.

      We have done this.

      “Ecologically, we hypothesize that dense, highly structured bacterial colonies, such as necessary for the SC phenotype, can enhance the uptake of metabolic degradation products from complex polysaccharides. These large macromolecules are often partially hydrolyzed extracellularly because they are too large to pass through bacterial cell membranes. For example, marine Vibrionaceae strains that produce lower levels of extracellular alginate lyases tend to aggregate more strongly, potentially facilitating localized degradation and uptake of polysaccharides (D’Souza et al., 2023). Additionally, certain marine bacteria employ a "selfish" mechanism to internalize large polysaccharide fragments into their periplasmic space, minimizing loss to the environment and enhancing substrate utilization (Reintjes et al., 2017). Bacteria secrete enzymes into the surrounding environment to break these polysaccharides down into more easily absorbable monosaccharides or oligosaccharides. This mechanism suggests that the colony structure could create a physical barrier that keeps these products concentrated and near the cells, allowing the colony to efficiently access and utilize these products, preventing the leakage into the surrounding environment. While SC may also yield other ecological benefits associated with growth in biofilms, the highly structured colonies that characterize SC may be more resistant against invasion by competitor species scavenging for degradation products, than an unstructured biofilm. This model is consistent with the observation that SC is associated with polysaccharide metabolism genes, and with the recent observation that SC is mainly localized on surface and interface environments such as airwater interfaces, tidal flats, and marine particles (Zomer et al., 2024).” [L650-670]

      (7) It would help the readers if you could expand on how polysaccharide metabolism is linked to motility in Line 610.

      As indicated previously, this is known and we will clarify.

      “Polysaccharide metabolism in IR1 has been linked to changes in colony color and motility through the study of fucoidan metabolism (van de Kerkhof et al., 2022).” [L622-623]

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer 1:

      In the article titled "Polyphosphate discriminates protein conformational ensembles more efficiently than DNA promoting diverse assembly and maturation behaviors," Goyal and colleagues investigate the role of negatively charged biopolymers, i.e., polyphosphate (polyP) and DNA, play in phase separation of cytidine repressor (CytR) and fructose repressor (FruR). The authors find that both negative polymers drive the formation of metastable protein/polymer condensates. However, polyPdriven condensates form more gel- or solid-like structures over time while DNA-driven condensates tend to dissipate over time. The authors link this disparate condensate behavior to polyP-induced structures within the enzymes. Specifically, they observe the formation of polyproline II-like structures within two tested enzyme variants in the presence of polyP. Together their results provide a unique insight into the physical and structural mechanism by which two unique negatively charged polymers can induce distinct phase transitions with the same protein. This study will be a welcomed addition to the condensate field and provide new molecular insights into how binding partner-induced structural changes within a given protein can affect the mesoscale behavior of condensates. The concerns outlined below are meant to strengthen the manuscript.

      Recommendation:

      We value the reviewer’s positive comments and appreciate time taken to provide detailed feedback that has certainly helped improve our manuscript.

      Major Concerns:

      (1) The biggest concern in this manuscript lies with experiments comparing polyP45, which has a net negative charge of -47, and double-stranded DNA of 45 base pairs (as stated in the methods), which will have a net negative charge of -90. Given the dependence of phase separation and phase transitions on not only net charge but charge density, this is an important factor to consider when comparing the effect of these molecules. It is unclear how or if the authors considered these factors in the design of their experiments. Because of the factor of 2 difference in net charge over the same number of polymer chain components, i.e. a chain of 45 pi vs. a chain of 45 double-stranded base pairs, it is unclear if the results from polyP vs. DNA are directly comparable. One solution would be to repeat all DNA experiments using single-stranded DNA so that the net charge is similar to polyP over the same chain length. Another possibility would be to repeat DNA experiments using a doublestranded DNA of 23 base pairs. This would allow for a nearly equal net charge (-46 vs. -47 for polyP), but the charge density would still be 2X polyP. As it stands now, the perceived differences in DNA vs. polyP behavior may be an artifact arising from the difference in net charge and charge density between DNA and polyP.

      To address the reviewer’s concerns regarding charge density differences between polyP and DNA, we conducted an experiment using a higher DNA concentration (11.24 µM) to obtain charge equivalence between the two experiments (i.e. the total concentration of charges). As shown in Figure S5, even at higher DNA concentration, the condensates undergo progressive dissolution over time. This observation indicates that the differential maturation of condensates, arising from distinct initial protein ensembles, are governed by the intrinsic properties of polyP. Charge density (i.e. the number of charges per unit volume of the polymer), on the other hand, is an intrinsic feature of the polymer which is naturally different between DNA and polyP. In fact, the primary result of our work is our observation that polyP can discern the starting ensembles more efficiently, likely through actively engaging and interacting with the ensemble while DNA appears to be a passive player. The differences are not an artifact as they arise from fundamental features of two natural anionic polymers found within cells. In other words, the outcomes could be very different if the concentration of one polymer dominates over the other (see the response below).

      (2) One outstanding question the authors do not address relates to how mixtures of CytR or FruR, DNA, and polyP behave. In the bacterial cytoplasm, these molecules are all in the same compartment (admittedly that compartment is not well mixed due to unique condensate-driven organization). Would the authors expect to see similar effects of polyP and DNA if they were in the same solution? Perhaps the authors could run a set of experiments where they vary the ratios of DNA and polyP to probe how increased levels of "stress", i.e. increased levels of polyP vs. DNA, alter the formation and behavior of enzymatic condensates.

      Following this comment, we investigated the phase separation behavior of CytR WT in the presence of different charge ratios of polyP-DNA mixtures. As seen in Author response image 1,panel A below, the outcomes are highly sensitive to the starting concentrations: at higher charge concentration of polyP (left panel), the OD and ThT fluorescence intensity is high at lower time points, both decrease and increase again. Fluorescence microscopy images (panel B) reveal similar trends, but the more fascinating outcome are the FRAP recovery profiles which recover extremely fast and fully at zero time point (panel C) despite aggregation-like tendencies observed in ThT fluorescence assays. However, at longer time points (20 and 40 mins) the FRAP recovery is significantly weaker but recovers to ~65% at 1 hour (panel C). At high relative polyP concentrations with respect to DNA, droplets are formed first which then transition into aggregates (liquid-to-solid transition; middle image in panel A). At relatively high DNA concentrations it appears that both droplets and aggregates co-exist as both OD and ThT fluorescence are moderately high. Given these complex behaviors, we have not included the same in the current manuscript as we still do not fully understand the origins of these differences. In fact, we are planning to extend this study by exploring the combinations in detail to understand the relative roles played by the two polymers in ternary mixtures.

      Author response image 1.

      (3) In Figure 1H, the recovery trace shows the fractional recovery of DM to near WT levels. It is clear from the images that recovery of the bleached region occurs, but the overall fluorescence intensity of DM is much lower than WT, even when accounting for the difference in starting condensate sizes in the Pre-Bleach images. Shouldn't this qualitative difference in total fluorescence be reflected in the quantitative trace?

      In Figure 2H, as the reviewer rightly points out, there is a clear difference in the absolute fluorescence intensity between WT and DM condensates. We would like to clarify that the recovery traces shown in Figure 2I were normalized to the pre-bleach intensity of each individual condensate to reflect fractional recovery. This normalization is intended to highlight the relative mobility of the protein within each condensate, but it does not capture the difference in total fluorescence intensity between WT and DM.

      (4) A description of the molten-globular variant Y19A FruR should be included in the main text where the variant is introduced. There is currently no additional description of the molten-globular variant in the Supplement as suggested by the manuscript.

      Figure 6A depicts the three-dimensional structure of FruR WT, with tyrosine residues Y19 and Y28, shown in red, forming stacking interactions. In the Y19A mutant, the loss of these interactions results in little changes in secondary structure (as shown in Figure 6E) but disrupts the protein’s tertiary structure, resulting in a molten globular state. The FruR work is now published in JPCB and can be found at https://doi.org/10.1021/acs.jpcb.4c03895, and is also appropriately cited in the revised version (reference 53).

      (5) Throughout the manuscript, the authors discuss polyP and DNA being able (or unable) to "distinguish" between different variants of CytR and FruR. This is confusing and suggests that DNA or polyP can choose to bind one form over another. The authors should re-work the language in this section to better reflect their direct observations for the behavior of protein in CD experiments and condensate behavior in imaging and turbidity experiments.

      We have now modified the text where necessary. The experiments were not done in the presence of both polyP and DNA, but in isolation (protein + polyP or protein + DNA). Hence, our aim is to convey that polyP is the polymer that leads to variable outcomes because of its ability to ‘interact’ differently with the different starting ensembles.

      Minor Concerns:

      (1) For all Figures, please include the number of measurements, i.e., N = ...

      We have updated all figure legends to include the number of measurements, indicated as N = ..., as suggested.

      (2) For all Figures, please place panel labels, i.e., A, B, C, etc., in the same respective location for each panel. As currently mapped out, it is difficult to easily determine which data are associated with each panel because the IDs are in various locations.

      Due to variations in data presentation and spacing within individual plots, it was challenging to place all labels in exactly the same position without obscuring important details. We have therefore maintained the labels as they were before.

      (3) In the introduction, it would be helpful for the authors to specify exactly what is meant by chaperone. Given the context, it seems that the authors refer to the chaperone activity as one that prevents aggregation. Is this correct?

      We refer to chaperone activity specifically as the ability to prevent aggregation of proteins. We have now clarified this definition in the Introduction section of the revised manuscript.

      (4) The results for experiments shown in Figure 3 need additional setup in the text. Were these measurements taken immediately after mixing WT, DM, or P33A with polyP? If so, why do condensates immediately appear and then dissipate before ThT-detected aggregates begin forming? Or were condensates allowed to form and then transferred to a different buffer, after which measurements were taken? Without a brief description of the experimental setup, interpreting the results is difficult.

      The condensates appear immediately after adding polyP to protein solutions, indicating that the condensate phase is kinetically accessible on mixing polyP with DM or the WT. As illustrated in Figure 3A and 3B, for WT protein, the condensates undergo liquid to solid transition over the time as this likely is the most thermodynamically stable phase. Effectively, this work is to convey that it is important to look at time-dependence of even droplets when formed as they may not be the most stable phase.

      (5) Please include images of P33A over the time course of the experiment in Figure 3B.

      We have included the representative images of P33A in presence of polyP over the time in Figure 3B in the revised manuscript.

      (6) In Figures 3D, E, G, and H, please plot each measurement separately with mean and standard deviation to enable the reader to see each data point.

      We have now revised Figures 3D, E, G, and H to show individual data points along with the mean and standard deviation.

      (7) In the top paragraph on page 12, "fast-moving molecules" can be replaced with "dynamic molecules", as this offers a better description of the FRAP data.

      We have incorporated the suggested changes.

      (8) In the "Structural changes within the condensates spans over three hours" results section on page 15, the conclusion reads "In summary, we find that both the WT and the DM 'unfold' on forming condensates with polyP..." The way this is written suggests that WT and DM behave in a similar manner. Given the CD data, however, it seems that by 4 hours, DM forms alpha helices while the WT does not. This suggests that while each unfolds, the conformation at 4 hours is different. The summary should reflect these differences.

      We fully agree with the reviewer on this. The summary is now modified to include the fact the DM forms alpha helices at 4 hours while the WT does not.

      (9) At the end of the first paragraph of the results section "DNA does not discriminate the conformational ensembles" the authors should refer to Figure 2G, where they show the altered morphology of polP-P33A condensates.

      We have now included the reference to Figure 2G.

      (10) The authors refer to droplets "solubilizing" throughout the manuscript. It seems that dissolve is a better term to use. Solubilize is better associated with individual biomolecules while dissolve is better associated with condensate behavior.

      We thank the reviewer for pointing this out. We have revised the manuscript to replace “solubilize” with “dissolve”.

      (11) In Figures 5L and 5N, please change the Y-axis scale so that each curve is visible on the plot.

      We have adjusted the Y-axis scale in Figures 5L, 5M, and 5N to ensure that each curve is clearly visible and for easier comparison among the variants.

      (12) The authors should show an image of FruR WT and Y19A with DNA for a direct comparison with experiments in which FruR and polyP were used. The addition of turbidity measurements of samples shown in Figure 6D will offer another direct comparison. As written, there is no way for the author to directly compare the effects of polyP and DNA on FruR phase transitions.

      As suggested, we have now included representative images of FruR WT and Y19A with DNA (Figure 6K and 6L) to enable a direct comparison with the FruR–polyP experiments. Also, we have already shown turbidity measurements in Figure 6B and 6C corresponding to the samples shown in Figure 6D.

      Reviewer 2:

      In this study, Goyal et al demonstrate that the assembly of proteins with polyphosphate into either condensates or aggregates can reveal information on the initial protein ensemble. They show that, unlike DNA, polyphosphate is able to effectively discriminate against initial protein ensembles with different conformational heterogeneity, structure, and compactness. The authors further show that the protein native ensemble is vital on whether polyphosphate induces phase separation or aggregation, whereas DNA induces a similar outcome regardless of the initial protein ensemble. This work provides a way to improve our mechanistic understanding of how conformational transitions of proteins may regulate or drive LLPS condensate and aggregate assemblies within biological systems.

      We thank the reviewer for the favorable comments on the manuscript.

      Major Concerns:

      (1) The authors are using bacterial proteins (CytR and FruR) and solely represent polyphosphates as polyP45 (a polyphosphate with 45 Pi units). However, in bacterial systems, polyphosphates can be significantly longer (in the order of 100s to 1000 Pi units). Additionally, the experiments were run at neutral pH (7.0), and though this is fairly appropriate for the cytoplasm, volutin granules (where polyphosphates often accumulate) are typically considered slightly acidic (pH 5.5-6.5). From a physiological perspective, understanding how pH and the length of polyphosphate influence the ability to induce condensates or aggregates could be of importance.

      We appreciate the reviewer’s insightful comments regarding the physiological relevance of polyphosphate length and pH. In our current study, we used polyP45 as it is easily available commercially and we conducted our experiments at pH 7 to mimic the general cytoplasm conditions. We agree that polyphosphates in bacterial cells can be significantly longer (hundreds to thousands of Pi units) and conducting experiments at slightly more acidic environment would be physiologically relevant. We plan to use longer polyP from Regene Tiss Inc. and acidic pH to explore how polyphosphate-induced phase separation of CytR vary with pH as a part of a future study. One could imagine doing all the experiments listed in the manuscript at different pH conditions for the different variants, but this could not be a part of the current work which has a specific focus on the differences in maturation properties depending on the nature of starting ensemble. However, the pKa values of the internal hydroxyl groups is ~2.2 (DOI:10.2147/IJN.S389819) indicating that the polyP carries near identical charges in the pH range between 4-7, and hence we expect little change in the charged status of polyP. On the other hand, the protonation states of charged amino acids within CytR could vary with pH, thus influencing its assembly properties.

      (2) In the study, the longest metastable condensate induced by polyphosphate lasted approximately 3 hours before resolubilizing. It would be nice if the authors were able to generate a longer-lived condensate phase that would enable further mechanistic studies (e.g., NMR).

      We agree that generating longer-lived condensates would be highly valuable for mechanistic studies. However, the formation and stability of condensates is an intrinsic property of protein, and optimizing different conditions for a longer-lived condensate phase is beyond the scope of the current study. It is possible that the condensates are long-lived with longer polyP, but it is not clear if this would indeed be the case. We would also like to state here that while it is common to report on the liquid-to-solid transition in condensates, the intrinsic metastability of droplets (when there is no aggregation) is rarely reported. One possibility is to mutationally introduce cysteine residues and induce the formation of disulphide bridges (as done in a recent work, doi: 10.1021/jacs.4c09557) that make the condensate highly stable kinetically; however, this would also complicate the interpretation as the mechanism of condensate formation might be very different. We have therefore reported our results as an observation arising from differences in the nature of the poly-anionic polymers.

      (3) The authors showed that CytR DM (fully folded), CytR WT (minor state folded), and CytR P33A (highly disordered) with polyphosphates lead to longer-lived condensates that resolubilize, shorterlived condensates that aggregate, and immediate aggregating, respectively. Whereas FruR (folded) and FruR Y19A (molten globular) with polyphosphate induce spontaneous aggregation and short-lived condensates, respectively. I would expect FruR to be more similar to CytR DM and FruR Y19A more similar to CytR WT in terms of structure and conformational dynamics and plasticity, yet they have opposing results. This raises a bit of concern. Meaning, that though polyphosphate discriminates between the different ensembles, is it actually possible to obtain information on the initial ensemble composition?

      In the current study, we show that CytR WT (less structured) and FruR Y19A (molten globule) form short-lived condensates that aggregate. We agree with the reviewer that while CytR DM (fully folded) forms condensates that dissolve over time, FruR WT (fully folded) variant forms aggregates immediately upon polyP addition. The observations show that polyP can discriminate between different protein conformations, in contrast to DNA, which does not show such selectivity. However, we acknowledge that while polyP-induced behavior reflects aspects of protein ensemble properties, it does not provide direct insight into the nature of the initial conformational ensemble.

      (4) In the case of FruR with polyphosphate, no CD for the secondary structure analysis was provided as it was for CytR. It would be useful to see if the polyphosphate-induced structural changes observed for CytR hold true for FruR as well.

      We thank the reviewer for the suggestion. In response, we have performed far-UV CD experiments on FruR variants in the presence of polyP. Similar to the CytR WT, FruR WT shows unfolding upon polyP addition. A similar outcome is noted for the Y19A variant though there is significant residual helix content in the condensate unlike the WT. The CD spectra of FruR variants have been added to Figure 6.

      Minor Concerns/Suggestions:

      Under conclusion, third paragraph, first sentence. This sentence reads, "Our observations thus establish that polyP efficiently discriminates the conformational features of proteins than DNA, contributing to the diverse outcomes."

      We thank the reviewer for pointing this out. The sentence has been revised for clarity. It now reads “Our observations establish that polyP is more sensitive to the conformational features of proteins than DNA, thereby contributing to the diverse outcomes.”

      One experimental suggestion. Seeing that protein dynamics and plasticity seem to play a role. For either CytR WT or DM, it would be interesting to see the influence of temperature. Altering the temperature is a good way to perturb the population distribution of conformation sub-states and to alter kinetics. It may be that at a lower temperature (maybe 5C) for the WT you reduce conformational dynamics and you obtain results more similar to that of the DM. Alternatively, heating the DM would be another option. Obviously, there are additional challenges that may arise with changing the temperature, but if it were to work I think it could add some value.

      We thank the reviewer for the thoughtful suggestion. Due to limitations in our current experimental setup (as the reviewer notes as ‘challenges’)- the confocal set up does not have a temperature controller - we will not be to perform temperature-controlled assays. However, the ‘structure’ of CytR variants do not vary much between 280 – 298 K, and this is one of the reasons for choosing three variants without altering any other thermodynamic property. If temperature were varied, the dynamics of polyP would also change and hence the true molecule origins of any differences we might observe will be confounded by the dynamic effects on polyP as well. In this work, we have eliminated any dynamic differences in polyP by performing the experiments at a fixed temperature.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      One enduring mystery involving the evolution of genomes is the remarkable variation they exhibit with respect to size. Much of that variation is due to differences in the number of transposable elements, which often (but not always) correlates with the overall quantity of DNA. Amplification of TEs is nearly always either selectively neutral or negative with respect to host fitness. Given that larger effective population sizes are more efficient at removing these mutations, it has been hypothesized that TE content, and thus overall genome size, may be a function of effective population size. The authors of this manuscript test this hypothesis by using a uniform approach to analysis of several hundred animal genomes, using the ratio of synonymous to nonsynonymous mutations in coding sequence as a measure of the overall strength of purifying selection, which serves as a proxy for effective population size over time. The data convincingly demonstrates that it is unlikely that effective population size has a strong effect on TE content and, by extension, overall genome size (except for birds).

      Strengths:

      Although this ground has been covered before in many other papers, the strength of this analysis is that it is comprehensive and treats all the genomes with the same pipeline, making comparisons more convincing. Although this is a negative result, it is important because it is relatively comprehensive and indicates that there will be no simple, global hypothesis that can explain the observed variation.

      Weaknesses:

      In several places, I think the authors slip between assertions of correlation and assertions of cause-effect relationships not established in the results.

      Several times in the previous version of the manuscript we used the expression “effect of dN/dS on…” which might suggest a causal relationship. We have rephrased these expressions and highlighted the changes in the main text, so that correlation is not mistaken with causation (see also responses to detailed comments below).

      In other places, the arguments end up feeling circular, based, I think, on those inferred causal relationships. It was also puzzling why plants (which show vast differences in DNA content) were ignored altogether.

      The analysis focuses on metazoans for two reasons: one practical and one fundamental.

      The practical reason is computational. Our analysis included TE annotation, phylogenetic estimation and dN/dS estimation, which would have been very difficult with the hundreds, if not thousands, of plant genomes available. If we had included plants, it would have been natural to include fungi as well, to have a complete set of multicellular eukaryotic genomes, adding to the computational burden. The second fundamental reason is that plants show important genome size differences due to more frequent whole genome duplications (polyploidization) than in animals. It is therefore possible that the effect of selection on genome size is different in these two groups, which would have led us to treat them separately, decreasing the interest of this comparison. For these reasons we chose to focus on animals that still provide very wide ranges of genome size and population size well suited to test the impact of genetic drift on the genomic TE content.

      Reviewer #2 (Public review):

      Summary:

      The Mutational Hazard Hypothesis (MHH) is a very influential hypothesis in explaining the origins of genomic and other complexity that seem to entail the fixation of costly elements. Despite its influence, very few tests of the hypothesis have been offered, and most of these come with important caveats. This lack of empirical tests largely reflects the challenges of estimating crucial parameters.

      The authors test the central contention of the MHH, namely that genome size follows effective population size (Ne). They martial a lot of genomic and comparative data, test the viability of their surrogates for Ne and genome size, and use correct methods (phylogenetically corrected correlation) to test the hypothesis. Strikingly, they not only find that Ne is not THE major determinant of genome size, as is argued by MHH, but that there is not even a marginally significant effect. This is remarkable, making this an important paper.

      Strengths:

      The hypothesis tested is of great importance.

      The negative finding is of great importance for reevaluating the predictive power of the tested hypothesis.

      The test is straightforward and clear.

      The analysis is a technical tour-de-force, convincingly circumventing a number of challenges of mounting a true test of the hypothesis.

      Weaknesses:

      I note no particular strengths, but I believe the paper could be further strengthened in three major ways.

      (1) The authors should note that the hypothesis that they are testing is larger than the MHH.

      The MHH hypothesis says that (i) low-Ne species have more junk in their genomes and

      (ii) this is because junk tends to be costly because of increased mutation rate to nulls, relative to competing non/less-junky alleles.

      The current results reject not just the compound (i+ii) MHH hypothesis, but in fact any hypothesis that relies on i. This is notably a (much) more important rejection. Indeed, whereas MHH relies on particular constructions of increased mutation rates of varying plausibility, the more general hypothesis i includes any imaginable or proposed cost to the extra sequence (replication costs, background transcription, costs of transposition, ectopic expression of neighboring genes, recombination between homologous elements, misaligning during meiosis, reduced organismal function from nuclear expansion, the list goes on and on). For those who find the MHH dubious on its merits, focusing this paper on the MHH reduces its impact - the larger hypothesis that the small costs of extra sequence dictate the fates of different organisms' genomes is, in my opinion, a much more important and plausible hypothesis, and thus the current rejection is more important than the authors let on.

      The MHH is arguably the most structured and influential theoretical framework proposed to date based on the null assumption (i), therefore setting the paper up with the MHH is somehow inevitable. Because of this, we mostly discuss the assumption (ii) (the mutational aspect brought about by junk DNA) and the peculiarities of TE biology that can drive the genome away from the expectations of (i). We however agree that the hazard posed by extra DNA is not limited to the gain of function via the mutation process, but can be linked to many other molecular processes as mentioned above. Moreover, we also agree that our results can be interpreted within the general framework of the nearly-neutral theory. They demonstrate that mutations, whether increasing or decreasing genome size, have a distribution of fitness effects that falls outside the range necessary for selection in larger populations. In the revised manuscript, we made the concept of hazard more comprehensive and further stressed that this applies not only to TEs but any nearly-neutral mutation affecting non-coding DNA (lines 491-496): “Notably, these results not only reject the theory of extra non-coding DNA being costly for its point mutational risk, but also challenges the more general idea of its accumulation depending on other kinds of detrimental effects, such as increased replication, pervasive transcription, or ectopic recombination. Therefore, our results can be considered more general than a mere rejection of the MHH hypothesis, as they do not support any theory predicting that species with low Ne would accumulate more non-coding DNA.”

      (2) In addition to the authors' careful logical and mathematical description of their work, they should take more time to show the intuition that arises from their data. In particular, just by looking at Figure 1b one can see what is wrong with the non-phylogenetically-corrected correlations that MHH's supporters use. That figure shows that mammals, many of which have small Ne, have large genomes regardless of their Ne, which suggests that the coincidence of large genomes and frequently small Ne in this lineage is just that, a coincidence, not a causal relationship. Similarly, insects by and large have large Ne, regardless of their genome size. Insects, many of which have large genomes, have large Ne regardless of their genome size, again suggesting that the coincidence of this lineage of generally large Ne and smaller genomes is not causal. Given that these two lineages are abundant on earth in addition to being overrepresented among available genomes (and were even more overrepresented when the foundational MHH papers collected available genomes), it begins to emerge how one can easily end up with a spurious non-phylogenetically corrected correlation: grab a few insects, grab a few mammals, and you get a correlation. Notably, the same holds for lineages not included here but that are highly represented in our databases (and all the more so 20 years ago): yeasts related to S. cerevisiae (generally small genomes and large median Ne despite variation) and angiosperms (generally large genomes (compared to most eukaryotes) and small median Ne despite variation). Pointing these clear points out will help non-specialists to understand why the current analysis is not merely a they-said-them-said case, but offers an explanation for why the current authors' conclusions differ from the MHH's supporters and moreover explain what is wrong with the MHH's supporters' arguments.

      We thank the referee for this perspective. We agree that comparing dispersion of the points from the non-phylogenetically corrected correlation with the results of the phylogenetic contrasts intuitively emphasizes the importance of accounting for species relatedness. We added on to the discussion to stress the phylogenetic structure present in the data (lines 408-417): “It is important to note how not treating species traits as non-independent leads to artifactual results (Figure 2B-C). For instance, mammals have on average small population sizes and the largest genomes. Conversely, insects tend to have large Ne and overall small genomes. With a high sampling power and phylogenetic inertia being taken into account, our meta-analysis clearly points at a phylogenetic structure in the data: the main clades are each confined to separate genome size ranges regardless of their dN/dS variation. The other way around, variability in genome size can be observed in insects, irrespective of their dN/dS. Relying on non phylogenetically corrected models based on a limited number of species (such as that available at the time of the MHH proposal) can thus result in a spurious positive scaling between genome size and Ne proxies.”

      (3) A third way in which the paper is more important than the authors let on is in the striking degree of the failure of MHH here. MHH does not merely claim that Ne is one contributor to genome size among many; it claims that Ne is THE major contributor, which is a much, much stronger claim. That no evidence exists in the current data for even the small claim is a remarkable failure of the actual MHH hypothesis: the possibility is quite remote that Ne is THE major contributor but that one cannot even find a marginally significant correlation in a huge correlation analysis deriving from a lot of challenging bioinformatic work. Thus this is an extremely strong rejection of the MHH. The MHH is extremely influential and yet very challenging to test clearly. Frankly, the authors would be doing the field a disservice if they did not more strongly state the degree of importance of this finding.

      We respectfully disagree with the review that there is currently no evidence for an effect of Ne on genome size evolution. While it is accurate that our large dataset allows us to reject the universality of Ne as the major contributor to genome size variation, this does not exclude the possibility of such an effect in certain contexts. Notably, there are several pieces of evidence that find support for Ne to determine genome size variation and to entail nearly-neutral TE dynamics under certain circumstances, e.g. of particularly strongly contrasted Ne and moderate divergence times (Lefébure et al., 2017 Genome Res 27: 1016-1028; Mérel et al., 2021 Mol Biol Evol 38: 4252-4267; Mérel et al., 2024 biorXiv: 2024-01; Tollis and Boissinot, 2013 Genome Biol Evol 5: 1754-1768; Ruggiero et al., 2017 Front Genet 8: 44). The strength of such works is to analyze the short-term dynamics of TEs in response to N<sub>e</sub> within groups of species/populations, where the cost posed by extra DNA is likely to be similar. Indeed, the MHH predicts genome size to vary according to the combination of drift and mutation under the nearly-neutral theory of molecular evolution. Our work demonstrates that it is not true universally but does not exclude that it could exist locally. Moreover, defence mechanisms against TEs proliferation are often complex molecular machineries that might or might not evolve according to different constraints among clades. We have detailed these points in the discussion (lines 503-518).

      Reviewer #3 (Public review):

      Summary

      The Mutational Hazard Hypothesis (MHH) suggests that lineages with smaller effective population sizes should accumulate slightly deleterious transposable elements leading to larger genome sizes. Marino and colleagues tested the MHH using a set of 807 vertebrate, mollusc, and insect species. The authors mined repeats de novo and estimated dN/dS for each genome. Then, they used dN/dS and life history traits as reliable proxies for effective population size and tested for correlations between these proxies and repeat content while accounting for phylogenetic nonindependence. The results suggest that overall, lineages with lower effective population sizes do not exhibit increases in repeat content or genome size. This contrasts with expectations from the MHH. The authors speculate that changes in genome size may be driven by lineage-specific host-TE conflicts rather than effective population size.

      Strengths

      The general conclusions of this paper are supported by a powerful dataset of phylogenetically diverse species. The use of C-values rather than assembly size for many species (when available) helps mitigate the challenges associated with the underrepresentation of repetitive regions in short-read-based genome assemblies. As expected, genome size and repeat content are highly correlated across species. Nonetheless, the authors report divergent relationships between genome size and dN/dS and TE content and dN/dS in multiple clades: Insecta, Actinopteri, Aves, and Mammalia. These discrepancies are interesting but could reflect biases associated with the authors' methodology for repeat detection and quantification rather than the true biology.

      Weaknesses

      The authors used dnaPipeTE for repeat quantification. Although dnaPipeTE is a useful tool for estimating TE content when genome assemblies are not available, it exhibits several biases. One of these is that dnaPipeTE seems to consistently underestimate satellite content (compared to repeat masker on assembled genomes; see Goubert et al. 2015). Satellites comprise a significant portion of many animal genomes and are likely significant contributors to differences in genome size. This should have a stronger effect on results in species where satellites comprise a larger proportion of the genome relative to other repeats (e.g. Drosophila virilis, >40% of the genome (Flynn et al. 2020); Triatoma infestans, 25% of the genome (Pita et al. 2017) and many others). For example, the authors report that only 0.46% of the Triatoma infestans genome is "other repeats" (which include simple repeats and satellites). This contrasts with previous reports of {greater than or equal to}25% satellite content in Triatoma infestans (Pita et al. 2017). Similarly, this study's results for "other" repeat content appear to be consistently lower for Drosophila species relative to previous reports (e.g. de Lima & Ruiz-Ruano 2022). The most extreme case of this is for Drosophila albomicans where the authors report 0.06% "other" repeat content when previous reports have suggested that 18%->38% of the genome is composed of satellites (de Lima & Ruiz-Ruano 2022). It is conceivable that occasional drastic underestimates or overestimates for repeat content in some species could have a large effect on coevol results, but a minimal effect on more general trends (e.g. the overall relationship between repeat content and genome size).

      There are indeed some discrepancies between our estimates of low complexity repeats and those from the literature due to the approach used. Hence, occasional underestimates or overestimates of repeat content are possible. As noted, the contribution of “Other” repeats to the overall repeat content is generally very low, meaning an underestimation bias. We thank the reviewer for providing this interesting review.

      We emphasized these points in the discussion of our revised manuscript (lines 358-376): “While the remarkable conservation of avian genome sizes has prompted interpretations involving further mechanisms (see discussion below), dnaPipeTE is known to generally underestimate satellite content (Goubert et al. 2015). This bias is more relevant for those species that exhibit large fractions of satellites compared to TEs in their repeatome. For instance, the portions of simple and low complexity repeats estimated with dnaPipeTE are consistently smaller than those reported in previous analyses based on assembly annotation for some species, such as Triatoma infestans (0.46% vs 25%; 7 Mbp vs 400 Mbp), Drosophila eugracilis (1.28% vs 10.89%; 2 Mbp vs 25 Mbp), Drosophila albomicans (0.06% vs 18 to 38%; 0.12 Mbp vs 39 to 85 Mbp) and some other Drosophila species (Pita et al. 2017; de Lima and Ruiz-Luano 2022; Supplemental Table S2). Although the accuracy of Coevol analyses might occasionally be affected by such underestimations, the effect is likely minimal on the general trends. Inability to detect ancient TE copies is another relevant bias of dnaPipeTE. However, the strong correlation between repeat content and genome size and the consistency of dnaPipeTE and earlGrey results, even in large genomes such as that of Aedes albopictus, indicate that dnaPipeTE method is pertinent for our large-scale analysis. Furthermore, such an approach is especially fitting for the examination of recent TEs, as this specific analysis is not biased by very repetitive new TE families that are problematic to assemble.”

      Not being able to correctly estimate the quantity of satellites might pose a problem for quantifying the total content of junk DNA. However, the overall repeat content mostly composed of TEs correlates very well with genome size, both in the overall dataset and within clades (with the notable exception of birds) so we are confident that this limitation is not the explanation of our negative results. Moreover, while satellite information might be missing, this is not problematic to test our hypothesis, as we focus on TEs, whose proliferation mechanism differs significantly from that of tandem repeats and largely account for genome size variation.

      Another bias of dnaPipeTE is that it does not detect ancient TEs as well as more recently active TEs (Goubert et al., 2015 Genome Biol Evol 7: 1192-1205). Thus, the repeat content used for PIC and coevolve analyses here is inherently biased toward more recently inserted TEs. This bias could significantly impact the inference of long-term evolutionary trends.

      Indeed, dnaPipeTE is not good at detecting old TE copies due to the read-based approach, biasing the outcome towards new elements. We agree that TE content can be underestimated, especially in those genomes that tend to accumulate TEs rather than getting rid of them. However, the sum of old TEs and recent TEs is extremely well correlated to genome size (Pearson’s correlation: r = 0.87, p-value < 2.2e-16; PIC: slope = 0.22, adj-R<sup>2</sup> = 0.42, p-value < 2.2e-16). Our main result therefore does not rely on an accurate estimation of old TEs. In contrast, we hypothesized that recent TEs could be interesting because selection could be more likely to act on TEs insertion and dynamics rather than on non-coding DNA as a whole. Our results demonstrate that this is not the case. It should be noted that in spite of its limits towards old TEs, dnaPipeTE is well-suited for this analysis as it is not biased by highly repetitive new TE families that are challenging to assemble. In the revised manuscript, we now emphasize the limitations of dnaPipeTE and discuss the consequences on our results. See lines 359-374 (reported above) and lines 449-455: “On the other hand, it is conceivable the avian TE diversity to be underappreciated due to the limits of sequencing technologies used so far in resolving complex repeat-rich regions. For instance, employment of long-reads technologies allowed to reveal more extended repeated regions that were previously ignored with short read assemblies (Kapusta and Suh 2017; Benham et al. 2024). Besides, quite large fractions might indeed be satellite sequences constituting relevant fractions of the genome that are challenging to identify with reference- or read-based methods (Edwards et al. 2025).”

      Finally, in a preliminary work on the dipteran species, we showed that the TE content estimated with dnaPipeTE is generally similar to that estimated from the assembly with earlGrey (Baril et al., 2024 Mol Biol Evol 38: msae068) across a good range of genome sizes going from drosophilid-like to mosquito-like (TE genomic percentage: Pearson’s r = 0.88, p-value = 1.951e-10; TE base pairs: Pearson’s r = 0.90, p-value = 3.573e-11; see also the corrected Supplementary Figure S2 and new Supplementary Figure S3). While TEs for these species are probably dominated by recent to moderately recent TEs, Ae. albopictus is an outlier for its genome size and the estimations with the two methods are largely consistent. However, the computation time required to estimate TE content using EarlGrey was significantly longer, with a ~300% increase in computation time, making it a very costly option (a similar issue applicable to other assembly-based annotation pipelines). Given the rationale presented above, we decided to use dnaPipeTE instead of EarlGrey.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Since I am not an expert in the field, some of these comments may simply reflect a lack of understanding on my part. However, in those cases, I hope they can help the authors clarify important points. I did have a bunch of comments concerning the complexity of the relationship between TEs and their hosts that would likely affect TE content, but I ended up deleting most of them because they were covered in the discussion. However, I do think that in setting up the paper, particularly given the results, it might have been useful to introduce those issues in the introduction. That is to say, treating TEs as a generic mutagen that will fit into a relatively simple model is unlikely to be correct. What will ultimately be more interesting are the particulars of the ways that the relationships between TEs and their host evolve over time. Finally, given the huge variation in plant genes with respect to genome size and TE content, along with really interesting variation in deletion rates, I'm surprised that they were not included. I get that you have to draw a line somewhere, and this work builds on a bunch of other work in animals, but it seems like a missed opportunity.

      We chose to restrict the introduction to the rationale behind the MHH as it is the starting point and focus of the manuscript. Because the aspects of the complexity of TE-host relationships are only covered in a speculative way, we limited them to the discussion but it is true that introducing them at the very beginning gives a more comprehensive overview. The introduction now includes a few sentences about lineage-specific selective effect of TEs and TE-host evolution (lines 83-86): “On top of that, an alternative TE-host-oriented perspective is that the accumulation of TEs in particular depends on their type of activity and dynamics, as well as on the lineage-specific silencing mechanisms evolved by host genomes (Ågren and Wright 2011).”

      Page 4. "The MHH is highly popular..." Evidence for this? It is fine as is, but it could also be seen as a straw man argument. Perhaps make clear this is an opinion of the authors?

      That MHH is popular and well-known is more a fact than an opinion: the original paper by Lynch and Conery (2003) and “The origins of genome architecture” by Lynch (2007) have respectively 1872 and 1901 citations to the present date (04/03/2025). Besides, the MHH is often invoked in highly cited reviews about TEs, e.g. Bourque et al., 2018 Genome Biol 19:1-12; Wells and Feschotte, 2020 Annu Rev Genet 54: 539-561.

      Page 4. "on phylogenetically very diverse datasets..." Given the fact that even closely related plants can show huge variation in genome size, it's a shame that they weren't included here. There are also numerous examples of closely related plants that are obligate selfers and out-crossers.

      This is true, and some studies already tested MHH in specific plant groups (Ågren et al., 2014 BMC Genom 15: 1-9; Hu et al., 2011 Nat Genet 43: 476-481; Wright et al., 2008 Int J Plant Sci 169: 105-118), including selfers vs out-crossers cases (Glémin et al., 2019 Evolutionary genomics: statistical and computational methods: 331-369). Further development in this kingdom would be interesting. However, the boundary was set to metazoans since the very beginning of analyses to maintain a large phylogenetic span and a manageable computational burden. Furthermore, some of the included animal clades are supposed to display good Ne contrasts according to known LHTs or to previous literature: for instance, the very different Ne of mammals and insects, as well as more narrowed examples like Drosophilidae and solitary vs eusocial hymenopterans.

      Page 6. "species-poor, deep-branching taxa were excluded" I see why this was done, as these taxa would not provide close as well as distant comparisons, but I would have thought they might have provided some interesting outlying data. As the geneticists say, value the exceptions.

      The reason to exclude them was not only that they would solely provide very distant comparisons. The lack of a rich and balanced sampling would imply calculating nucleotide substitution rates over hundreds of millions of years, which typically lead to saturation of synonymous sites. In case of saturation of synonymous sites, the synonymous divergence will be underestimated, and therefore, the dN/dS ratio no longer a valuable estimate of N<sub>e</sub>. Outside vertebrates and insects, the available genomes in a clade would mostly correspond to a few species from an entire phylum, making it challenging to estimate dN/dS and to correlate present day genome size with Ne estimated over hundreds of millions of years.

      Figure 1. What are the scaling units for each of these values? I get that dN/dS is between 0 and 1, but what about genome sizes? Are these relative sizes? Are TE content values a percent of the total? This may be mentioned elsewhere, but I think it is worth putting that information here as well.

      Thanks for pointing this out. Both genome sizes and TE contents are in bp, we added this information in the legend of the figure.

      Page 8. TE content estimates are invariably wrong given the diversity of TEs and, in many genomes, the presence of large numbers of low copy number "dead" elements. If that varies between taxa, this could cause problems. Given that, I would have liked to see the protocols used here be compared to a set of "gold standard" genomes with exceptionally well-annotated TEs (Humans and D. melanogaster, for instance).

      As already mentioned, dnaPipeTE is indeed biased towards young TEs (elements older than 25-30% are generally not detected). TE content can therefore be underestimated, especially in those genomes that tend to accumulate TEs rather than getting rid of them. Although most of them do not have “gold-standard” genomes, a comparison of dnaPipeTE with TE annotations from assemblies is already provided for a subset of species. Some variation can be present - see Supplemental Figure S6 and comments of Reviewer#3 about detection of satellite sequences. However, the subset covers a good range of genome sizes and overall dnaPipeTE emerges as an appropriate tool to characterize the general patterns of repeat content variation.

      Page 11. "close to 1 accounts for more..." I would say "closer" rather than "close".

      Agreed and changed.

      Page 11. "We therefore employed this parameter..." I know you made the point earlier, but maybe reiterate the general point here that selection is lower on average with a lower effective population size. Actually, I'm wondering if we don't need a different term for long-term net effective population size, which dN/dS is measuring.

      We reiterated here the relationship among dN/dS, Ne and magnitude of selection (lines 200-204): “a dN/dS closer to 1 accounts for more frequent accumulation of mildly deleterious mutations over time due to increased genetic drift, while a dN/dS close to zero is associated with a stronger effect of purifying selection. We therefore employed this parameter as a genomic indicator of N<sub>e</sub>, as the two are expected to scale negatively between each other.”

      Page 11. "We estimated dN/dS with a mapping method..." I very much appreciate that the authors are using the same pipeline for the analysis of all of these taxa, but I would also be interested in how these dN/dS values compare with previously obtained values for a subset of intensively studied taxa.

      The original publication of the method demonstrated that dN/dS estimations using mapping are highly similar to those obtained with maximum likelihood methods, such as implemented in CODEML (Romiguier et al., 2014 J Evol Biol 27: 593-603). Below is the comparison for 16 vertebrate species from Figuet et al. (2016 Mol Biol Evol 33: 1517-1527), where dN/dS are reasonably correlated (slope = 0.57, adjusted-R<sup>2</sup> = 0.39, p-value=0.006). That being said, some noise can be present as the compared genes and the phylogeny used are different. Although we expect some value between 0 and 1, some range of variation is to be expected depending on both the species used and the markers, as substitution rates and/or selection strength might be different. Differences in dN/dS for the same species would not necessarily imply an issue with one of the methods.

      Author response image 1.

      Page 12. " As expected, Bio++ dN/dS scales positively with..." Should this be explicitly referenced earlier? I do see that references mentioning both body mass and longevity are included earlier, but the terms themselves are not.

      We added a list of the expected correlations for dN/dS and LHTs at the beginning of the paragraph (lines 205-208): “In general, dN/dS is expected to scale positively with body length, age at first birth, maximum longevity, age at sexual maturity and mass, and to scale negatively with metabolic rate, population density and depth range.”

      Page 12. "dN/dS estimation on the trimmed phylogeny deprived of short and long branches results in a stronger correlation with LHTs, suggesting that short branches..." and what about the long branches? Trimming them helps because LHTs change over long periods of time?

      Trimming of long branches should avoid saturation in the signal of synonymous substitutions if present (whereby increase in dN is not parallelled by corresponding increase in dS due to depletion of all sites). Excluding very long branches was one of the reasons why we excluded taxonomic groups with few species. See lines 131-133: “For reliable estimation of substitution rates, this dataset was further downsized to 807 representative genomes as species-poor, deep-branching taxa were excluded”. Correlating present-day genome size with Ne estimates over long periods of time could weaken a potential correlation. However, exploratory analyses (not included) did not indicate that excluding long branches improved the relationship between Ne and genome size/TE content. The rationale is explained in Materials and Methods but was wrongly formulated. We rephrased it and added a reference (lines 636-638): “Estimation of dN/dS on either very long or short terminal branches might lead to loss of accuracy due to branch saturation (Weber et al. 2014) or to a higher variance of substitution rates, respectively”.

      Table 2. "Expected significant correlations are marked in bold black; significant correlations opposite to the expected trend are marked in bold red." Expected based on the initial hypothesis? Perhaps frame it as a test of the hypothesis?

      As per the comment above, we added a sentence in the main text to clarify the expected correlations for dN/dS and LHTs (lines 205-208): “In general, dN/dS is expected to scale positively with body length, age at first birth, maximum longevity, age at sexual maturity and mass, and to scale negatively with metabolic rate, population density and depth range.”. The second expected correlation is that between dN/dS and genome size/TE content, which is stated at the beginning of paragraph 2.5 (lines 244-245): “If increased genetic drift leads to TE expansions, a positive relationship between dN/dS and TE content, and more broadly with genome size, should be observed.”.

      Page 14. "Based on the available traits, the two kinds of Ne proxies analyzed here correspond in general..." the two kinds being dN/dS and a selection of LHT?

      We rephrased the sentence as such (lines 233-234): “Based on the available traits, the estimations of dN/dS ratios obtained using two different methods correspond in general to each other”.

      Table 3. Did you explain why there is a distinction between GC3-poor and GC3-rich gene sets?

      No, the explanation is missing, thank you for pointing it out. The choice comes from the observations made by Mérel et al. (2024 biorXiv: 2024-01), who do find a stronger relationship between dN/dS and genome size in Drosophila using the same tool (Coevol) in GC3-poor genes than in GC3-rich ones or in random sets of genes exhibiting heterogeneity in GC3 content. There are several possible explanations for this. First, mixing genes with various base compositions in the same concatenate can alter the calculation of codon frequency and impair the accuracy of the model estimating substitution rates.

      Moreover, base composition and evolutionary rates may not be two independent molecular traits, at the very least in Drosophila, and more generally in species experiencing selection on codon bias. Because optimal codons are enriched in G/C bases at the third position (Duret and Mouchiroud, 1999 PNAS 96: 4482-4487), GC3-rich genes are likely to be more expressed and therefore evolve under stronger purifying selection than GC3-poor genes in Drosophila.

      Accordingly, Merel and colleagues observed significantly higher dN/dS estimates for GC3-poor genes than for GC3-rich genes. Additionally, selection on codon usage acting on these highly expressed genes, that are GC3-rich, violates the assumed neutrality of dS. This implies that dN/dS estimates based on genes under selection on codon bias are likely less appropriate proxies of Ne than expected.

      Although some of these observations may be specific to Drosophila, this criterion was taken into consideration as taking restricted gene subsets was required for Coevol runs. We added this explanation in materials and methods (lines 723-738).

      Page 16. "Coevol dN/dS scales negatively with genome size across the whole dataset (Slope = -0.287, adjusted-R<sup>2</sup> = 0.004, p-value = 0.039) and within insects" Should I assume that none of the other groups scale negatively on their own, but cumulatively, all of them do?

      Yes, and this is an “insect-effect”: the regression of the whole dataset is negative but it is not anymore when insects are removed (with the model still being far from significant).

      Page 16. "Overall, we find no evidence for a recursive association of dN/dS with genome size and TE content across the analysed animal taxa as an effect of long-term Ne variation." I get the point, but this is starting to feel a bit circular. What you see is a lack of an association between dN/dS and TE content, but what do you mean by "as an effect of..." here? You are using dN/dS as a proxy, so the wording here feels odd.

      See the reply below.

      Page 17. I'm not sure that "effect" here is the word to use. You are looking at associations, not cause-effect relationships. Certainly, dN/dS is not causing anything; it is an effect of variation in purifying selection.

      Agreed, dN/dS is the ratio reflecting the level of purifying selection, not the cause itself. dN/dS is employed here as the independent variable in the correlation with genome size or TE content. dN/dS has an “effect” on the dependent variables in the sense that it can predict their variation, not in the sense that it is causing genome size to vary. We rephrased this and similar sentences to avoid misunderstandings (changes are highlighted in the revised text).

      Page 17. "Instead, mammalian TE content correlates positively with metabolic rate and population density, and negatively with body length, mass, sexual maturity, age at first birth and longevity." I guess I'm getting tripped up by measures of current LHTs and historical LHTs which, I'm assuming, varies considerably over the long periods of time that impact TE content evolution.

      PIC analyses can be considered as correlations on current LHTs as we compare values (or better, contrasts) at the tips of phylogenies. In the case of Coevol, traits are inferred at internal nodes, in such a way that the model should take into account the historical variation of LHTs, too.

      Page 18. "positive effect of dN/dS on recent TE insertions..." Again, this is not a measure of the effect of dN/dS on TE insertions, it is a measure of correlation. I know it's shorthand, but in this case, I think it really matters that we avoid making cause inferences.

      We have rephrased this as ”...very weak positive correlation of dN/dS with recent TE insertions…”.

      Page 18. "are consistent with the scenarios depicted by genome size and overall TE content in the corresponding clades." Maybe be more explicit here at the very end of the results about what those scenarios are.

      Correlating the recent TE content with dN/dS and LHTs basically recapitulates the relationship found using the other genomic traits (genome size and overall TE content). We have rephrased the closing sentence as “Therefore, the coevolution patterns between population size and recent TE content are consistent with the pictures emerging from the comparison of population size proxies with genome size and overall TE content in the corresponding clades” (lines 312-315).

      Page 19. "However, the difficulty in assembling repetitive regions..." I would say the same is true of TE content, which is almost always underestimated for the same reasons.

      “Repetitive regions” is here intended as an umbrella term including all kinds of repeats, from simple ones to transposable elements.

      Page 20. "repeat content has a lower capacity to explain size compared to other clades." Perhaps, but I'm not convinced this is not due to large numbers of low copy number elements, perhaps purged at varying rates. Are we certain that dnaPipeTE would detect these? Have rates of deletion in the various taxa examined been estimated?

      It is possible that low copy number elements are detected differently, according to the rate of decay in different species and depending also on the annotation method (indeed low copy families are less likely to be captured during read sampling by dnaPipeTE). A negative correlation between assembly size and deletion rate was observed in birds (Ji et al., 2023 Sci Adv 8: eabo0099). So we should expect a rate of TE removal inversely proportional to genome size, a positive correlation between TE content and genome size, and negative relationship between TE content and deletion rate, too. The relationship of TE content with deletion rate and genome size however appears more complex than this, even this paper using assembly-based TE annotations. However, misestimations of repeat content are also potentially due to the limited capacity of dnaPipeTE of detecting simple and low complexity repeats (see comments from Reviewer#3), which might be important genomic components in birds (see a few comments below).

      Page 21. "DNA gain, and their evolutionary dynamics appear of prime importance in driving genome size variation." How about DNA loss over time?

      See response to the comment below.

      Page 22. "in the latter case, the pace of sequence erosion could be in the long run independent of drift and lead to different trends of TE retention and degradation in different lineages." Ah, I see my earlier question is addressed here. How about deletion as a driver as well?

      Deletion was not investigated here. However, deletion processes are surely very different across animals and their impact merits to be studied as well within a comparative framework. Small scale deletion events have even been proposed to contrast the increase in genome size by TE expansion (Petrov et al., 2002 Theor Popul Biol 61: 531-544). In fact, their magnitude would not be high enough to effectively contrast processes of genome expansion in most organisms (Gregory, 2004 Gene 324: 15-34). However, larger-scale deletions might play an important role in genome size determinism by counterbalancing DNA gain (Kapusta et al., 2017 PNAS 114: E1460-E1469; Ji et al., 2023 Sci Adv 8: eabo0099). For sake of space we do not delve in detail into this issue, but we do provide some perspectives about the role of deletion (see lines 518-521 and 535-541).

      Page 22. "however not surprising given the higher variation of TE load compared to the restricted genome size range." I admit, I'm struggling with this. If it isn't genes, and it isn't satellites, and it isn't TEs, what is it?

      Most birds having ~1Gb genomes and displaying very low TE contents. Other studies annotated TEs in avian genome assemblies and also found a not so strong correlation between amount of TEs and genome size (Ji et al., 2023 Sci Adv 8: eabo0099, Kapusta and Suh, 2016 Ann N Y Acad Sci 1389: 164-185). It is possible that the TE diversity is underappreciated in birds due to the limits of sequencing technologies used so far in resolving complex repeat-rich regions. For instance, employment of long-reads technologies allowed to reveal more extended repeated regions that were previously ignored with short read assemblies (Kapusta and Suh, 2016 Ann N Y Acad Sci 1389: 164-185). Besides, quite large fractions might indeed be satellite sequences constituting relevant fractions of the genome (Edwards et al., 2025 biorXiv: 2025-02). We added this perspective in the discussion (lines 446-455): “As previous studies find relatively weak correlations between TE content and genome size in birds (Ji et al. 2022; Kapusta and Suh 2017), it is possible for the very narrow variation of the avian genome sizes to impair the detection of consistent signals. On the other hand, it is conceivable the avian TE diversity to be underappreciated due to the limits of sequencing technologies used so far in resolving complex repeat-rich regions. For instance, employment of long-reads technologies allowed to reveal more extended repeated regions that were previously ignored with short read assemblies (Kapusta and Suh 2017; Benham et al. 2024). Besides, quite large fractions might indeed be satellite sequences constituting relevant fractions of the genome that are challenging to identify with reference- or read-based methods (Edwards et al. 2025).” See also responses to Reviewer#3’s concerns about dnaPipeTE.

      Page 24. "Our findings do not support the quantity of non-coding DNA being driven in..." Many TEs carry genes and are "coding".

      Yes. Non-coding DNA intended as the non-coding portion of genomes not directly involved in organisms’ functions and fitness (in other words sequences not undergoing purifying selection). TEs do have coding parts but are in most part molecular parasites hijacking hosts’ machinery.

      Page 25. "There is some evidence of selection acting against TEs proliferation." Given that the vast majority of TEs are recognized and epigenetically silenced in most genomes, I'd say the evidence is overwhelming. Here I suspect you mean evidence for success in preventing proliferation. Actually, since we know that systems of TE silencing have a cost, it might be worth considering how the costs and benefits of these systems may have influenced overall TE content.

      We meant selection against TE proliferation in the making, notably visible at the level of genome-wide signatures for relaxed/effective selection. We rephrased it as “Evidence for signatures of negative selection against TE proliferation exist at various degrees.” (line 543).

      Reviewer #3 (Recommendations for the authors):

      Page 14: Please define GC3-rich and GC3-poor gene sets and how they were established, as well as why the analyses were conducted separately on GC3-rich and GC3-poor genes.

      We added a detailed explanation for the choice of GC3-rich and GC3-poor genes (see modified section Methods - Phylogenetic independent contrasts and Coevol reconstruction, lines 723-738).

      “Genes were selected according to their GC content at the third codon position (GC3). Indeed, mixing genes with heterogeneous base composition in the same concatenate might result in an alteration of the calculation of codon frequencies, and consequently impair the accuracy of the model estimating substitution rates (Mérel et al. 2024). Moreover, genes with different GC3 levels can reflect different selective pressures, as highly expressed genes should be enriched in optimal codons as a consequence of selection on codon usage. In Drosophila, where codon usage bias is at play, most optimal codons present G/C bases at the third position (Duret and Mouchiroud, 1999), meaning that genes with high GC3 content should evolve under stronger purifying selection than GC3-poor genes. Accordingly, Mérel et al. (2024) do find a stronger relationship between dN/dS and genome size when using GC3-poor genes, as compared to GC3-rich genes or gene concatenates of random GC3 composition. Finally, dN/dS can be influenced by GC-biased gene conversion (Bolívar et al. 2019; Ratnakumar et al. 2010), and the strength at which such substitution bias acts can be reflected by base composition. For these reasons, two sets of 50 genes with similar GC3 content were defined in order to employ genes undergoing similar evolutionary regimes.”

      Please add lines between columns and rows in tables. Table 3 is especially difficult to follow due to its size, and lines separating columns and rows would vastly help with readability.

      We added lines delimiting cells in all the main tables.

      Throughout the text and figures, please be consistent with either scientific names or common names for lineages or clades.

      Out of the five groups, for four of them the common name is the same as the scientific one (except Aves/birds).

      Regarding the title for section 3.1, I don't believe "underrate" is the best word here. I find this title confusing.

      We replaced the term “underrate” with “underestimate” in the title.

      The authors report that read type (short vs. long) does not have a significant effect on assembly size relative to C-value. However, the authors (albeit admittedly in the discussion) removed lower-quality assemblies using a minimum N50 cutoff. Thus, this lack of read-type effect could be quite misleading. I strongly recommend the authors either remove this analysis entirely from the manuscript or report results both with and without their minimum N50 cutoff. I expect that read type should have a strong effect on assembly size relative to C-value, especially in mammals where TEs and satellites comprise ~50% of the genome.

      Yes, it's likely that if we took any short-read assembly, we would have a short-read effect. We do not mean to suggest that in general short reads produce the same assembly quality as long reads, but that in this dataset we do not need to account for the read effect in the model to predict C-values. Adding the same test including all assemblies will be very time-consuming because C-values should be manually checked as already done for the species. If we removed this test, readers might wonder whether our genome size predictions are not distorted by a short-read effect. We now make it clear that this quality filter likely has an outcome on our observations: “This suggests that the assemblies selected for our dataset can mostly provide a reliable measurement of genome size, and thus a quasi-exhaustive view of the genome architecture.” (lines 333-335).

      There seem to be some confusing inconsistencies between Supplementary Table S2 and Supplementary Figure S2. In Supplementary Table S2, the authors report ~24% of the Drosophila pectinifera genome as unknown repeats. This is not consistent with the stacked bar plot for D. pectinifera in Supplementary Figure S2.

      True, the figure is wrong, thank you for spotting the error. The plot of Supplemental Figure S2 was remade with the correct repeat proportions as in Supplementary Tables S2 and S4. Because the reference genome sizes on which TE proportions are calculated are different for the two methods, we added another supplemental figure showing the same comparison in Kbp (now Supplemental Figure S3).

      At the bottom of page 20: "many species with a high duplication score in our dataset correspond to documented duplication" How many?

      Salmoniformes (9), Acipenseriformes (1), Cypriniformes (3) out of 23 species with high duplication score. It’s detailed in the results (lines 193-196): “Of the 24 species with more than 30% of duplicated BUSCO genes, 13 include sturgeon, salmonids and cyprinids, known to have undergone whole genome duplication (Du et al. 2020; Li and Guo 2020; Lien et al. 2016), and five are dipteran species, where gene duplications are common (Ruzzante et al. 2019).”

      Top of page 21: "However, the contribution of duplicated genes to genome size is minimal compared to the one of TEs, and removing species with high duplication scores does not affect our results: this implies that duplication does not impact genome size strongly enough to explain the lack of correlation with dN/dS." This sentence is confusing and needs rewording.

      We reworded the sentence (lines 383-384): “this implies that duplication is unlikely to be the factor causing the relationship between genome size and dN/dS to deviate from the pattern expected from the MHH”.

      Beginning of section 3.3: "Our dN/dS calculation included several filtering steps by branch length and topology: indeed, selecting markers by such criteria appears to be an essential step to reconcile estimations with different methodologies" A personal communication is cited here. Are there really no peer-reviewed sources supporting this claim?

      This mainly comes from a comparison of dN/dS calculation with different methods (notably ML method of bpp vs Coevol bayesian framework) on a set of Zoonomia species. We observed that estimations with different methods appeared correlated but with some noise: filtering out genes with deviant topologies (by a combination of PhylteR and of an unpublished Bayesian shrinkage model) reconciled even more the estimations obtained from different methods. Results are not shown here but the description of an analogous procedure is presented in Bastian, M. (2024). Génomique des populations intégrative: de la phylogénie à la génétique des populations (Doctoral dissertation, Université lyon 1) that we added to the references.

      Figure 2 needs to be cropped to remove the vertical gray line on the right of the figure as well as the portion of visible (partly cropped) text at the top. What is the "Tree scale" in Figure 1?

      Quality of figure 2 in the main text was adjusted. The tree scale is in amino acid substitutions, we added it in the legend of the figure.

      It is also unclear whether the authors used TE content or overall repeat content for their analyses.

      The overall repeat content includes both TEs and other kinds of repeats (simple repeats, low complexity repeats, satellites). The contribution of such other repeats to the total content is generally quite low for most species compared to that of TEs (only 13 genomes in all dataset have more than 3% of “Other” repeats). Conversely, the “other” repeats were not included in the recent content since the divergence of a copy from its consensus sequence is pertinent only for TEs.

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Overall, the data presented in this manuscript is of good quality. Understanding how cells control RPA loading on ssDNA is crucial to understanding DNA damage responses and genome maintenance mechanisms. The authors used genetic approaches to show that disrupting PCNA binding and SUMOylation of Srs2 can rescue the CPT sensitivity of rfa1 mutants with reduced affinity for ssDNA. In addition, the authors find that SUMOylation of Srs2 depends on binding to PCNA and the presence of Mec1.

      Comments on revisions:

      I am satisfied with the revisions made by the authors, which helped clarify some points that were confusing in the initial submission.

      Thank you.

      Reviewer #2 (Public Review):

      This revised manuscript mostly addresses previous concerns by doubling down on the model without providing additional direct evidence of interactions between Srs2 and PCNA, and that "precise sites of Srs2 actions in the genome remain to be determined." One additional Srs2 allele has been examined, showing some effect in combination with rfa1-zm2. Many of the conclusions are based on reasonable assumptions about the consequences of various mutations, but direct evidence of changes in Srs2 association with PNCA or other interactors is still missing. There is an assumption that a deletion of a Rad51-interacting domain or a PCNA-interacting domain have no pleiotropic effects, which may not be the case. How SLX4 might interact with Srs2 is unclear to me, again assuming that the SLX4 defect is "surgical" - removing only one of its many interactions.

      Previous studies have already provided direct evidence for the interaction between Srs2 and PCNA through the Srs2’s PIM region (Armstrong et al, 2012; Papouli et al, 2005); we have added these citations in the text. Similarly. Srs2 associations with SUMO and Rad51 have also been demonstrated (Colavito et al, 2009; Kolesar et al, 2016; Kolesar et al., 2012), and these studies were cited in the text.

      We did not state that a deletion of a Rad51-interacting domain or a PCNA-interacting domain have no pleiotropic effects. We only assessed whether these previously characterized mutant alleles could mimic srs2∆ in rescuing rfa1-zm2 defects.

      We assessed the genetic interaction between slx4-RIM and srs2-∆PIM mutants, and not the physical interaction between the two proteins. As we described in the text, our rationale for this genetic test is based on that the reports that both slx4 and srs2 mutants impair recovery from the Mec1 induced checkpoint, thus they may affect parallel pathways of checkpoint dampening.

      One point of concern is the use of t-tests without some sort of correction for multiple comparisons - in several figures. I'm quite sceptical about some of the p < 0.05 calls surviving a Bonferroni correction. Also in 4B, which comparison is **? Also, admittedly by eye, the changes in "active" Rad53 seem much greater than 5x. (also in Fig. 3, normalizing to a non-WT sample seems odd).

      Claims made in this work were based only on pairwise comparison not multi-comparison. We have now made this point clearer in the graphs and in Method. As the values were compared between a wild-type strain and a specific mutant strain, or between two mutants, we believe that t-test is suitable for statistical analysis.

      Figure 4B, ** indicates that the WT value is significantly different from that of the slx4-RIM srs2-∆PIM double mutant and from that of srs2-∆PIM single mutant. We have modified the graph to indicate the pair-wide comparison. The 5-fold change of active Rad53 levels was derived by comparing the values between the srs2∆ PIM slx4<sup>RIM</sup>-TAP double mutant and wild-type Slx4-TAP. In Figure 3, normalization to the lowest value affords better visualization. This is rather a stylish issue; we would like to maintain it as the other reviewers had no issues.

      What is the WT doubling time for this strain? From the FACS it seems as if in 2 h the cells have completed more than 1 complete cell cycle. Also in 5D. Seems fast...

      Wild-type W303 strain has less than 90 min doubling time as shown by many labs, and our data are consistent with this. The FACS profiles for wild-type cells shown in Figures 3C, 4C, and 5C are consistent with each other, showing that after G1 cells entered the cell cycle, they were in G2 phase at the 1-hour time points, and then a percentage of the cells exited the first cell cycle by two hours.

      I have one over-arching confusion. Srs2 was shown initially to remove Rad51 from ssDNA and the suppression of some of srs2's defects by deleting rad51 made a nice, compact story, though exactly how srs2's "suppression of rad6" fit in isn't so clear (since Rad6 ties into Rad18 and into PCNA ubiquitylation and into PCNA SUMOylation). Now Srs2 is invoked to remove RPA. It seems to me that any model needs to explain how Srs2 can be doing both. I assume that if RPA and Rad51 are both removed from the same ssDNA, the ssDNA will be "trashed" as suggested by Symington's RPA depletion experiments. So building a model that accounts for selective Srs2 action at only some ssDNA regions might be enhanced by also explaining how Rad51 fits into this scheme.

      While the anti-recombinase function of Srs2 was better studied, its “anti-RPA” role in checkpoint dampening was recently described by us (Dhingra et al, 2021) following the initial report by the Haber group some time ago (Vaze et al, 2002). A better understanding of this new role is required before we can generate a comprehensive picture of how Srs2 integrates the two functions (and possibly other functions). Our current work addresses this issue by providing a more detailed understanding of this new role of Srs2.

      Single molecular data showed that Srs2 strips both RPA and Rad51 from ssDNA, but this effect is highly dynamic (i.e. RPA and Rad51 can rebind ssDNA after being displaced) (De Tullio et al, 2017). As such, generation of “deserted” ssDNA regions lacking RPA and Rad51 in cells can be an unlikely event. Rather, Srs2 can foster RPA and Rad51 dynamics on ssDNA. Additional studies will be needed to generate a model that integrates the anti-recombinase and the anti-RPA roles of Srs2.

      As a previous reviewer has pointed out, CPT creates multiple forms of damage. Foiani showed that 4NQO would activate the Mec1/Rad53 checkpoint in G1- arrested cells, presumably because there would be singlestrand gaps but no DSBs. Whether this would be a way to look specifically at one type of damage is worth considering; but UV might be a simpler way to look. As also noted, the effects on the checkpoint and on viability are quite modest. Because it isn't clear (at least to me) why rfa1 mutants are so sensitive to CPT, it's hard for me to understand how srs2-zm2 has a modest suppressive effect: is it by changing the checkpoint response or facilitating repair or both? Or how srs2-3KR or srs2-dPIM differ from rfa1-zm2 in this respect. The authors seem to lump all these small suppressions under the rubric of "proper levels of RPA-ssDNA" but there are no assays that directly get at this. This is the biggest limitation.

      CPT treatment is an ideal condition to examine how cells dampen the DNA damage checkpoint, because while most genotoxic conditions (e.g. 4NQO, MMS) induce both the DNA replication checkpoint and the DNA damage checkpoint, CPT was shown to only induced the latter (Menin et al, 2018; Minca & Kowalski, 2011; Redon et al, 2003; Tercero et al, 2003). Future studies examining 4NQO and UV conditions can further expand our understanding of checkpoint dampening in different conditions.

      We have previously provided evidence to support the conclusion that srs2 suppression of rfa1-zm is partly mediated by changing checkpoint levels (Dhingra et al., 2021). We cannot exclude the possibility that the suppression may also be related to changes of DNA repair; we have now added this note in the text.

      Regarding direct testing RPA levels on DNA, we have previously shown that srs2∆ increased the levels of chromatin associated Rfa1 and this is suppressed by rfa1-zm2 (Dhingra et al., 2021). We have now included chromatin fractionation data to show that srs2-∆PIM also led to an increase of Rfa1 on chromatin, and this was suppressed by rfa1-zm2 (new Fig. S2).

      Srs2 has also been implicated as a helicase in dissolving "toxic joint molecules" (Elango et al. 2017). Whether this activity is changed by any of the mutants (or by mutations in Rfa1) is unclear. In their paper, Elango writes: "Rare survivors in the absence of Srs2 rely on structure-specific endonucleases, Mus81 and Yen1, that resolve toxic joint-molecules" Given the involvement of SLX4, perhaps the authors should examine the roles of structure-specific nucleases in CPT survival?

      Srs2 has several roles, and its role in RPA antagonism can be genetically separated from its role in Rad51 regulation as we have shown in our previous work (Dhingra et al., 2021) and this notion is further supported by evidence presented in the current work. Srs2’s role in dissolving "toxic joint molecules” was mainly observed during BIR (Elango et al, 2017). Whether it is related to checkpoint dampening will be interesting to address in the future but is beyond of the scope of the current work that seeks to answer the question how Srs2 regulates RPA during checkpoint dampening. Similarly, determining the roles of Mus81 and Yen1 and other structural nucleases in CPT survival is a worthwhile task but it is a research topic well separated from the focus of this work.

      Experiments that might clarify some of these ambiguities are proposed to be done in the future. For now, we have a number of very interesting interactions that may be understood in terms of a model that supposes discriminating among gaps and ssDNA extensions by the presence of PCNA, perhaps modified by SUMO. As noted above, it would be useful to think about the relation to Rad6.

      Several studies have shown that Srs2’s functional interaction with Rad6 is based on Srs2-mediated recombination regulation (reviewed by (Niu & Klein, 2017). Given that recombinational regulation by Srs2 is genetically separable from the Srs2 and RPA antagonism (Dhingra et al., 2021), we do not see a strong rationale to examine Rad6 in this work, which addresses how Srs2 regulates RPA. With this said, this study has provided basis for future studies of possible cross-talks among different Srs2-mediated pathways.

      Reviewer #3 (Public Review):

      The superfamily I 3'-5' DNA helicase Srs2 is well known for its role as an anti-recombinase, stripping Rad51 from ssDNA, as well as an anti-crossover factor, dissociating extended D-loops and favoring non-crossover outcome during recombination. In addition, Srs2 plays a key role in in ribonucleotide excision repair. Besides DNA repair defects, srs2 mutants also show a reduced recovery after DNA damage that is related to its role in downregulating the DNA damage signaling or checkpoint response. Recent work from the Zhao laboratory (PMID: 33602817) identified a role of Srs2 in downregulating the DNA damage signaling response by removing RPA from ssDNA. This manuscript reports further mechanistic insights into the signaling downregulation function of Srs2.

      Using the genetic interaction with mutations in RPA1, mainly rfa1-zm2, the authors test a panel of mutations in Srs2 that affect CDK sites (srs2-7AV), potential Mec1 sites (srs2-2SA), known sumoylation sites (srs2-3KR), Rad51 binding (delta 875-902), PCNA interaction (delta 1159-1163), and SUMO interaction (srs2SIMmut). All mutants were generated by genomic replacement and the expression level of the mutant proteins was found to be unchanged. This alleviates some concern about the use of deletion mutants compared to point mutations. Double mutant analysis identified that PCNA interaction and SUMO sites were required for the Srs2 checkpoint dampening function, at least in the context of the rfa1-zm2 mutant. There was no effect of this mutants in a RFA1 wild type background. This latter result is likely explained by the activity of the parallel pathway of checkpoint dampening mediated by Slx4, and genetic data with an Slx4 point mutation affecting Rtt107 interaction and checkpoint downregulation support this notion. Further analysis of Srs2 sumoylation showed that Srs2 sumoylation depended on PCNA interaction, suggesting sequential events of Srs2 recruitment by PCNA and subsequent sumoylation. Kinetic analysis showed that sumoylation peaks after maximal Mec1 induction by DNA damage (using the Top1 poison camptothecin (CPT)) and depended on Mec1. This data are consistent with a model that Mec1 hyperactivation is ultimately leading to signaling downregulation by Srs2 through Srs2 sumoylation. Mec1-S1964 phosphorylation, a marker for Mec1 hyperactivation and a site found to be needed for checkpoint downregulation after DSB induction, did not appear to be involved in checkpoint downregulation after CPT damage. The data are in support of the model that Mec1 hyperactivation when targeted to RPA-covered ssDNA by its Ddc2 (human ATRIP) targeting factor, favors Srs2 sumoylation after Srs2 recruitment to PCNA to disrupt the RPA-Ddc2-Mec1 signaling complex. Presumably, this allows gap filling and disappearance of long-lived ssDNA as the initiator of checkpoint signaling, although the study does not extend to this step.

      Strengths:

      (1) The manuscript focuses on the novel function of Srs2 to downregulate the DNA damage signaling response and provide new mechanistic insights.

      (2) The conclusions that PCNA interaction and ensuing Srs2-sumoylation are involved in checkpoint downregulation are well supported by the data.

      Weaknesses:

      (1) Additional mutants of interest could have been tested, such as the recently reported Pin mutant, srs2-Y775A (PMID: 38065943), and the Rad51 interaction point mutant, srs2-F891A (PMID: 31142613).

      (2) The use of deletion mutants for PCNA and RAD51 interaction is inferior to using specific point mutants, as done for the SUMO interaction and the sites for post-translational modifications.

      (3) Figure 4D and Figure 5A report data with standard deviations, which is unusual for n=2. Maybe the individual data points could be plotted with a color for each independent experiment to allow the reader to evaluate the reproducibility of the results.

      Comments on revisions:

      In this revision, the authors adequately addressed my concerns. The only issue I see remaining is the site of Srs2 action. The authors argue in favor of gaps and against R-loops and ssDNA resulting from excessive supercoiling. The authors do not discuss ssDNA resulting from processing of onesided DSBs, which are expected to result from replication run-off after CPT damage but are not expected to provide the 3'-junction for preferred PCNA loading. Can the authors exclude PCNA at the 5'-junction at a resected DSB?

      We have now added a sentence stating that we cannot exclude the possibility that PCNA may be positioned at a 5’-junction, as this can be observed in vitro, albert that PCNA loading was seen exclusively at a 3’-junction in the presence of RPA (Ellison & Stillman, 2003; Majka et al, 2006).

      Recommendations For the authors:

      Reviewer #2 (Recommendations For the authors):

      A Bonferroni correction should be made for the multiple comparisons in several figures.

      Specific comments:

      l. 41. This is a too long and confusing sentence.

      Sentence shortened: “These data suggest that Srs2 recruitment to PCNA proximal ssDNA-RPA filaments followed by its sumoylation can promote checkpoint recovery, whereas Srs2 action is minimized at regions with no proximal PCNA to permit RPA-mediated ssDNA protection”.

      l. 60. Identify Ddc2 and Mec1 as ATRIP and ATR.

      Done.

      l. 125 "fails to downregulate RPA levels on chromatin and Mec1-mediated DDC..." fails to downregulate RPA and fails to reduce Mec1-mediated DDC?

      Sentence modified: “fails to downregulate both the RPA levels on chromatin and the Mec1-mediated DDC”

      l. 204 "consistent with the notion that Srs2 has roles beyond RPA regulation"... What other roles? It's stripping of Rad51? Removing toxic joint molecules? Something else?

      Sentence modified: “consistent with the notion that Srs2 has roles beyond RPA regulation, such as in Rad51 regulation and removing DNA joint molecules”.

      l. 249 "Significantly, srs2-ΔPIM and -3KR increased the percentage of rfa1-zm2 cells transitioning into the G1 phase" No. Just back to normal. As stated in l. 258: "258 We found that srs2-ΔPIM and srs2-3KR mutants on their own behaved normally in the two DDC assays described above." All of these effects are quite small.

      Sentence modified: “Compared with rfa1-zm2 cells, srs2-∆PIM rfa1-zm2 and srs2-3KR rfa1-zm2 cells showed increased percentages of cells transitioning into the G1 phase”.

      l. 468 "Our previous work has provided several lines of evidence to support that Rad51 removal by Srs2 is separable from the Srs2-RPA antagonism (Dhingra et al., 2021). What evidence? See my comment above about not having both proteins removed at the same time.

      We have addressed this point in our initial rebuttal and some key points are summarized below. In our previous report (Dhingra et al., 2021), we provided several lines of evidence to support the conclusion that Rad51 is not relevant to the Srs2-RPA antagonism. For example, while rad51∆ rescues the hyper-recombination phenotype of srs2∆ cells, rad51∆ did not affect the hyper-checkpoint phenotype of srs2∆. In contrast, rfa1-zm1/zm2 have the opposite effects, that is, rfa1zm1/zm2 suppressed the hyper-checkpoint, but not the hyper-recombination, phenotype of srs2∆ cells. The differential effects of rad51∆ and rfa1-zm1/zm2 were also seen for the ATPase dead allele of Srs2 (srs2K41A). For example, rfa1-zm2 rescued hyper-checkpoint and CPT sensitivity of srs2-K41A cells, while rad51∆ had neither effect. These and other data described by Dhingra et al (2021) suggest that Srs2’s effects on checkpoint vs. recombination can be separated genetically. Consistent with our conclusion summarized above, deleting the Rad51 binding domain in Srs2 (srs2-∆Rad51BD) has no effect on rfa1-zm2 phenotype in CPT (Fig. 2D). This data provides yet another evidence that Srs2 regulation of Rad51 is separable from the Srs2RPA antagonism.

      l. 525 "possibility, we tested the separation pin of Srs2 (Y775), which was shown to enables its in vitro helicase activity during the revision of our work..." ?? there was helicase activity during the revision of your work? Please fix the sentence.

      Sentence modified: “we tested the separation pin of Srs2 (Y775). This residue was shown to be key for the Srs2’s helicase activity in vitro in a report that was published during the revision of our work (Meir et al, 2023).”

      Fig. 3. "srs2-ΔPIM and -3KR allow better G1 entry of rfa1-zm2 cells." is it better entry or less arrest at G2/M? One implies better turning off of a checkpoint, the other suggests less activation of the checkpoint.

      This is a correct statement. For all strains examined in Figure 3, cells were seen in G2/M phase after 1-hour CPT treatment, suggesting proper arrest.

      References:

      Armstrong AA, Mohideen F, Lima CD (2012) Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2. Nature 483: 59-63

      Colavito S, Macris-Kiss M, Seong C, Gleeson O, Greene EC, Klein HL, Krejci L, Sung P (2009) Functional significance of the Rad51-Srs2 complex in Rad51 presynaptic filament disruption. Nucleic Acids Res 37: 6754-6764.

      De Tullio L, Kaniecki K, Kwon Y, Crickard JB, Sung P, Greene EC (2017) Yeast Srs2 helicase promotes redistribution of single-stranded DNA-bound RPA and Rad52 in homologous recombination regulation. Cell Rep 21: 570-577

      Dhingra N, Kuppa S, Wei L, Pokhrel N, Baburyan S, Meng X, Antony E, Zhao X (2021) The Srs2 helicase dampens DNA damage checkpoint by recycling RPA from chromatin. Proc Natl Acad Sci U S A 118: e2020185118

      Elango R, Sheng Z, Jackson J, DeCata J, Ibrahim Y, Pham NT, Liang DH, Sakofsky CJ, Vindigni A, Lobachev KS et al (2017) Break-induced replication promotes formation of lethal joint molecules dissolved by Srs2. Nat Commun 8: 1790

      Ellison V, Stillman B (2003) Biochemical characterization of DNA damage checkpoint complexes: clamp loader and clamp complexes with specificity for 5' recessed DNA. PLoS Biol 1: E33

      Kolesar P, Altmannova V, Silva S, Lisby M, Krejci L (2016) Pro-recombination Role of Srs2 Protein Requires SUMO (Small Ubiquitin-like Modifier) but Is Independent of PCNA (Proliferating Cell Nuclear Antigen) Interaction. J Biol Chem 291: 7594-7607.

      Kolesar P, Sarangi P, Altmannova V, Zhao X, Krejci L (2012) Dual roles of the SUMO-interacting motif in the regulation of Srs2 sumoylation. Nucleic Acids Res 40: 7831-7843.

      Majka J, Binz SK, Wold MS, Burgers PM (2006) Replication protein A directs loading of the DNA damage checkpoint clamp to 5'-DNA junctions. J Biol Chem 281: 27855-27861

      Meir A, Raina VB, Rivera CE, Marie L, Symington LS, Greene EC (2023) The separation pin distinguishes the pro- and anti-recombinogenic functions of Saccharomyces cerevisiae Srs2. Nat Commun 14: 8144

      Menin L, Ursich S, Trovesi C, Zellweger R, Lopes M, Longhese MP, Clerici M (2018) Tel1/ATM prevents degradation of replication forks that reverse after Topoisomerase poisoning. EMBO Rep 19: e45535

      Minca EC, Kowalski D (2011) Replication fork stalling by bulky DNA damage: localization at active origins and checkpoint modulation. Nucleic Acids Res 39: 2610-2623

      Niu H, Klein HL (2017) Multifunctional roles of Saccharomyces cerevisiae Srs2 protein in replication, recombination and repair. FEMS Yeast Res 17: fow111

      Papouli E, Chen S, Davies AA, Huttner D, Krejci L, Sung P, Ulrich HD (2005) Crosstalk between SUMO and ubiquitin on PCNA is mediated by recruitment of the helicase Srs2p. Mol Cell 19: 123-133

      Redon C, Pilch DR, Rogakou EP, Orr AH, Lowndes NF, Bonner WM (2003) Yeast histone 2A serine 129 is essential for the efficient repair of checkpoint-blind DNA damage. EMBO Rep 4: 678-684

      Tercero JA, Longhese MP, Diffley JFX (2003) A central role for DNA replication forks in checkpoint activation and response. Mol Cell 11: 1323-1336

      Vaze MB, Pellicioli A, Lee SE, Ira G, Liberi G, Arbel-Eden A, Foiani M, Haber JE (2002) Recovery from checkpointmediated arrest after repair of a double-strand break requires Srs2 helicase. Mol Cell 10: 373-385

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      I In this manuscript, Jiao D et al reported the induction of synthetic lethal by combined inhibition of anti-apoptotic BCL-2 family proteins and WSB2, a substrate receptor in CRL5 ubiquitin ligase complex. Mechanistically, WSB2 interacts with NOXA to promote its ubiquitylation and degradation. Cancer cells deficient in WSB2, as well as heart and liver tissues from Wsb2-/- mice exhibit high susceptibility to apoptosis induced by inhibitors of BCL-2 family proteins. The anti-apoptotic activity of WSB2 is partially dependent on NOXA.

      Overall, the finding, that WSB2 disruption triggers synthetic lethality to BCL-2 family protein inhibitors by destabilizing NOXA, is rather novel. The manuscript is largely hypothesis-driven, with experiments that are adequately designed and executed. However, there are quite a few issues for the authors to address, including those listed below.

      Specific comments:

      (1) At the beginning of the Results section, a clear statement is needed as to why the authors are interested in WSB2 and what brought them to analyze "the genetic co-dependency between WSB2 and other proteins".

      We thank the reviewer for raising this important point. We agree that a clear rationale should be provided at the beginning of the Results section. As reported in previous studies [Ref: 1, 2, 3], strong synthetic interactions have been observed between WSB2 and several mitochondrial apoptosis-related factors, including MCL-1, BCL-xL, and MARCH5. We have referenced these findings in the Discussion section. Motivated by these studies, we became interested in the role of WSB2 and aimed to investigate the specific mechanisms underlying its synthetic lethality with anti-apoptotic BCL-2 family members. We will revise the beginning of the Results section to clearly state this rationale.

      (1) McDonald, E.R., 3rd et al. Project DRIVE: A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening. Cell 170, 577-592 e510 (2017).

      (2) DeWeirdt, P.C. et al. Genetic screens in isogenic mammalian cell lines without single cell cloning. Nat Commun 11, 752 (2020).

      (3) DeWeirdt, P.C. et al. Optimization of AsCas12a for combinatorial genetic screens in human cells. Nat Biotechnol 39, 94-104 (2021).

      (2) In general, the biochemical evidence supporting the role of WSB2 as a SOCS box-containing substrate-binding receptor of CRL5 E3 in promoting NOXA ubiquitylation and degradation is relatively weak. First, since NOXA binds to WSB2 on its SOCS box, which consists of a BC box for Elongin B/C binding and a CUL5 box for CUL5 binding, it is crucial to determine whether the binding of NOXA on the SOCS box affects the formation of CRL5WSB2 complex. The authors should demonstrate the endogenous binding between NOXA and the CRL5WSB2 complex. Additionally, the authors may also consider manipulating CUL5, SAG, or ElonginB/C to assess if it would affect NOXA protein turnover in two independent cell lines.

      We thank the reviewer for raising this important point. To determine whether endogenous NOXA binds to the intact CRL5<sup>WSB2</sup> complex, we performed co-immunoprecipitation assays using an antibody against NOXA. Indeed, NOXA co-immunoprecipitated with all subunits of the CRL5<sup>WSB2</sup> complex (Figure 2—figure supplement 1D), suggesting that NOXA binding to WSB2 does not disrupt interactions between WSB2 and the other CRL5 subunits. Moreover, depletion of CRL5 complex components (RBX2/SAG, CUL5, ELOB, or ELOC) through siRNAs in C4-2B or Huh-7 cells also resulted in a marked increase in NOXA protein levels.

      Second, in all the experiments designed to detect NOXA ubiquitylation in cells, the authors utilized immunoprecipitation (IP) with FLAG-NOXA/NOXA, followed by immunoblotting (IB) with HA-Ub. However, it is possible that the observed poly-Ub bands could be partly attributed to the ubiquitylation of other NOXA binding proteins. Therefore, the authors need to consider performing IP with HA-Ub and subsequently IB with NOXA. Alternatively, they could use Ni-beads to pull down all His-Ub-tagged proteins under denaturing conditions, followed by the detection of FLAG-tagged NOXA using anti-FLAG Ab. The authors are encouraged to perform one of these suggested experiments to exclude the possibility of this concern. Furthermore, an in vitro ubiquitylation assay is crucial to conclusively demonstrate that the polyubiquitylation of NOXA is indeed mediated by the CRL5WSB2 complex.

      We appreciate the reviewer for raising these important considerations regarding our ubiquitylation assays. We fully acknowledge the reviewer's concern that classical ubiquitination assays could potentially detect ubiquitination of proteins interacting with NOXA. However, we would like to clarify that our experimental conditions effectively mitigate this issue. Specifically, cells were lysed using buffer containing 1% SDS followed by boiling at 105°C for 5 minutes. These rigorous denaturing conditions ensure disruption of non-covalent protein interactions, thereby effectively eliminating the possibility of detecting ubiquitination signals from NOXA-associated proteins.

      Regarding the suggestion to perform an in vitro ubiquitination assay, we agree this experiment would indeed provide additional evidence. However, due to significant technical complexities associated with reconstituting CRL5-based E3 ubiquitin ligase activity in vitro—which would require the expression and purification of at least six recombinant proteins—such experiments are rarely performed in this context. Furthermore, NOXA is uniquely localized as a membrane protein on the mitochondrial outer membrane, posing additional significant challenges for protein expression and purification. Given the robustness of our current in vivo ubiquitylation assay under stringent denaturing conditions, we believe our existing data sufficiently and conclusively demonstrate NOXA ubiquitination mediated by the CRL5<sup>WSB2</sup> complex.

      (3) In their attempt to map the binding regions between NOXA and WSB2, the authors utilized exogenous proteins of both WSB2 and NOXA. To strengthen their findings, it would be more convincing to perform IP with exogenous wt/mutant WSB2 or NOXA and subsequently perform IB to detect endogenous NOXA or WSB2, respectively. Additionally, an in vitro binding assay using purified proteins would provide further evidence of a direct binding between NOXA and WSB2.

      We thank the reviewer for raising these important issues. In response to the reviewer’s suggestion to map the binding regions between NOXA and WSB2 more convincingly, we have indeed performed semi-endogenous Co-IP assays, which yielded results consistent with our exogenous protein experiments (Figure 3—figure supplement 1A, B). Concerning the recommendation to further validate direct interaction using purified recombinant proteins, we encountered substantial technical difficulties in obtaining pure and soluble recombinant WSB2 protein. Additionally, given that NOXA is an outer mitochondrial membrane protein and the interaction occurs on mitochondria, we believe that an in vitro binding assay may have limited physiological relevance. We hope the reviewer can appreciate these practical challenges and our current evidence supporting the strong interaction between NOXA and WSB2.

      Reviewer #2 (Public Review):

      Summary:

      Exploring the DEP-MAP database and two drug-screen databases, the authors identify WSB2 as an interactor of several BCL2 proteins. In follow-up experiments, they show that CRL5/WSB2 controls NOXA protein levels via K48 ubiquitination following direct protein-protein interaction, and cell death sensitivity in the context of BH3 mimetic treatment, where WSB2 depletion synergizes with drug treatment.

      Strengths:

      The authors use a set of orthogonal methods across different model cell lines and a new WSB2 KO mouse model to confirm their findings. They also manage to correlate WSB2 expression with poor prognosis in prostate and liver cancer, supporting the idea that targeting WSB2 may sensitize cancers for treatment with BH3 mimetics.

      Weaknesses:

      The conclusions drawn based on the findings in cancer patients are very speculative, as regulation of NOXA cannot be the sole function of CRL5/WSB2 and it is hence unclear what causes correlation with patient survival. Moreover, the authors do not provide a clear mechanistic explanation of how exactly higher levels of NOXA promote apoptosis in the absence of WSB2. This would be important knowledge, as usually high NOXA levels correlate with high MCL1, as they are turned over together, but in situations like this, or loss of other E3 ligases, such as MARCH, the buffering capacity of MCL1 is outrun, allowing excess NOXA to kill (likely by neutralizing other BCL2 proteins it usually does not bind to, such as BCLX). Moreover, a necroptosis-inducing role of NOXA has been postulated. Neither of these options is interrogated here.

      Recommendations For The Authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) Figure 2J. The authors showed that "the mRNA levels of NOXA were even reduced in WSB2-KO cells compared to parental cells". What is the possible mechanism? This point should at least be discussed.

      We thank the reviewer for raising these important issues. The underlying mechanisms for the significantly lower mRNA levels of NOXA following the KO of WSB2 are not fully understood at present. However, we propose that this could represent a form of negative feedback regulation at the level of gene expression. Specifically, when the protein levels of BNIP3/3L rise sharply, it may activate mechanisms that suppress their own mRNA synthesis or stability, serving as a buffering system to prevent further protein accumulation. Such negative feedback loops may be critical for maintaining cellular homeostasis and avoiding excessive protein production. Moreover, this phenomenon is frequently observed in other studies investigating substrates targeted by E3 ubiquitin ligases for degradation. We have elaborated on this point in the Discussion section.

      (2) Figure 2M. A previous study has clearly demonstrated that NOXA is subjected to ubiquitylation and degradation by CRL5 E3 ligase (PMID: 27591266). This paper should be cited. Also, in that publication, NOXA ubiquitylation is via the K11 linkage, not the K48 linkage. The authors should include K11R mutant in their assay.

      We thank the reviewer for raising this important issue. We thank the reviewer for suggesting the relevant reference (PMID: 27591266), which we have now cited accordingly. Additionally, we would like to clarify that our new in vivo ubiquitination assays included the K11R and K11-only ubiquitin mutants, and our data demonstrate that WSB2-mediated NOXA ubiquitination indeed involves the K11 linkage ubiquitination(Figure 2—figure supplement 1E).

      (3) Figure 3H, J. The authors stated, "By mutating these lysine residues to arginine, we found that WSB2-mediated NOXA ubiquitination was completely abolished". Which one of the three lysine residues is playing the dominant role?

      We thank the reviewer for raising this important issue. To address this, we generated FLAG-NOXA mutants individually substituting lysine residues K35, K41, and K48 with arginine. In vivo ubiquitination assays demonstrated that lysine 48 (K48) is the predominant residue responsible for WSB2-mediated NOXA ubiquitination (Figure 3—figure supplement 1C).

      (4) Figure 3N. The authors need to show that the fusion peptide containing C-terminal NOXA peptide competitively inhibits the interaction between endogenous WSB2 and NOXA and extends the protein half-life of NOXA, leading to NOXA accumulation.

      We sincerely thank the reviewer for raising these important issues. As suggested, we investigated whether the fusion peptide containing the C-terminal NOXA sequence competitively disrupts the interaction between endogenous WSB2 and NOXA, subsequently influencing NOXA stability. Our results demonstrated that treatment with this fusion peptide indeed significantly reduced the endogenous interaction between WSB2 and NOXA (Figure 3—figure supplement 1D). Furthermore, we observed that the peptide dose-dependently increased endogenous NOXA protein levels and prolonged its protein half-life, thereby resulting in the accumulation of NOXA (Figure 3N; Figure 3—figure supplement 1E, F). These findings collectively indicate that the fusion peptide competitively inhibits the WSB2-NOXA interaction, stabilizes NOXA protein, and enhances its accumulation.

      (5) Figure 4. a) It would be better to investigate whether WSB2 knockdown can sensitize cancer cells to the treatment with ABT-737 or AZD5991, evidenced by a decrease in both IC50 values and clonogenic survival rates and whether such sensitization is dependent on NOXA. b) The authors need to show the levels of cleaved caspase-3/7/9 and the percentages of apoptotic cells in shNC cells upon silencing of WSB2 in Figure 4A-F. c) It will be more convincing to repeat the experiment to show synthetic lethality by WSB2 disruption and MCL-1 inhibitor AZD5991 treatment using another cell line, such as WSB2-deficient Huh-7 cells in Figure 4 I&J.

      We sincerely thank the reviewer for these valuable and constructive suggestions. Regarding point (a): We believe that our current Western blot and flow cytometry data (Figure 4G–L) have already provided strong evidence that WSB2 depletion enhances apoptosis in response to ABT-737 and AZD5991. Therefore, we consider that additional IC50 and clonogenic survival assays, while informative, may not be essential for supporting our conclusion. Furthermore, as shown in Figure 5A–F, we found that silencing NOXA largely, though not completely, reversed the enhanced apoptosis triggered by these inhibitors in WSB2-deficient cells, suggesting that the sensitization effect is at least partially dependent on NOXA.

      Regarding point (b): We have shown that WSB2 knockout alone had no impact on the levels of cleaved caspase-3/7/9 or the percentages of apoptotic cells in Huh-7 and C4-2B cells (Figure 4G-L and Figure 4—figure supplement 1A-D), indicating that WSB2 loss does not induce apoptosis on its own under basal conditions.

      Regarding point (c): We appreciate the reviewer’s suggestion and have now repeated the experiment in WSB2 knockout Huh-7 cells. The new results further support the synthetic lethality between WSB2 loss and AZD5991 treatment (Figure 4—figure supplement 1C, D).

      (6) Figure 5A/C/E. The effect of siNOXA is minor, if any, for cleavage of caspases. The same thing for Figure 6F/H.

      We appreciate the reviewer’s insightful observation regarding the relatively modest effect of shNOXA on caspase cleavage in Figures 5A/C/E and Figures 6F/H. Indeed, we acknowledge that the reduction in caspase cleavage following NOXA knockdown is moderate. However, consistent with our discussions in the manuscript, NOXA knockdown significantly—but not completely—rescued the increased apoptosis observed in WSB2-deficient cells treated with BCL-2 family inhibitors. This suggests that while NOXA plays a notable role, additional mechanisms or unidentified targets may also be involved in WSB2-mediated regulation of apoptosis.

      (7) Figure 5 I&J. The authors may consider performing IHC staining, immunofluorescence, or WB analysis to show the levels of NOXA and cleaved caspases or PARP in xenograft tumors. This would provide in vivo evidence of significant apoptosis induction resulting from the co-administration of ABT-737 and R8-C-terminal NOXA peptide.

      We appreciate the reviewer's thoughtful suggestion regarding additional immunohistochemical or immunofluorescence analyses in xenograft tumors. However, due to current limitations in available antibodies suitable for reliable detection of NOXA by IHC and IF, we are unable to perform these experiments. We greatly appreciate the reviewer's understanding of this technical constraint. Nevertheless, our existing data collectively supports the conclusion that the combination of ABT-737 and R8-C-terminal NOXA peptide significantly enhances apoptosis in vivo.

      (8) Figure 7. Does an inverse correlation exist between the protein levels of WSB2 and NOXA in RPAD or LIHC tissue microarrays? On page 12, in the first paragraph, Figure 7M-P was cited incorrectly.

      We sincerely thank the reviewer for raising this important issue. As mentioned above, due to current limitations regarding the availability of suitable antibodies that can reliably detect NOXA by IHC, we regret that it is not feasible to experimentally address this question at this time.

      Additionally, we have carefully corrected the citation error involving Figure 7M-P on page 12, as pointed out by the reviewer.

      (9) Figure S1D. BCL-W levels were reduced upon WSB2 overexpression, which should be acknowledged.

      We sincerely thank the reviewer for raising this important issue. We acknowledge that BCL-W protein levels were slightly reduced upon WSB2 overexpression in Figure S1D. However, this effect is distinct from the pronounced reduction observed in NOXA protein levels. We have revised the manuscript to clarify this point. Additionally, we recognize that transient overexpression systems may occasionally lead to non-specific or artifactual changes. Our exogenous expression and co-immunoprecipitation experiments did not support an interaction between BCL-W and WSB2. Therefore, the observed reduction of BCL-W under these conditions may not reflect a physiologically relevant regulation.

      (10) Figure S4. Given WSB2 KO mice are viable; the authors may consider determining whether these mice are more sensitive to radiation-induced tissue damage or but more resistant to radiation-induced tumorigenesis?

      We sincerely thank the reviewer for this insightful and biologically meaningful suggestion. We agree that investigating the potential role of WSB2 in radiation-induced tissue damage and tumorigenesis would be of great interest. However, conducting such experiments requires access to specialized irradiation facilities, which are currently unavailable to us. Nevertheless, we recognize the value of this line of investigation and plan to explore it in our future studies.

      (11) All data were displayed as mean{plus minus}SD. However, for data from three independent experiments, it is more appropriate to present the results as mean{plus minus}SEM, not mean{plus minus}SD.

      We sincerely thank the reviewer for highlighting this important issue. In line with the reviewer's suggestion, we have revised the manuscript accordingly and now present data from three independent experiments as mean ± SEM.

      (12) The figure legends require careful review: i) The low dose of ABT-199 (Figure 6H) and the dose of ABT-199 used in Figure 6I are missing. ii) The legends for Figure S1D-E are incorrect. iii) The name of the antibody in the legend of Figure S3C is incorrect.

      We sincerely thank the reviewer for raising these important issues. We have carefully corrected all the errors mentioned. In addition, we have thoroughly reviewed the manuscript to prevent similar errors.

      Reviewer #2 (Recommendations For The Authors):

      The authors focus on NOXA, after initially identifying WSB2 to interact with several BCL2 proteins. The rationale behind this is that WSB2 depletion or overexpression affects NOXA levels, but none of the other BCL2 proteins tested, as stated in the text. Yet, BCLW is also depleted upon overexpression of WSB2 (Supplementary Figure 1). How does this phenomenon relate to the sensitization noted, is BCL-W higher in WSB2 KO cells? It does not seem so though. This warrants discussion.

      We appreciate the reviewer for raising this important issue. Our results showed that overexpression of WSB2 markedly reduced NOXA levels, while the levels of other BCL-2 family proteins remained unaffected or minimally affected, such as BCL-W (Figure 2—figure supplement 1A). Furthermore, depletion of WSB2 through shRNA-mediated KD or CRISPR/Cas9-mediated KO in C4-2B cells or Huh-7 cells led to a marked increase in the steady-state levels of endogenous NOXA, without affecting other BCL-2 family proteins examined, included BCL-W (Figure 2A-C, Figure 2—figure supplement 2A, B).

      If WSB2 depletion does not affect MCL1 levels, how does excess NOXA actually kill? Does it bind to any (other) prosurvival proteins under conditions of WSB2 depletion? Is the MCL1 half-life changed?

      We appreciate the reviewer for raising this important point. NOXA is a BH3-only protein known to promote apoptosis primarily by binding to and neutralizing anti-apoptotic BCL-2 family members, especially MCL-1, via its BH3 domain. It can inhibit MCL-1 either through competitive binding or by facilitating its ubiquitination and subsequent proteasomal degradation. In our system, the total protein levels of MCL-1 remained unchanged in WSB2 knockout cells, suggesting that NOXA may not be promoting apoptosis through enhanced MCL-1 degradation. Instead, we speculate that the accumulation of NOXA in WSB2-deficient cells enhances apoptosis by sequestering MCL-1 through direct binding, thereby freeing pro-apoptotic effectors such as BAK and BAX. In line with our observations, Nakao et al. reported that deletion of the mitochondrial E3 ligase MARCH5 led to a pronounced increase in NOXA expression, while leaving MCL-1 protein levels unchanged in leukemia cell lines (Leukemia. 2023 ;37:1028-1038., PMID: 36973350).

      Additionally, NOXA has been reported to interact with other anti-apoptotic proteins, including BCL-XL. It is therefore possible that under conditions of WSB2 depletion, excess NOXA may also bind to BCL-XL and relieve its inhibition of BAX/BAK, further contributing to apoptosis. Future experiments assessing NOXA binding partners in WSB2-deficient cells would help clarify this mechanism.

      I think some initial insights into the mechanism underlying the sensitization would add a lot to this study. Is there a role of BFL1/A1 in any of these cell lines, as it can also rather selectively bind to NOXA and is sometimes deregulated in cancer?

      We appreciate the reviewer for raising this important issue. While BFL1/A1 is indeed another anti-apoptotic BCL-2 family member that can selectively bind to NOXA and has been implicated in cancer, our study primarily focuses on the WSB2-NOXA axis. However, given its potential involvement in apoptosis regulation, it would be an interesting direction for future studies to explore whether BFL1/A1 contributes to NOXA-mediated sensitization in specific cellular contexts.

      Otherwise, this is a very nice and convincing study.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript focuses on the olfactory system of Pieris brassicae larvae and the importance of olfactory information in their interactions with the host plant Brassica oleracea and the major parasitic wasp Cotesia glomerata. The authors used CRISPR/Cas9 to knockout odorant receptor coreceptors (Orco), and conducted a comparative study on the behavior and olfactory system of the mutant and wild-type larvae. The study found that Orco-expressing olfactory sensory neurons in antennae and maxillary palps of Orco knockout (KO) larvae disappeared, and the number of glomeruli in the brain decreased, which impairs the olfactory detection and primary processing in the brain. Orco KO caterpillars show weight loss and loss of preference for optimal food plants; KO larvae also lost weight when attacked by parasitoids with the ovipositor removed, and mortality increased when attacked by untreated parasitoids. On this basis, the authors further studied the responses of caterpillars to volatiles from plants attacked by the larvae of the same species and volatiles from plants on which the caterpillars were themselves attacked by parasitic wasps. Lack of OR-mediated olfactory inputs prevents caterpillars from finding suitable food sources and from choosing spaces free of enemies.

      Strengths:

      The findings help to understand the important role of olfaction in caterpillar feeding and predator avoidance, highlighting the importance of odorant receptor genes in shaping ecological interactions.

      Weaknesses:

      There are the following major concerns:

      (1) Possible non-targeted effects of Orco knockout using CRISPR/Cas9 should be analyzed and evaluated in Materials and Methods and Results.

      Thank you for your suggestion. In the Materials and Methods, we mention how we selected the target region and evaluated potential off-target sites by Exonerate and CHOPCHOP. Neither of these methods found potential off-target sites with a more-than-17-nt alignment identity. Therefore, we assumed no off-target effect in our Orco knockout. Furthermore, we did not find any developmental differences between wildtype and knockout caterpillars when these were reared on leaf discs in Petri dishes (Fig S4). We will further highlight this information on the off-target evaluation in the Results section.

      (2) Figure 1E: Only one olfactory receptor neuron was marked in WT. There are at least three olfactory sensilla at the top of the maxillary palp. Therefore, to explain the loss of Orcoexpressing neurons in the mutant (Figure 1F), a more rigorous explanation of the photo is required.

      Thank you for pointing this out. The figure shows only a qualitative comparison between WT and KO and we did not aim to determine the total number of Orco positive neurons in the maxillary palps or antennae of WT and KO caterpillars, but please see our previous work for the neuron numbers in the caterpillar antennae (Wang et al., 2024). We did indeed find more than one neuron in the maxillary palps, but as these were in very different image planes it was not possible to visualize them together. However, we will add a few sentences in the Results and Discussion section to explain the results of the maxillary palp Orco staining.

      (3) In Figure 1G, H, the four glomeruli are circled by dotted lines: their corresponding relationship between the two figures needs to be further clarified.

      Thank you for pointing this out. The four glomeruli in Figure 1G and 1H are not strictly corresponding. We circled these glomeruli to highlight them, as they are the best visualized and clearly shown in this view. In this study, we only counted the number of glomeruli in both WT and KO, however, we did not clarify which glomeruli are missing in the KO caterpillar brain. We will further clarify this in the figure legend.

      (4) Line 130: Since the main topic in this study is the olfactory system of larvae, the experimental results of this part are all about antennal electrophysiological responses, mating frequency, and egg production of female and male adults of wild type and Orco KO mutant, it may be considered to include this part in the supplementary files. It is better to include some data about the olfactory responses of larvae.

      Thank you for your suggestion. We do agree with your suggestion, and we will consider moving this part to the supplementary information. Regarding larval olfactory response, we unfortunately failed to record any spikes using single sensillum recordings due to the difficult nature of the preparation; however we do believe that this would be an interesting avenue for further research.

      (5)Line 166: The sentences in the text are about the choice test between " healthy plant vs. infested plant", while in Fig 3C, it is "infested plant vs. no plant". The content in the text does not match the figure.

      Thank you for pointing this out. The sentence is “We compared the behaviors of both WT and Orco KO caterpillars in response to clean air, a healthy plant and a caterpillar-infested plant”. We tested these three stimuli in two comparisons: healthy plant vs no plant, infested plant vs no plant. The two comparisons are shown in Figure 3C separately. We will aim to describe this more clearly in the revised version of this manuscript.

      (6) Lines 174-178: Figure 3A showed that the body weight of Orco KO larvae in the absence of parasitic wasps also decreased compared with that of WT. Therefore, in the experiments of Figure 3A and E, the difference in the body weight of Orco KO larvae in the presence or absence of parasitic wasps without ovipositors should also be compared. The current data cannot determine the reduced weight of KO mutant is due to the Orco knockout or the presence of parasitic wasps.

      Thank you for pointing this out. We did not make a comparison between the data of Figures 3A and 3E since the two experiments were not conducted at the same time due to the limited space in our BioSafety III greenhouse. We do agree that the weight decrease in Figure 3E is partly due to the reduced caterpillar growth shown in Figure 3A. However, we are confident that the additional decrease in caterpillar weight shown in Figure 3E is mainly driven by the presence of disarmed parasitoids. To be specific, the average weight in Figure 3A is 0.4544 g for WT and 0.4230 g for KO, KO weight is 93.1% of WT caterpillars. While in Figure 3E, the average weight is 0.4273 g for WT and 0.3637 g for KO, KO weight is 85.1% of WT caterpillars. We will discuss this interaction between caterpillar growth and the effect of the parasitoid attacks more extensively in the revised version of the manuscript.

      (7) Lines 179-181: Figure 3F shows that the survival rate of larvae of Orco KO mutant decreased in the presence of parasitic wasps, and the difference in survival rate of larvae of WT and Orco KO mutant in the absence of parasitic wasps should also be compared. The current data cannot determine whether the reduced survival of the KO mutant is due to the Orco knockout or the presence of parasitic wasps.

      We are happy that you highlight this point. When conducting these experiments, we selected groups of caterpillars and carefully placed them on a leaf with minimal disturbance of the caterpillars, which minimized hurting and mortality. We did test the survival of caterpillars in the absence of parasitoid wasps from the experiment presented in Figure 3A, although this was missing from the manuscript. There is no significant difference in the survival rate of caterpillars between the two genotypes in the absence of wasps (average mortality WT = 8.8 %, average mortality KO = 2.9 %; P = 0.088, Wilcoxon test), so the decreased survival rate is most likely due to the attack of the wasps. We will add this information to the revised version of the manuscript.

      (8) In Figure 4B, why do the compounds tested have no volatiles derived from plants? Cruciferous plants have the well-known mustard bomb. In the behavioral experiments, the larvae responses to ITC compounds were not included, which is suggested to be explained in the discussion section.

      Thank you for the suggestion. We assume you mean Figure 4D/4E instead of Figure 4B. In Figure 4B, many of the identified chemical compounds are essentially plant volatiles, especially those from caterpillar frass and caterpillar spit. In Figure 4D/4E, most of the tested chemicals are derived from plants. But indeed, we did not include ITCs, based on information from the EAG results in Figures 2A & 2B. Butterfly antennae did not respond strongly to ITCs, so we did not include ITCs in the larval behavioural tests. Instead, the tested chemicals in Figure 4D/4E either elicit high EAG responses of butterflies or have been identified as “important” by VIP scores in the chemical analyses. In the EAG results of Plutella xylostella (Liu et al., 2020), moths responded well to a few ITCs, the tested ITCs in our study are actually adopted from this study except for those that were not available to us. However, butterflies did not show a strong response to the tested ITCs; therefore, we did not include ITCs because we expected that Pieris brassicae caterpillars are not likely to show good responses to ITCs. We will add this explanation to the revised version of our manuscript.

      (9) The custom-made setup and the relevant behavioral experiments in Figure 4C need to be described in detail (Line 545).

      We will add more detailed descriptions for the setup and method in the Materials and Methods.

      (10) Materials and Methods Line 448: 10 μL paraffin oil should be used for negative control.

      Thank you for pointing this out. We used both clean filter paper and clean filter paper with 10 μL paraffin oil as negative controls, but we did not find a significant difference between the two controls. Therefore, in the EAG results of Figure 2A/2B, we presented paraffin oil as one of the tested chemicals. We will re-run our statistical tests with paraffin oil as negative control, although we do not expect any major differences to the previous tests.

      Reviewer #2 (Public review):

      Summary:

      This manuscript investigated the effect of olfactory cues on caterpillar performance and parasitoid avoidance in Pieris brassicae. The authors knocked out Orco to produce caterpillars with significantly reduced olfactory perception. These caterpillars showed reduced performance and increased susceptibility to a parasitoid wasp.

      Strengths:

      This is an impressive piece of work and a well-written manuscript. The authors have used multiple techniques to investigate not only the effect of the loss of olfactory cues on host-parasitoid interactions, but also the mechanisms underlying this.

      Weaknesses:

      (1) I do have one major query regarding this manuscript - I agree that the results of the caterpillar choice tests in a y-maze give weight to the idea that olfactory cues may help them avoid areas with higher numbers of parasitoids. However, the experiments with parasitoids were carried out on a single plant. Given that caterpillars in these experiments were very limited in their potential movement and source of food - how likely is it that avoidance played a role in the results seen from these experiments, as opposed to simply the slower growth of the KO caterpillars extending their period of susceptibility? While the two mechanisms may well both take place in nature - only one suggests a direct role of olfaction in enemy avoidance at this life stage, while the other is an indirect effect, hence the distinction is important.

      We do agree with your comment that both mechanisms may be at work in nature and we do address this in the Discussion section. In our study, we did find that wildtype caterpillars were more efficient in locating their food source and did grow faster on full plants than knockout caterpillars. This faster growth will enable wildtype caterpillars to more quickly outgrow the life-stages most vulnerable to the parasitoids (L1 and L2). The olfactory system therefore supports the escape from parasitoids indirectly by enhancing feeding efficiency directly.

      Figure 3D shows that WT caterpillars prefer infested plants without parastioids to infested plants with parasitoids. In addition, we observed that caterpillars move frequently between different leaves. Therefore, we speculate that WT caterpillars make use of volatiles from the plant or from (parasitoid-exposed) conspecifics via their spit or faeces to avoid parts of the plant potentially attracting natural enemies. Knockout caterpillars are unable to use these volatile danger cues and therefore do not avoid plant parts that are most attractive to their natural enemies, making KO caterpillars more susceptible and leading to more natural enemy harassment. Through this, olfaction also directly impacts the ability of a caterpillar to find an enemy-free feeding site.

      We think that olfaction supports the enemy avoidance of caterpillars via both these mechanisms, although at different time scales. Unfortunately, our analysis was not detailed enough to discern the relative importance of the two mechanisms we found. However, we feel that this would be an interesting avenue for further research. Moreover, we will sharpen our discussion on the potential importance of the two different mechanisms in the revised version of this manuscript.

      (2) My other issue was determining sample sizes used from the text was sometimes a bit confusing. (This was much clearer from the figures).

      We will revise the sample size in the text to make it more clear.

      (3) I also couldn't find the test statistics for any of the statistical methods in the main text, or in the supplementary materials.

      Thank you for pointing this out. We will provide more detailed test statistics in the main text and in the supplementary materials of the revised version of the manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Abstract

      Line 24: "optimal food plant" should be changed to "optimal food plants"

      Thank you for the suggestion, we will revise it.

      (2) Introduction

      Lines 44-46: The sentence should be rephrased.

      Thank you for the suggestion, we will revise it.

      Line 50: "are" should be changed to "is".

      Thank you for the suggestion, we will revise it.

      Lines 57 and 58: Please provide the Latin names of "brown planthoppers" and "striped stem borer".

      Thank you for the suggestion, we will revise it.

      Line 85: "investigate the influence of odor-guided behavior by this primary herbivore on the next trophic levels"; similarly, Line 160: "investigate if caterpillars could locate the optimal host-plant when supplied with differently treated plants". These sentences are not very accurate in describing the relevant experiments. A: Thank you for the suggestion, we will revise them.

      Reviewer #2 (Recommendations for the authors):

      (1) L53 Remove the "the" from "Under the strong selection pressure"

      Thank you for the suggestion, we will revise it.

      (2) L80 I suggest adding a reference for the spitting behaviour, e.g. Muller et al 2003.

      Thank you for the suggestion, we will add it.

      (3) L89 establishing a homozygous KO insect colony.

      Thank you for the suggestion, we will revise it.

      (4) L107 perhaps this goes against the journal style but I always like to see acronyms explained the first time they are used.

      Thank you for the suggestion, we will try to make it more understandable.

      (5) L146-148 sentence difficult to read - consider rephrasing.

      Thank you for the suggestion, we will revise it.

      (6) L230 do you mean still produce? Rather than still reproduce?

      Thank you for the suggestion, we will revise it.

      (7) L233 missing an and before "a greater vulnerability to the parasitoid wasp".

      Thank you for pointing this out, we will revise it.

      (8) L238 malfunctional is a strange word choice.

      Thank you for pointing this out, we will revise it.

      (9) L181 - can the authors confirm that this lower survival was due to parasitism by the wasps?

      This question is similar to Q(7) of Reviewer 1, so we quote our answer for Q(7) here:

      When conducting these experiments, we selected groups of caterpillars and carefully placed them on a leaf with minimal disturbance of the caterpillars, which minimized hurting and mortality. We did test the survival of caterpillars in the absence of parasitoid wasps from the experiment presented in Figure 3A, although this was missing from the manuscript. There is no significant difference in the survival rate of caterpillars between the two genotypes in the absence of wasp (average mortality WT = 8.8 %, average mortality KO = 2.9 %; P = 0.088, Wilcoxon test), so the decreased survival rate is most likely due to the attack of the wasps. We will add this information to the revised version of the manuscript.

      (10) L474 - has it been tested if wasps still behave similarly after their ovipositor has been removed?

      Thank you for pointing out this issue. We did not strictly compare if disarmed and untreated wasps have similar behaviors. However, we did observe if disarmed wasps can actively move or fly after recovering from anesthesia before releasing into a cage, otherwise we would replace with another active one.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study aims to identify the proteins that compose the electrical synapse, which are much less understood than those of the chemical synapse. Identifying these proteins is important to understand how synaptogenesis and conductance are regulated in these synapses. The authors identified more than 50 new proteins and used immunoprecipitation and immunostaining to validate their interaction of localization. One new protein, a scaffolding protein, shows particularly strong evidence of being an integral component of the electrical synapse. However, many key experimental details are missing (e.g. mass spectrometry), making it difficult to assess the strength of the evidence.

      Strengths:

      One newly identified protein, SIPA1L3, has been validated both by immunoprecipitation and immunohistochemistry. The localization at the electrical synapse is very striking.<br /> A large number of candidate interacting proteins were validated with immunostaining in vivo or in vitro.

      Weaknesses:

      There is no systematic comparison between the zebrafish and mouse proteome. The claim that there is "a high degree of evolutionary conservation" was not substantiated.

      We have added a table as supplementary figure 3 that shows a comparison of all candidates. While there are differences in both proteomes, components such as ZO proteins and the endocytosis machinery are clearly conserved.

      No description of how mass spectrometry was done and what type of validation was done.

      We have contacted the mass spec facility we worked with and added a paragraph explaining the mass spec. procedure in the material and methods section.

      The threshold for enrichment seems arbitrary.

      Yes, the thresholds are somewhat arbitrary. This is due to the fact that experiments that captured larger total amounts of protein (mouse retina samples) had higher signal-to-noise ratio than those that captured smaller total amounts of protein (zebrafish retina). This allowed us to use a more stringent threshold in the mouse dataset to focus on high probability captured proteins.

      Inconsistent nomenclature and punctuation usage.

      We have scanned through the manuscript and updated terms that were used inconsistently in the interim revision of the manuscript.

      The description of figures is very sparse and error-prone (e.g. Figure 6).

      In Figure 1B, there is very broad non-specific labeling by avidin in zebrafish (In contrast to the more specific avidin binding in mice, Figure 2B). How are the authors certain that the enrichment is specific at the electrical synapse?

      The enrichment of the proteins we identified is specific for electrical synapses because we compared the abundance of all candidates between Cx35b-V5-TurboID and wildtype retinas. Proteins that are components of electrical synapses, will only show up in the Cx35b-V5-TurboID condition. The western blot (Strep-HRP) in figure 1C shows the differences in the streptavidin labeling and hence the enrichment of proteins that are part of electrical synapses. Moreover, while the background appears to be quite abundant in sections, biotinylation is a rare posttranslational modification and mainly occurs in carboxylases: The two intense bands that show up above 50 and 75 kDa. The background mainly originates from these two proteins. Therefore, it is easy to distinguish specific hits from non-specific background.

      In Figure 1E, there is very little colocalization between Cx35 and Cx34.7. More quantification is needed to show that it is indeed "frequently associated."

      We agree that “frequently associated” is too strong as a statement. We corrected this and instead wrote “that Cx34.7 was only expressed in the outer plexiform layer (OPL) where it was associated with Cx35b at some gap junctions” in line 151. There are many gap junctions at which Cx35b is not colocalized with Cx34.7.

      Expression of GFP in HCs would potentially be an issue, since GFP is fused to Cx36 (regardless of whether HC expresses Cx36 endogenously) and V5-TurboID-dGBP can bind to GFP and biotinylate any adjacent protein.

      Thank you for this suggestion! There should be no Cx36-GFP expression in horizontal cells, which means that the nanobody cannot bind to anything in these cells. Moreover, to recognize specific signals from non-specific background, we included wild type retinas throughout the entire experiments. This condition controls for non-specific biotinylation.

      Figure 7: the description does not match up with the figure regarding ZO-1 and ZO-2.

      It appears that a portion of the figure legend was left out of the submitted version of the manuscript. We have put the legend for panels A through C back into the manuscript in the interim revision.

      Reviewer #2 (Public review):

      Summary:

      This study aimed to uncover the protein composition and evolutionary conservation of electrical synapses in retinal neurons. The authors employed two complementary BioID approaches: expressing a Cx35b-TurboID fusion protein in zebrafish photoreceptors and using GFP-directed TurboID in Cx36-EGFP-labeled mouse AII amacrine cells. They identified conserved ZO proteins and endocytosis components in both species, along with over 50 novel proteins related to adhesion, cytoskeleton remodeling, membrane trafficking, and chemical synapses. Through a series of validation studies¬-including immunohistochemistry, in vitro interaction assays, and immunoprecipitation - they demonstrate that novel scaffold protein SIPA1L3 interacts with both Cx36 and ZO proteins at electrical synapse. Furthermore, they identify and localize proteins ZO-1, ZO-2, CGN, SIPA1L3, Syt4, SJ2BP, and BAI1 at AII/cone bipolar cell gap junctions.

      Strengths:

      The study demonstrates several significant strengths in both experimental design and validation approaches. First, the dual-species approach provides valuable insights into the evolutionary conservation of electrical synapse components across vertebrates. Second, the authors compare two different TurboID strategies in mice and demonstrate that the HKamac promoter and GFP-directed approach can successfully target the electrical synapse proteome of mouse AII amacrine cells. Third, they employed multiple complementary validation approaches - including retinal section immunohistochemistry, in vitro interaction assays, and immunoprecipitation-providing evidence supporting the presence and interaction of these proteins at electrical synapses.

      Weaknesses:

      The conclusions of this paper are supported by data; however, some aspects of the quantitative proteomics analysis require clarification and more detailed documented. The differential threshold criteria (>3 log2 fold for mouse vs >1 log2 fold for zebrafish) will benefit from biological justification, particularly given the cross-species comparison. Additionally, providing details on the number of biological or technical replicates used in this study, along with analyses of how these replicates compare to each other, would strengthen the confidence in the identification of candidate proteins. Furthermore, including negative controls for the histological validation of proteins interacting with Cx36 could increase the reliability of the staining results.

      While the study successfully characterized the presence of candidate proteins at the electrical synapses between AII amacrine cells and cone bipolar cells, it did not compare protein compositions between the different types of electrical synapses within the circuit. Given that AII amacrine cells form both homologous (AII-AII) and heterologous (AII-cone bipolar cell) electrical synapses-connections that serve distinct functional roles in retinal signaling processing-a comparative analysis of their molecular compositions could have provided important insights into synapse specificity.

      Reviewer #3 (Public review):

      Summary:

      This study by Tetenborg S et al. identifies proteins that are physically closely associated with gap junctions in retinal neurons of mice and zebrafish using BioID, a technique that labels and isolates proteins proximal to a protein of interest. These proteins include scaffold proteins, adhesion molecules, chemical synapse proteins, components of the endocytic machinery, and cytoskeleton-associated proteins. Using a combination of genetic tools and meticulously executed immunostaining, the authors further verified the colocalizations of some of the identified proteins with connexin-positive gap junctions. The findings in this study highlight the complexity of gap junctions. Electrical synapses are abundant in the nervous system, yet their regulatory mechanisms are far less understood than those of chemical synapses. This work will provide valuable information for future studies aiming to elucidate the regulatory mechanisms essential for the function of neural circuits.

      Strengths:

      A key strength of this work is the identification of novel gap junction-associated proteins in AII amacrine cells and photoreceptors using BioID in combination with various genetic tools. The well-studied functions of gap junctions in these neurons will facilitate future research into the functions of the identified proteins in regulating electrical synapses.

      Thank you for these comments.

      Weaknesses:

      I do not see major weaknesses in this paper. A minor point is that, although the immunostaining in this study is beautifully executed, the quantification to verify the colocalization of the identified proteins with gap junctions is missing. In particular, endocytosis component proteins are abundant in the IPL, making it unclear whether their colocalization with gap junction is above chance level (e.g. EPS15l1, HIP1R, SNAP91, ITSN in Figure 3B).

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) It would be helpful to include a comprehensive summary of the results from the quantitative proteomics analyses, such as the number of proteins detected in each species and the number of proteins associated with each GO term. Additionally, a clear figure or table highlighting the specific proteins conserved between zebrafish and mice would strengthen the evidence for evolutionary conservation of proteins at electrical synapses.

      We have added the raw data we received from our mass spec facility including a comparison of all the candidates for different species. Supplementary figure 3.

      (2) A more detailed description of the number of experimental and/or technical replicates would improve the technical rigor of the study. For example, what was the rationale for using different log2 fold-change cutoffs in mice versus zebrafish? Are the replicates consistent in terms of protein enrichment?

      We have added raw data from individual experiments as a supplement (Excel spreadsheet). We have two replicates from zebrafish and two from mice. The first experiment in mice was conducted with fewer retinas and a different promoter (human synapsin promoter) and didn’t yield nearly as many candidates. We are currently running a third experiment with 35 mouse retinas which will most likely detect more candidates as we have identified currently. We can update the proteome in this paper once the analysis is complete. It is not feasible to conduct these experiments with multiple replicates at the same time, since the number of animals that have to be used is simply too high, especially since very specific genotypes are required that are difficult obtain.

      (3) It would be interesting to determine whether there are differences in the presence of candidate proteins between AII-AII gap junctions and AII-cone bipolar cell gap junctions. Given that the subcellular localization of AII-AII gap junctions differs from that of AII-cone bipolar cell gap junctions (with most AII-AII gap junctions located below AII-cone ones), histological validations of the proteins shown in Figure 6 can be repeated for AII-AII gap junctions. This would help reveal similarities or differences in the protein compositions of these two types of gap junctions.

      Thank you for this suggestion. We had similar plans. However, we realized that homologous gap junctions are difficult to recognize with GFP. The dense GFP labeling in the proximal IPL, where AII-AII gap junctions are formed, does not allow us to clearly trace the location of individual dendrites from different cells. Detecting AII-AII gap junctions would require intracellular dye Injections of neighboring AII cells. Unfortunately, we don’t have a set up that would allow this. Bipolar cell terminals, on the contrary, are a lot easier to detect with markers such as SCGN, which is why we decided to focus on AII/ONCB gap junctions.

      (4) In Figures 1 and 2, it would be helpful to clarify in the figure legends whether the proteins in the interaction networks represent all detected proteins or only those selected based on log2 fold-change or other criteria.

      Thank you for this suggestion! We have added a description in lines 643 and 662.

      (5) In Figure 1A (bottom panel), please include a negative control for the Neutravidin staining result from the non-labeling group.

      We only tested the biotinylation for wild type retinas in cell lysates and western blots as shown in figure 1C, which shows an entirely different biotinylation pattern.

      (6) In Figure 2B, please include the results of Neutravidin staining for both the labeling and non-labeling groups.

      Same comment: We see the differences in the biotinylation pattern on western blots, which is distinct for Cx36-EGFP and wild type retinas, although both genotypes were injected with the same AAV construct and the same dose of biotin. We hope that this provides sufficient evidence for the specificity of our approach.

      (7) In Figure 5B, the sizes of multiple proteins detected by Western blotting are inconsistent and confusing. For example, the size of Cx36 in the "FLAG-SJ2BP" panel differs from that in the other three panels. Additionally, in the "Myc-SIPA1L3+" panel, the size of SIPA1l3 appears different between the input and IP conditions.

      Thank you for pointing this out! The differences in the molecular weight can be explained by dimerization. We have indicated the position of the dimer and the monomer bands with arrows. Especially, when larger amounts of Cx36 are coprecipitated Cx36 preferentially occurs as a dimer. This can also be seen in our previous publication:

      S. Tetenborg et al., Regulation of Cx36 trafficking through the early secretory pathway by COPII cargo receptors and Grasp55. Cellular and Molecular Life Sciences 81, 1-17 (2024). Figure 1D

      The band that occurs above 150kDa in the SIPA1L3 input is most likely a non-specific product. The specific band for SIPA1L3 can be seen in the IP sample, which has the appropriate molecular weight. We often see much better immuno reactivity for the protein of interest in IP samples, because the protein is concentrated in these experiments which facilitates its detection.

      (8) How specific are the antibodies used for validating the proteins in this study? Given that many proteins, such as EPS15l1, HIP1R, SNAP91, GPrin1, SJ2BP, Syt4, show broad distribution in the IPL (Figure 3B, 4A, 6D), it is important to validate the specificity of these antibodies. Additionally, including negative controls in the histological validation would strengthen the reliability of the results.

      We carefully selected the antibodies based on western blot data, that confirmed that each antibody detected an antigen of appropriate size. Moreover, the distribution of the proteins mentioned is consistent with function of each protein described in the literature. EPS15L1 and GPrin1 for instance are both membrane-associated, which is evident in Hek cells. Figure 5C.

      A true negative control would require KO tissue and we don’t think that this is feasible at this point.

      (9) In Figure 7F, the model could be improved by highlighting which components may be conserved between zebrafish and mice, as well as which components are conserved between the AII-AII junction and AII-cone bipolar cell junction?

      Thank you for this suggestion. However, we don’t think that this is necessary as our study primarily focuses on the AII amacrine cell.

      Currently we are unable to distinguish differences in the composition of AII-AII and AII-ONCB junctions as described above.

      (10) Are there any functional measurements that could support the conclusion that "loss of Cx36 resulted in a quantitative defect in the formation of electrical synapse density complex"?

      The loss of electrical synapse density proteins is shown by these immunostaining comparisons. Functional measurements necessarily depend on the function of the electrical synapse itself, which is gone in the case of the Cx36 KO. It is not clear that a different functional measurement can be devised.

      Reviewer #3 (Recommendations for the authors):

      (1) It would be very helpful if there were page and line numbers on the manuscript.

      Line and page numbers have been added.

      (2) Typos in the 3rd paragraph, the sentence 'which is triggered by the influx of Calcium though non-synaptic NMDA...'

      Should it read '... Calcium THROUGH non-synaptic NMDA'?

      We have corrected this typo.

      (3) Figure 1B: please add a description of the top panels, 'Cx36 S293'.

      A description of the top panels has been added to the figure legend in line. Line 639.

      (4) Figure 1C: what do the arrows indicate?

      We apologize for the confusion. The arrows in the western blot indicate the position of the Cx35-V5-TurboID construct, which can be detected with streptavidin-HRP and the V5 antibody. We have added a description for these arrows to the figure legend. See line 641.

      (5) Related to the point in the 'Weakness', there are some descriptions of how well some of the gap junction-associated proteins colocalize with Cx36 in immunostaining. For example, 'In comparison to the scaffold proteins, however, the colocalization of Cx36 with each of these endocytic components, was clearly less frequent and more heterogenous, which appears to reflect different stages in the life cycle of Cx36' and 'All of these proteins showed considerable colocalization with Cx36 in AII amacrine cell dendrites'. It would be nice to see quantification data to support these claims.

      Thank you for this suggestion. We have added a colocalization analysis to figure 3 (C & D). We quantified the colocalization for the endocytosis proteins Eps15l1 and Hip1r. This quantification included a flipped control to rule out random overlap. For both proteins we confirmed true colocalization (Figure 3D).

      (6) In Figure 5B, it would be helpful if there were arrows or some kind in western blottings to indicate which bands are supposed to be the targeted proteins.

      We have added arrows in IP samples to indicate bands representing the corresponding protein.

      (7) In the sentence including 'for the PBM of Cx36, as it is the case for ZO-1', what is PBM?

      The PBM means PDZ binding motif. We have added an explanation for this abbreviation in line 244.

      (8) Please add a description of the Cx35b promoter construct in the Method section.

      The Cx35b Promoter is a 6.5kb fragment. We will make the clone available via Addgene to ensure that all details of the clone can be accessed via snapgene or alternative software.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Formins are complex proteins with multiple effects on actin filament assembly, including nucleation, capping with processive elongation, and bundling. Determining which of these activities is important for a given biological process and normal cellular function is a major challenge.

      Here, the authors study the formin FHOD3L, which is essential for normal sarcomere assembly in muscle cells. They identify point mutants of FHOD3L in which formin nucleation and elongation/bundling activities are functionally separated. Expression of these mutants in neonatal rat ventricular myocytes shows that the control of actin filament elongation by formin is the major activity required for the normal assembly of functional sarcomeres.

      Strengths:

      The strength of this work is to combine sensitive biochemical assays with excellent work in neonatal rat ventricular myocytes. This combination of approaches is highly effective for analyzing the function of proteins with multiple activities in vitro.

      Weaknesses:

      FHOD3L does not seem to be the easiest formin to study because of its relatively weak nucleation activity and the short duration of capping events. This difficulty imposes rigorous biochemical analysis and careful interpretation of the data, which should be improved in this work.

      We thank the reviewer for their praise and appreciation of our work. Indeed, FHOD3L is a challenging formin to work with.

      Important points are raised here and below regarding the brief elongation events we reported. As suggested, we performed more rigorous analysis of the data and present it in the revised manuscript. We now report that from 45 dim regions analyzed, in three independent experiments with wild type FHOD3L, we detected 40 bursts. (The remaining five could be formin falling off too quickly to detect or the dim spots could be regions of inhomogeneity in intensity, not due to formin.) For comparison to the presented data with FHOD3L-CT, we analyzed the filaments in TIRF assays with no formin present. As the reviewers point out, inhomogeneities in filament intensity are normal. Thus, we examined any dim spots for pauses and/or bursts. As is now reported in Figure 2G,H, the velocity of growth of these dim spots is indistinguishable from the velocity of the rest of the filament. We acknowledge that our numbers may not be perfectly accurate, due to the noise in our system, we believe that the difference of 3-4 fold increase versus no change in rate is substantial and convincing.

      We also determined the number of dim spots per length of filament. We found a higher frequency when FHOD3L-CT or FHOD3S-CT was present vs no formin, as now shown in Figure 2 – supplements 1G and 2E.

      We were asked about the pauses we observe before bursts of elongation and how we know they are functionally relevant. The short answer is that we do not know. We reported them because they were so common: Of the 40 bursts, pauses preceded the burst in 38 cases. We cannot rule out that this pause reflects an interaction with the surface but might expect the frequency to be lower if it were. We revise the text to make our conclusions about pauses more circumspect.

      We are convinced that the brief dim events we observed in the presence of FHOD3L-CT, in fact, reflect formin-mediated elongation and worked hard to improve their presentation, in addition to the added analysis. We include new kymographs, including examples from FHOD3L, FHOD3S, K1193L, and actin alone. We hope that the reviewers are also convinced.

      This does not preclude our interest in the microfluidics and two-color assays, which will be pursued in the future. We have reached out to a colleague who is set up to repeat these measurements with microfluidics-assisted TIRF. The noise should be greatly reduced and the system is also optimal for directly visualizing labeled FHOD3, as suggested. We expect these experimental approaches will provide additional insights.

      Reviewer #2 (Public review):

      This article elucidates the biochemical and cellular mechanisms by which the FHOD-family of formins, particularly FHOD3, contributes to sarcomere formation and contractility in cardiomyocytes. Formins are mainly known to nucleate and elongate actin filaments, with certain family members also exhibiting capping, severing, and bundling activities. Although FHOD3 has been well-established as essential for sarcomere assembly in cardiomyocytes, its precise biochemical functions and contributions to actin dynamics remain poorly understood.

      In this study, the authors combine in vitro biochemical assays with cellular experiments to dissect FHOD3's roles in actin assembly and sarcomere formation. They demonstrate that FHOD3 nucleates actin filaments and acts as a transient elongator, pausing elongation after an initial burst of filament growth. Using separation-of-function mutants, they show thatFHOD3's elongation activity - rather than its nucleation, capping, or bundling capabilities - is key for its sarcomeric function.

      The experiments have been conducted rigorously and well-analyzed, and the paper is clearly written. The data presented support the authors' conclusions. I appreciate the detailed description and rationale behind the FHOD3 constructs used in this study.

      We are happy to hear others find paper to be clearly written and well described.

      However, I was somewhat surprised and a bit disappointed that while the authors conducted single-color TIRF experiments to observe the effects of FHOD3 on single filaments, they did not use fluorescently labeled FHOD3 to directly visualize its behavior. Incorporating such experiments would significantly strengthen their conclusions regarding FHOD3's bursts of elongation interspersed with capping activity. While I understand this might require a few additional weeks of experiments, these data would add considerable value by directly testing the proposed mechanism.

      We appreciate the suggestion and hope to incorporate a two-color approach soon. As noted, FHOD3L is not always easy to work with and we do not have a functional labeled copy of the protein at this time.

      There is a typo in the word "required" in line number 30. The authors also use fit data to extract parameters in several panels (e.g., Figures 2b, 2d, 3a, and 3b). While these fit functions may be intuitive to actin experts, explicitly describing the fit functions in the figure legends or methods would greatly benefit the broader readership.

      Thank you for these comments. We updated the indicated figures and described the analysis in greater detail.

      Reviewer #3 (Public review):

      Valencia et al. aim to elucidate the biochemical and cellular mechanisms through which the human formin FHOD3 drives sarcomere assembly in cardiomyocytes. To do so, they combined rigorous in vitro biochemical assays with comprehensive in vivo characterizations, evaluating two wild-type FHOD3 isoforms and two function-separating mutants. Surprisingly, they found that both wild-type FHOD3 isoforms can nucleate new actin filaments, as well as elongate existing actin filaments in conjunction with profilin following barbed-end capping. This is in addition to FHOD3's proposed role as an actin bundler. Next, the authors asked whether FHOD3L promotes sarcomere assembly in cardiomyocytes through its activity in actin nucleation or rather elongation. With two function-separating mutants, the authors evaluated the numbers and morphology of sarcomeres, as well as their ability to beat and generate cardiac rhythm. The authors found that while the wild-type FHOD3L and the K1193L mutant can rescue sarcomere morphology and physiology, the GS-FH1 mutant fails to do so. Given that in GS-FH1 mainly elongation activity is compromised, the authors concluded that the elongation activity of FHOD3 is essential for its role in sarcomere assembly in cardiomyocytes, while its nucleator activity is dispensable. Overall, this important study provided a broadened view on the biochemical activities of FHOD3, and a pioneering view on a possible cellular mechanism of how FHOD3L drives sarcomere assembly. If further validated, this can lead to new mechanistic models of sarcomere assembly and potentially new therapeutic targets of cardiomyopathy.

      The conclusions of this paper are mostly well supported by the comprehensive biochemical analyses performed by the authors. However, the sarcomere assembly defect phenotype in the GS-FH1 rescue condition requires further investigation, as the extremely low level of GS-FH1 signal in transfected cells in Figure 6A may reflect a failure of actin-binding by this construct in vivo, rather than its inability to drive elongation. Though the authors do show in Figure 6 that GS-FH1 can bind to normal-looking sarcomeres when they are present, this may be due to a lack of siRNA activity in these cells, such that endogenous FHOD3L is still present. In this possible scenario, GS-FH1 may dimerize with endogenous FHOD3L. The authors should demonstrate that GS-FH1 alone can indeed interact with existing actin filaments in vivo. While this has been clearly demonstrated in vitro, given the more complex biochemical environment in vivo where additional unknown binding partners may present, cautions should be made when extrapolating findings from the former to the latter.

      The reviewer is concerned about the low protein levels in the GS-FH1 rescue experiments as reflected in the HA fluorescence intensity distributions shown in Fig. 5 Supplement 2A. While the scenario proposed could explain our observations with the GSFH1 rescues it is quite complex. Nor does the scenario preclude the conclusion that the FH1 domain is critical. We agree that the observed sarcomeres are likely to be residual in cells with incomplete RNAi. We now include the image of a cell that is still full of sarcomeres and note that the GH-FH1 is expressed at a relatively high level and striated throughout the cell. We interpret this as evidence that GS-FH1 is stable when suitable binding sites are available. We cannot exclude that there is more GS-FH1 because there was more endogenous FHOD3L with which to heterodimerize. If the GS-FH1 heterodimer were simply poisoning the wild type protein, we do not expect that it would be bound correctly to sarcomeres. If, instead, heterodimers have some activity, it seems far from sufficient to rescue sarcomere formation, suggesting that two functional FH1 domains are critical.

      Furthermore, we do not see evidence of correlation between protein levels and rescue at the level present in these cells (addressed below). Unfortunately, the proposed IP to test whether FHOD3L binds actin in vivo would only potentially report on filament side binding (both direct and indirect). It would not address whether the GS-FH1 mutant functions as a nucleator, elongator, bundler and/or capping protein in vivo.

      The critical question that we can address is whether the phenotype is due to low protein levels, assuming the protein present is functional, or due to loss of elongation activity by FHOD3L. To address this question, we returned to our data.

      First, we plotted the distributions of the intensities of the cells we analyzed further, in addition to the automated readout of all of the cells in the dish (Fig. 4 supplement 1). These cells were selected randomly and, as should be the case, the distributions of their intensities agree well with the original distributions for the three different rescue constructs: FHOD3L, K1193L, and GS-FH1 (Fig. 6 supplement 1). We then asked whether there was any correlation in HA intensities with the sarcomere metrics. As seen in our pilot data, no correlation is evident in any of the three cases across the range of intensities we collected (400 – 2700 a.u.) (old Fig. 6 supplement C,D,E). We now replace the data from pilot experiments with analysis of HA intensities and sarcomere metrics from the data sets included in the paper (new Fig 6. Supplement 1). Again, little to no correlation was observed (the single highest r-squared value is 0.2 and the remaining eight values are less than or equal to 0.08).

      To more specifically address the question of whether low HA fluorescence intensity is likely to reflect sufficient protein levels to build sarcomeres we re-examined two data sets from the FHOD3L WT rescue data. We found that, by chance, the first replicate of data from the wild type rescue has a comparable intensity distribution to that of the GSFH1 rescues (580 +/- 261 / cell vs. 548 +/- 105 / cell). In addition, we collected all of the data from cells with intensity levels <720, designed to mimic the distribution of the GS-FH1 cells (Fig. 6 supplement 3). We then compared the sarcomere metrics (sarcomere number, sarcomere length, sarcomere width) between the full data set and the two low intensity subsets:

      • Sarcomere number is the only non-normal metric. We therefore used the Mann Whitney U test, which shows no difference between all 3 WT distributions.

      • We compared Z-line lengths by one-way ANOVA and Tukey's post hoc tests, again finding no significant difference for all distributions.

      • Sarcomere length shows a weakly significant difference (p=0.038) between the whole WT data set and bio rep 1, but no difference between the whole WT data set and the HA<720 group.

      Thus, cells expressing wild type FHOD3L at levels comparable to levels detected in GS-FH1 mutant rescues, are fully rescued. Based on these findings we conclude that the expression levels in the GS-FH1 are high enough to rescue the FHOD3 knock down, supporting our conclusion that the defect is due to loss of elongation activity. We have added this analysis and discussion to the revised manuscript.

      Recommendations for the authors:

      Reviewing Editor Comments:

      You will see that the 3 reviewers are very positive about your work and appreciate the elegant combination of biochemical assays and functional tests in cardiomyocytes. We've had a long discussion with them and we all agree that two experiments deserve further effort to make the conclusions of your paper more convincing.

      Thank you.

      The first experiment is the TIRF elongation assay, where the two biochemist Reviewers remain doubtful that these short events are really due to the presence of a formin at the end of the filament. One of them suggests that two-color imaging with a labeled formin should clearly prove this point.

      We agree that the elongation assays can be improved. Given the similarity of processivity of Fhod3L, Fhod3S and Drosophila FhodA (measured by a distinct method), we are inclined to believe them. However, the reviewer raises an excellent point about the accuracy of the measurements given the resolution (and noise) of the data. We are interested in the two-color imaging assay but do not believe it will necessarily simplify the analysis. We suspect that Fhod spends more time at/near the barbed end than is apparent based on elongation rates. The fact that we see repeated events on individual filaments at such low concentrations of FHOD3L (0.1 nM) supports this idea. Otherwise, the likelihood of FHOD3L finding barbed ends so often is really quite low.

      We will return to these experiments, using alternate methods, curious to see what else we learn. In the meantime, we conducted more thorough analysis, including controls, and improved visualization of example traces. Data for elongation analysis and kymographs were acquired with Jfilament. We stretched the x-axis (time) in kymographs for FHOD3L-CT (Fig. 2F), FHOD3S-CT (Fig. 2, supplement 2C), FHOD3L-CT K1193L (Fig. 3, supplement 1A), and actin alone (Fig 2G), and highlighted regions of analysis. The slopes for these regions, separated based on intensity, were fit to the data in KaleidaGraph. The fits are offset from the data such that they do not obscure the filaments and corresponding rates are given. The fact that we never see fast dim regions when FHOD3 is not present, as shown in Fig. 2H and that the frequency of dim events is markedly increased (Fig. 2-supplements 1G and 2E) give us confidence that the events are real. We acknowledge in the text that the precise values of the short events may be inaccurate due to the resolution of our experiments. We hope the reviewers are convinced by the improved analysis.

      The second experiment is the sarcomere assembly defect phenotype in the GS-FH1 rescue condition. This requires further investigation, as the extremely low level of GS-FH1 signal in transfected cells in Figure 6A may reflect a failure of actin-binding/nucleation in vivo, rather than its inability to elongate F-actin. Although you show that GS-FH1 can bind to sarcomeres when they are present, this may be due to a lack of siRNA activity in these cells, such that endogenous FHOD3L is still present. In this possible scenario, GS-FH1 could dimerize with endogenous FHOD3L.

      We agree that the sarcomeres we see are likely to be residual and could reflect some remaining endogenous FHOD3. The reviewers are concerned about the low protein levels in the GSFH1 rescues. First, we do not agree that the levels are “extremely” low. Through careful analysis, we established that 3xHA-FHOD3L intensities between 300 and 3000 a.u./um<sup>2</sup> were sufficient for full rescue. The mean for the GSFH1 experiments is 533 +/- 93, which is well within this range. Furthermore, we did not observe correlation between sarcomere number, length, or width and HA intensity over the full range collected for wild type FHOD3L or within the GS-FH1 data. We previously showed pilot data but now show correlation analysis for every analyzed cell (Fig. 4 – figure supplement 1 D-F). We conducted this analysis on all of the mutant rescue experiments (Fig. 6-supplement 1). Finally, we identified two subpopulations of the wildtype rescue data. One is all of the cells with HA intensity < 720, which gives a distribution of mean 545 +/- 85. The second set is the first biological replicate of wild type rescue, which has a distribution of mean 560 +/- 160. Again correlation shows little relationship between HA levels and sarcomere metrics. Nevertheless, we show intensity level matched images in Fig 6, as opposed to images reflecting average intensities.

      The critical question remains whether the phenotype is due to low protein levels or due to loss of elongation by FHOD3L. Notably, we now show a cell that is full of sarcomeres and has relatively high FHOD3L levels as well, consistent with available binding sites stabilizing mutant protein but not ruling out heterodimerization (Fig. 6 – figure supplement 2C). Others have expressed mutant FHOD3L in a wild type background in mice. They observed poisoning, consistent with heterodimerization. Thus, it is possible that, as suggested, the FHOD3L-GSFH1 detected in sarcomeres is in fact heterodimerized with residual endogenous FHOD3L. In this case, we would still conclude that the protein is not functional enough to rescue, supporting a role for the FH1 domain.

      In the future, we plan to perform experiments with compromised, but not inactive, FH1 domains, as we discuss in the paper.

      We hope that you will find these comments useful.

      Yes, the comments were thoughtful and helped us write a better paper. Thank you.

      Reviewer #1 (Recommendations for the authors):

      Some experiments should be described and analyzed more carefully. This lack of clarity calls into question the interpretation of some experiments. Overall, this study is not yet as convincing as it should be.

      Main recommendations:

      (1) Formin elongation phases in the TIRF experiment are not convincing. They are rare and it is difficult to see any significant difference between the control movie without FHOD3L-CT and the movie with FHOD3L-CT. Filaments assembled in the absence of FHOD3L-CT also show some fluorescence inhomogeneity (which is normal), and measurements of formin elongation rates and capping times are not convincing (for example, the kymograph of the control profilin-actin situation in Figure 2F also shows a fast elongation phase on the right).

      Please see response above. We conducted more thorough analysis and created improved visualizations. We hope the data are more convincing now.

      It is also difficult to understand how an accurate measurement can be made from these noisy kymographs, and the method section should explain that precisely.

      This is a valid point. We added details of analysis to the methods section and we discuss the fact that the measurements are at the limit of our resolution in the paper. We rely on the large (~3-fold) difference in elongation, more than specific elongation rates for our interpretation.

      One of the problems is that these events are too transient to quantify well with noisy data. I noticed that the formin concentration used in these movies is quite low (0.1 nM FHOD3L-CT). Is there a reason for this? Is it possible to increase the formin concentration to increase the number of formin capping/elongation events and provide more convincing movies?

      We acknowledge that the data are noisy. We felt that it was necessary to perform experiments with filaments only tethered at one end, leaving the growing end free. We did so, in part, because when we did experiments with biotinylated actin to anchor the filaments down, we observed pauses in the absence of formin. Ultimately, we compromised, using anchored seeds and a relatively low concentration of NEM-myosin to decrease motion of the actin filaments.

      The experiments were performed with such low FHOD3L-CT because it was a potent nucleator in TIRF assays, making data analysis nearly impossible with more formin present. FHOD3S-CT and FHOD3L-CT K1193L behaved somewhat differently between these experiments and we were able to perform them with 1 nM formin.

      Not seeing formin at the tip of the filaments is an additional difficulty because we do not know if these pauses occur because formin is stuck to the coverslips (which could very well happen with these sticky proteins) or freely bound at the end of a filament as the text suggests. Is there any argument in favor of one scenario over the other?

      This will be an important experiment. As described above, we suspect that Fhod spends more time at/near the barbed end than is apparent based on elongation data. The fact that we see repeated events on individual filaments at such low concentrations of FHOD3L (0.1 nM) supports this idea. Otherwise, the likelihood of FHOD3L finding barbed ends so often is really quite low. In order to address the question about the cause of pauses, we reviewed our data, finding that 38 of 40 bursts were preceded by pauses. We do, however, discuss that we cannot rule out non-specific interactions with the surface.

      (2) Pyrene elongation assays in the presence of profilin are actually more convincing to test the elongation ability of formins. However, such an assay is not presented for all mutants. It should be.

      While we agree to some extent with this comment, we did not include the pyrene data for all of the mutants because the shapes of the curves were even more complicated than those seen with wild type FHOD3L-CT rendering them uninterpretable.

      (3) Some experiments (e.g. in Figure 2E) are performed with yeast profilin, while others (e.g. in Figure 2F) are performed with human profilin. Obviously, both profilins could modulate formin activity differently and the side-by-side interpretation of both experiments is difficult. Could the authors stick to human profilin for all experiments?

      We used to always perform pyrene assays with yeast profilin because it was known to be insensitive to pyrene. These data were collected before we realized that the affinity of human profilin for actin is so high that we could probably do everything with this profilin. We have compared the two profilins for other formins, e.g. Delphilin, Capu, and did not observe detectable differences.

      Minor recommendations:

      (1) The pyrene assays with the light blue colored curve choice are not ideal. I have difficulties seeing some of the curves.

      Thank you. We added symbols to a subset of the traces to make them more visible.

      (2) In the same curves, I can't understand what the +3.75 and 0.078 numbers mean. Could these results be plotted in a clearer way?

      These values are the lowest concentrations in the range tests. They were matching light blue with black outline for visibility. We added symbols and changed the color of the numbering for improved visibility/understanding.

      (3) In Figure 2D, is the Kd of I1163A really determined only from 2 experimental data points?

      Of course not. We now show the figure with extended axes in Fig. 2 - figure supplement 1C.

      (4) In Figure 2C, the shape of the curves suggests that this is not a pure capping assay, but a mix of capping and nucleation. It's not dramatic but could lead to an under-estimation of the capping efficiency.

      We agree with the reviewer that the complicated shapes confound interpretation. Our analysis is based on the earliest slopes, in part, for this reason. We added discussion of this complication to the text.

      Reviewer #3 (Recommendations for the authors):

      Suggestions for additional experiments:

      (1) To evaluate whether GS-FH1 alone can indeed interact with existing actin filaments in vivo, the authors may consider performing immunoprecipitation assays with GS-FH1 extracted from rescued NRVMs.

      An IP of GS-FH1 from cells could show actin filament side binding but, unfortunately, will not provide any information about filament end binding, which is of much greater interest.

      It will be helpful to show phalloidin staining in GS-FH1 rescues in a similar manner as in Figure 6-supplement 1, panel B, and compare that with mock rescue in Figure 4 panel D. It will be essential to prove this prior to concluding that actin elongation activity is essential for sarcomere assembly.

      This is an excellent suggestion. We now include images of phalloidin stained cells from both K1193L and GS-FH1 rescues (Fig. 6A’ – supplement 2A,B). We were intrigued to see small actin punctae that were sometimes aligned. We speculate that these could be pre-premyofibrils and suggest that this is further evidence that the GS-FH1 protein is not completely unstable.

      (2) Prior to sarcomere assembly, a-actinin is known to form short bundles with actin filaments (I-Z-I complex) without clearly defined periodicity. This semi-ordered state then transforms into the more ordered sarcomeres with periodic spacing. It will be valuable to show the phalloidin staining in addition to the a-actinin IF consistently across all conditions. This may lead to further insights into the defects of sarcomere assembly. Along the same vein, higher magnification images showcasing several sarcomeres will help the readers evaluate these defects.

      We agree that there are additional valuable measurements to be made. In order to favor synchronized contraction, we plated the cells at too high a density to reliably identify IZI complexes. We have included some zoomed in images of the phalloidin staining.

      Recommendations for improving the writing:

      The authors mentioned the interaction between cardiac MyBP-C and FHOD3L as essential for the localization of FHOD3L to the C-line of the sarcomere. Can they discuss whether this interaction is important for the role of FHOD3L in sarcomere assembly? If so, how?

      This is a very interesting question that we cannot answer at this time.

      Minor corrections to the text and figures:

      In the legend of Figure 2-Figure Supplement 1, the labels of (F) and (E) are swapped.

      Thank you for catching this.

    1. Author response:

      eLife Assessment

      This useful study presents Altair-LSFM, a solid and well-documented implementation of a light-sheet fluorescence microscope (LSFM) designed for accessibility and cost reduction. While the approach offers strengths such as the use of custom-machined baseplates and detailed assembly instructions, its overall impact is limited by the lack of live-cell imaging capabilities and the absence of a clear, quantitative comparison to existing LSFM platforms. As such, although technically competent, the broader utility and uptake of this system by the community may be limited.

      We thank the reviewers and editors for their thoughtful evaluation of our work and for recognizing the technical strengths of the Altair-LSFM platform, including the custom-machined baseplates and detailed documentation provided to support accessibility and reproducibility. We respectfully disagree, however, with the assessment that the system lacks live-cell imaging capabilities. We are fully confident in the system’s suitability for live-cell applications and will demonstrate this by including representative live-cell imaging data in the revised manuscript, along with detailed instructions for implementing environment control. Moreover, we will expand our discussion to include a broader, more quantitative comparison to existing LSFM platforms—highlighting trade-offs in cost, performance, and accessibility—to better contextualize Altair’s utility and adaptability across diverse research settings.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The article presents the details of the high-resolution light-sheet microscopy system developed by the group. In addition to presenting the technical details of the system, its resolution has been characterized and its functionality demonstrated by visualizing subcellular structures in a biological sample.

      Strengths:

      (1) The article includes extensive supplementary material that complements the information in the main article.

      (2) However, in some sections, the information provided is somewhat superficial.

      Our goal was to make the supplemental content as comprehensive and useful as possible. In addition to the materials provided with the manuscript, our intention is for the online documentation (available at thedeanlab.github.io/altair) to serve as a living resource that evolves in response to user feedback. For this reason, we are especially interested in identifying and expanding any sections that are perceived as superficial, and we would greatly appreciate the reviewer’s guidance on which areas would benefit from further elaboration.

      Weaknesses:

      (1) Although a comparison is made with other light-sheet microscopy systems, the presented system does not represent a significant advance over existing systems. It uses high numerical aperture objectives and Gaussian beams, achieving resolution close to theoretical after deconvolution. The main advantage of the presented system is its ease of construction, thanks to the design of a perforated base plate.

      We appreciate the reviewer’s assessment and the opportunity to clarify our intent. Our primary goal was not to introduce new optical functionality beyond that of existing high-performance light-sheet systems, but rather to reduce the barrier to entry for non-specialist labs.

      (2) Using similar objectives (Nikon 25x and Thorlabs 20x), the results obtained are similar to those of the LLSM system (using a Gaussian beam without laser modulation). However, the article does not mention the difficulties of mounting the sample in the implemented configuration.

      We agree that there are practical challenges associated with handling 5 mm diameter coverslips. However, the Nikon 25x can readily be replaced by a Zeiss W Plan-Apochromat 20x/1.0 objective, which eliminates the need for the 5 mm coverslip[1]. In the revised manuscript, we will more explicitly detail the practical challenges in handling a 5 mm coverslip and mention the alternative detection objective.

      (3) The authors present a low-cost, open-source system. Although they provide open source code for the software (navigate), the use of proprietary electronics (ASI, NI, etc.) makes the system relatively expensive. Its low cost is not justified.

      We understand the reviewer’s concern regarding the use of proprietary control hardware such as the ASI Tiger Controller and NI data acquisition cards. While lower-cost alternatives for analog and digital control (e.g., microcontroller-based systems) do exist, our choice was intentional. By relying on a unified and professionally supported platform, we minimize the complexity of sourcing, configuring, and integrating components from disparate vendors—each of which would otherwise demand specialized technical expertise. Moreover, in future releases, we aim to further streamline the system by eliminating the need for the NI card, consolidating all optoelectronic control through the ASI Tiger Controller. This approach allows users to purchase a fully assembled and pre-configured system that can be operational with minimal effort.

      It is worth noting that the ASI components are not the primary cost driver. The full set—including XYZ and focusing stages, a filter wheel, a tube lens, the Tiger Controller, and basic optomechanical adapters—costs approximately $27,000, or ~18% of the total system cost. Additional cost reductions are possible. For example, replacing the motorized sample positioning and focusing stages with manual alternatives could reduce the cost by ~$12,000. However, this would eliminate key functionality such as autofocusing, 3D tiling, and multi-position acquisition. Open-source mechanical platforms such as OpenFlexure could in principle be adapted, but they would require custom assembly and would need to be integrated into our control software. Similarly, the filter wheel could be omitted in favor of a multi-band emission filter, reducing the cost by ~$5,000. However, this comes at the expense of increased spectral crosstalk, often necessitating spectral unmixing. An industrial CMOS camera—such as the Ximea MU196CR-ON, recently demonstrated in a Direct View Oblique Plane Microscopy configuration[2]—could substitute for the sCMOS cameras typically used in high-end imaging. However, these industrial sensors often exhibit higher noise floors and lower dynamic range, limiting sensitivity for low-signal imaging applications.

      While a $150,000 system represents a significant investment, we consider it relatively cost-effective in the context of advanced light-sheet microscopy. For comparison, commercially available systems with similar optical performance—such as LLSM systems from 3i or Zeiss—are several-fold more expensive.

      (4) The fibroblast images provided are of exceptional quality. However, these are fixed samples. The system lacks the necessary elements for monitoring cells in vivo, such as temperature or pH control.

      We thank the reviewer for their positive comment regarding the quality of our fibroblast images. As noted, the current manuscript focuses on the optical design and performance characterization of the system, using fixed specimens to validate resolution and imaging stability. We acknowledge the importance of environmental control for live-cell imaging. Temperature regulation is routinely implemented in our lab using flexible adhesive heating elements paired with a power supply and PID controller. For pH stabilization in systems that lack a 5% CO<sub>2</sub> atmosphere, we typically supplement the imaging medium with 10–25 mM HEPES buffer. In the revised manuscript, we will introduce a modified sample chamber capable of maintaining user-specified temperatures, along with detailed assembly instructions. We will also include representative live-cell imaging data to demonstrate the feasibility of in vitro imaging using this system.

      Reviewer #2 (Public review):

      Summary:

      The authors present Altair-LSFM (Light Sheet Fluorescence Microscope), a high-resolution, open-source microscope, that is relatively easy to align and construct and achieves sub-cellular resolution. The authors developed this microscope to fill a perceived need that current open-source systems are primarily designed for large specimens and lack sub-cellular resolution or are difficult to construct and align, and are not stable. While commercial alternatives exist that offer sub-cellular resolution, they are expensive. The authors' manuscript centers around comparisons to the highly successful lattice light-sheet microscope, including the choice of detection and excitation objectives. The authors thus claim that there remains a critical need for high-resolution, economical, and easy-to-implement LSFM systems.

      Strengths:

      The authors succeed in their goals of implementing a relatively low-cost (~ USD 150K) open-source microscope that is easy to align. The ease of alignment rests on using custom-designed baseplates with dowel pins for precise positioning of optics based on computer analysis of opto-mechanical tolerances, as well as the optical path design. They simplify the excitation optics over Lattice light-sheet microscopes by using a Gaussian beam for illumination while maintaining lateral and axial resolutions of 235 and 350 nm across a 260-um field of view after deconvolution. In doing so they rest on foundational principles of optical microscopy that what matters for lateral resolution is the numerical aperture of the detection objective and proper sampling of the image field on to the detection, and the axial resolution depends on the thickness of the light-sheet when it is thinner than the depth of field of the detection objective. This concept has unfortunately not been completely clear to users of high-resolution light-sheet microscopes and is thus a valuable demonstration. The microscope is controlled by an open-source software, Navigate, developed by the authors, and it is thus foreseeable that different versions of this system could be implemented depending on experimental needs while maintaining easy alignment and low cost. They demonstrate system performance successfully by characterizing their sheet, point-spread function, and visualization of sub-cellular structures in mammalian cells, including microtubules, actin filaments, nuclei, and the Golgi apparatus.

      We thank the reviewer for their thoughtful summary of our work. We are pleased that the foundational optical principles, design rationale, and emphasis on accessibility came through clearly. We agree that the approach used to construct the microscope is highly modular, and we anticipate that these design principles will serve as the basis for additional system variants tailored to specific biological samples and experimental contexts. To support this, we provide all Zemax simulations and CAD files openly on our GitHub repository, enabling advanced users to build upon our design and create new functional variants of the Altair system.

      Weaknesses:

      There is a fixation on comparison to the first-generation lattice light-sheet microscope, which has evolved significantly since then:

      (1) The authors claim that commercial lattice light-sheet microscopes (LLSM) are "complex, expensive, and alignment intensive", I believe this sentence applies to the open-source version of LLSM, which was made available for wide dissemination. Since then, a commercial solution has been provided by 3i, which is now being used in multiple cores and labs but does require routine alignments. However, Zeiss has also released a commercial turn-key system, which, while expensive, is stable, and the complexity does not interfere with the experience of the user. Though in general, statements on ease of use and stability might be considered anecdotal and may not belong in a scientific article, unreferenced or without data.

      The referee is correct that our comparisons reference the original LLSM design, which was simultaneously disseminated as an open-source platform and commercialized by 3i. While we acknowledge that newer variants of LLSM have been developed—including systems incorporating adaptive optics[3] and the MOSAIC platform (which remains unpublished)—the original implementation remains the most widely described and cited in the literature. It is therefore the most appropriate point of comparison for contextualizing Altair’s performance, complexity, and accessibility. Importantly, this version of LLSM is far from obsolete; it continues to be one of the most commonly used imaging systems at Janelia Research Campus’s Advanced Imaging Center.

      We acknowledge that more recent commercial implementation by Zeiss has addressed several of the practical limitations associated with the original design. In particular, we agree that the Zeiss Lattice Lightsheet 7 system, which integrates a meniscus lens to facilitate oblique imaging through a coverslip, offers a user-friendly experience—albeit with a modest tradeoff in resolution (reported deskewed resolution: 330 nm × 330 nm × 500–1000 nm).

      While we recognize that statements on usability and stability can be subjective, one objective proxy for system complexity is the number of optical elements that require precise alignment during assembly. The original LLSM setup includes approximately 29 optical components that must each be carefully positioned laterally, angularly, and coaxially along the optical path. In contrast, the first-generation Altair system contains only 9 such elements. By this metric, Altair is considerably simpler to assemble and align, supporting our overarching goal of making high-resolution light-sheet imaging more accessible to non-specialist laboratories. In the revised manuscript, we will clarify the scope of our comparison and provide more precise language about what we mean by complexity (e.g., number of optical elements needed to align).

      (2) One of the major limitations of the first generation LLSM was the use of a 5 mm coverslip, which was a hinderance for many users. However, the Zeiss system elegantly solves this problem, and so does Oblique Plane Microscopy (OPM), while the Altair-LSFM retains this feature, which may dissuade widespread adoption. This limitation and how it may be overcome in future iterations is not discussed.

      We agree that the use of 5 mm diameter coverslips, while enabling high-NA imaging in the current Altair-LSFM configuration, may serve as an inconvenience for many users. We will discuss this more explicitly in the revised manuscript. Specifically, we note that changing the detection objective is sufficient to eliminate the need for a 5 mm coverslip. For example, as demonstrated in Moore et al., Lab Chip 2021, pairing the Zeiss W Plan-Apochromat 20x/1.0 objective with the Thorlabs TL20X-MPL allows imaging beyond the physical surfaces of both objectives, removing the constraint imposed by small-format coverslips[1]. In the revised manuscript, we will propose this modification as a straightforward path for increasing compatibility with more conventional sample mounting formats.

      (3) Further, on the point of sample flexibility, all generations of the LLSM, and by the nature of its design, the OPM, can accommodate live-cell imaging with temperature, gas, and humidity control. It is unclear how this would be implemented with the current sample chamber. This limitation would severely limit use cases for cell biologists, for which this microscope is designed. There is no discussion on this limitation or how it may be overcome in future iterations.

      We appreciate the reviewer’s emphasis on the importance of environmental control for live-cell imaging applications. It is worth noting that the original LLSM design, including the system commercialized by 3i, provided temperature control only, without integrated gas or humidity regulation. Despite this, it has been successfully used by a wide range of scientists to generate important biological insights.

      We agree that both OPM and the Zeiss implementation of LLSM offer clear advantages in terms of environmental control, as we previously discussed in detail in Sapoznik et al., eLife, 2020[4]. However, assembly of high numerical aperture OPM systems is highly technical, and no open-source variant of OPM delivers sub-cellular scale resolution yet.

      (4) The authors' comparison to LLSM is constrained to the "square" lattice, which, as they point out, is the most used optical lattice (though this also might be considered anecdotal). The LLSM original design, however, goes far beyond the square lattice, including hexagonal lattices, the ability to do structured illumination, and greater flexibility in general in terms of light-sheet tuning for different experimental needs, as well as not being limited to just sample scanning. Thus, the Alstair-LSFM cannot compare to the original LLSM in terms of versatility, even if comparisons to the resolution provided by the square lattice are fair.

      We thank the reviewer for this comment. It is true that our discussion focused primarily on the square lattice implementation of LLSM. While this could be viewed as a subset of the system’s broader capabilities, we chose this focus intentionally, as the square lattice remains by far the most commonly used variant in practice. Even in the original LLSM publication, 16 out of 20 figure subpanels utilized the square lattice, with only one panel each representing the hexagonal lattice in SIM mode, a standard Bessel beam in incoherent SIM mode, a hex lattice in dithered mode, and a single Bessel in dithered mode. This usage pattern largely reflects the operational simplicity of the square lattice: it minimizes sidelobe growth and enables more straightforward alignment and data processing compared to hexagonal or structured illumination modes.

      In 2019, we performed an exhaustive accounting of published illumination modes in LLSM and found that the SIM mode had only been used in two additional peer-reviewed publications at that time. We will consider updating this table in the revised manuscript and will expand our discussion to acknowledge the broader flexibility of the LLSM platform—including its capacity for structured illumination and alternative light-sheet geometries. However, we will also emphasize that, despite these advanced capabilities, the square lattice remains the dominant mode used by the community and therefore serves as a fair and practical benchmark for comparison.

      (5) There is no demonstration of the system's live-imaging capabilities or temporal resolution, which is the main advantage of existing light-sheet systems.

      In the revised manuscript, we will include a demonstration of live-cell imaging to directly validate the system’s suitability for dynamic biological applications. We will also characterize the temporal resolution of the system. As a sample-scanning microscope, the imaging speed is primarily limited by the performance of the Z-piezo stage. For simplicity and reduced optoelectronic complexity, we currently power the piezo through the ASI Tiger Controller. We will expand the supplementary material to describe the design criteria behind this choice, including potential trade-offs, and provide data quantifying the achievable volume rates under typical operating conditions.

      While the microscope is well designed and completely open source, it will require experience with optics, electronics, and microscopy to implement and align properly. Experience with custom machining or soliciting a machine shop is also necessary. Thus, in my opinion, it is unlikely to be implemented by a lab that has zero prior experience with custom optics or can hire someone who does. Altair-LSFM may not be as easily adaptable or implementable as the authors describe or perceive in any lab that is interested, even if they can afford it. The authors indicate they will offer "workshops," but this does not necessarily remove the barrier to entry or lower it, perhaps as significantly as the authors describe.

      We appreciate the reviewer’s perspective and agree that building any high-performance custom microscope—Altair-LSFM included—requires a baseline familiarity with optics and instrumentation. Our goal is not to eliminate this requirement entirely, but to significantly reduce the technical and logistical barriers that typically accompany custom light-sheet microscope construction.

      Importantly, no machining experience or in-house fabrication capabilities are required—users can simply submit provided design files and specifications directly to the vendor. We will make this process as straightforward as possible by supplying detailed instructions, recommended materials, and vendor-ready files. Additionally, we draw encouragement from the success of related efforts such as mesoSPIM, which has seen over 30 successful implementations worldwide using a similar model of exhaustive online documentation, open-source control software, and community support through user meetings and workshops.

      We recognize that documentation alone is not always sufficient, and we are committed to further lowering barriers to adoption. To this end, we are actively working with commercial vendors to streamline procurement and reduce the logistical burden on end users. Additionally, Altair-LSFM is supported by a Biomedical Technology Development and Dissemination (BTDD) grant, which provides dedicated resources for hosting workshops, offering real-time community support, and generating supplementary materials such as narrated video tutorials. We will expand our discussion in the revised manuscript to better acknowledge these implementation challenges and outline our ongoing strategies for supporting a broad and diverse user base.

      There is a claim that this design is easily adaptable. However, the requirement of custom-machined baseplates and in silico optimization of the optical path basically means that each new instrument is a new design, even if the Navigate software can be used. It is unclear how Altair-LSFM demonstrates a modular design that reduces times from conception to optimization compared to previous implementations.

      We appreciate the reviewer’s comment and agree that our language regarding adaptability may have been too strong. It was not our intention to suggest that the system can be easily modified without prior experience. Meaningful adaptations of the optical or mechanical design would require users to have expertise in optical layout, optomechanical design, and alignment.

      That said, for labs with sufficient expertise, we aim to facilitate such modifications by providing comprehensive resources—including detailed Zemax simulations, CAD models, and alignment documentation. These materials are intended to reduce the development burden for those seeking to customize the platform for specific experimental needs.

      In the revised manuscript, we will clarify this point and explicitly state in the discussion what technical expertise is required to modify the system. We will also revise our language around adaptability to better reflect the intended audience and realistic scope of customization.

      Reviewer #3 (Public review):

      Summary:

      This manuscript introduces a high-resolution, open-source light-sheet fluorescence microscope optimized for sub-cellular imaging.

      The system is designed for ease of assembly and use, incorporating a custom-machined baseplate and in silico optimized optical paths to ensure robust alignment and performance. The authors demonstrate lateral and axial resolutions of ~235 nm and ~350 nm after deconvolution, enabling imaging of sub-diffraction structures in mammalian cells.

      The important feature of the microscope is the clever and elegant adaptation of simple gaussian beams, smart beam shaping, galvo pivoting and high NA objectives to ensure a uniform thin light-sheet of around 400 nm in thickness, over a 266 micron wide Field of view, pushing the axial resolution of the system beyond the regular diffraction limited-based tradeoffs of light-sheet fluorescence microscopy.

      Compelling validation using fluorescent beads and multicolor cellular imaging highlights the system's performance and accessibility. Moreover, a very extensive and comprehensive manual of operation is provided in the form of supplementary materials. This provides a DIY blueprint for researchers who want to implement such a system.

      Strengths:

      (1) Strong and accessible technical innovation: With an elegant combination of beam shaping and optical modelling, the authors provide a high-resolution light-sheet system that overcomes the classical light-sheet tradeoff limit of a thin light-sheet and a small field of view. In addition, the integration of in silico modelling with a custom-machined baseplate is very practical and allows for ease of alignment procedures. Combining these features with the solid and super-extensive guide provided in the supplementary information, this provides a protocol for replicating the microscope in any other lab.

      (2) Impeccable optical performance and ease of mounting of samples: The system takes advantage of the same sample-holding method seen already in other implementations, but reduces the optical complexity. At the same time, the authors claim to achieve similar lateral and axial resolution to Lattice-light-sheet microscopy (although without a direct comparison (see below in the "weaknesses" section). The optical characterization of the system is comprehensive and well-detailed. Additionally, the authors validate the system imaging sub-cellular structures in mammalian cells.

      (3) Transparency and comprehensiveness of documentation and resources: A very detailed protocol provides detailed documentation about the setup, the optical modeling, and the total cost.

      Weaknesses:

      (1) Limited quantitative comparisons: Although some qualitative comparison with previously published systems (diSPIM, lattice light-sheet) is provided throughout the manuscript, some side-by-side comparison would be of great benefit for the manuscript, even in the form of a theoretical simulation. While having a direct imaging comparison would be ideal, it's understandable that this goes beyond the interest of the paper; however, a table referencing image quality parameters (taken from the literature), such as signal-to-noise ratio, light-sheet thickness, and resolutions, would really enhance the features of the setup presented. Moreover, based also on the necessity for optical simplification, an additional comment on the importance/difference of dual objective/single objective light-sheet systems could really benefit the discussion.

      In the revised manuscript, we will expand our discussion to include a broader range of light-sheet microscope designs and imaging modes, including both single- and dual-objective configurations. We agree that highlighting the trade-offs between these approaches—such as working distance, sample geometry constraints, and alignment complexity—will enhance the overall context and utility of the manuscript.

      To further aid comparison, we will include a summary table referencing key image quality parameters such as lateral and axial resolution, and illumination beam NA for Altair-LSFM. Where available, we will reference values from published work—such as the axial resolution reported in Valm et al. (Nature, 2017)—to provide a clearer benchmark. Because such comparisons can be technically nuanced, especially when comparing across systems with different geometries and sample mounting constraints, we will also include a supplementary note outlining the assumptions and limitations of these comparisons.

      (2) Limitation to a fixed sample: In the manuscript, there is no mention of incubation temperature, CO₂ regulation, Humidity control, or possible integration of commercial environmental control systems. This is a major limitation for an imaging technique that owes its popularity to fast, volumetric, live-cell imaging of biological samples.

      We thank the reviewer for highlighting this important consideration. In the revised manuscript, we will provide a detailed description of how temperature control can be implemented using flexible adhesive heating elements, a power supply, and a PID controller. Step-by-step assembly instructions and recommended components will be included to facilitate adoption by users interested in live-cell imaging. We also note that most light-sheet microscopy systems capable of sub-cellular resolution—including the original LLSM design, diSPIM, and ASLM—typically do not incorporate integrated CO<sub>2</sub> or humidity control. These systems often rely on HEPES-buffered media to maintain pH stability, which is generally sufficient for short- to intermediate-term imaging. While full environmental control may be necessary for extended time-lapse studies, it is not a prerequisite for high-resolution volumetric imaging in many applications. Nonetheless, we will include a discussion of the challenges associated with adding CO<sub>2</sub> and humidity control to open or semi-enclosed architectures like Altair-LSFM, and outline potential future paths for integration with commercial incubation systems.

      (3) System cost and data storage cost: While the system presented has the advantage of being open-source, it remains relatively expensive (considering the 150k without laser source and optical table, for example). The manuscript could benefit from a more direct comparison of the performance/cost ratio of existing systems, considering academic settings with budgets that most of the time would not allow for expensive architectures. Moreover, it would also be beneficial to discuss the adaptability of the system, in case a 30k objective could not be feasible. Will this system work with different optics (with the obvious limitations coming with the lower NA objective)? This could be an interesting point of discussion. Adaptability of the system in case of lower budgets or more cost-effective choices, depending on the needs.

      We thank the reviewer for raising this important point. First, we would like to clarify that the quoted $150k cost estimate includes the optical table and laser source. We apologize for any confusion and will communicate this more effectively in the revised manuscript.

      We agree that adaptability is a key concern, especially in academic settings with limited budgets. The detection path can be readily altered depending on experimental needs and cost constraints. For example, in our discussion of alternatives to the 5 mm coverslip geometry, we will describe how switching to a Zeiss W Plan-Apochromat 20x/1.0 in combination with a compatible excitation objective allows high-resolution imaging while accommodating more conventional sample formats. We will expand this to include cost-effective alternatives as well.

      We will also expand our discussion on cost-reduction strategies and the associated trade-offs. These include replacing motorized stages with manual ones, omitting the filter wheel in favor of a multi-band emission filter, or using industrial-grade cameras in place of scientific CMOS detectors. While each change entails some loss in functionality or sensitivity, such modifications allow users to tailor the system to their specific budget and application.

      Finally, we recognize the challenge in communicating exact costs of commercial systems due to variability in configuration and pricing. Nonetheless, we will include approximate figures where possible and note that comparable commercial systems—such as LLSM platforms from 3i and Zeiss—are several-fold more expensive than the system presented here.

      Last, not much is said about the need for data storage. Light-sheet microscopy's bottleneck is the creation of increasingly large datasets, and it could be beneficial to discuss more about the storage needs and the quantity of data generated.

      Data storage is indeed a critical consideration in light-sheet microscopy. In the revised manuscript, we will provide a note outlining typical volume dimensions for live-cell imaging experiments along with the associated data overhead. This will include estimates for voxel counts, bit depth, time-lapse acquisitions, and multi-channel datasets to help users anticipate storage needs. We will also briefly discuss strategies for managing large datasets, file types and compression formats.

      Conclusion:

      Altair-LSFM represents a well-engineered and accessible light-sheet system that addresses a longstanding need for high-resolution, reproducible, and affordable sub-cellular light-sheet imaging. While some aspects-comparative benchmarking and validation, limitation for fixed samples-would benefit from further development, the manuscript makes a compelling case for Altair-LSFM as a valuable contribution to the open microscopy scientific community.

      References

      (1) Moore, R. P. et al. A multi-functional microfluidic device compatible with widefield and light sheet microscopy. Lab Chip 22, 136-147 (2021). https://doi.org/10.1039/d1lc00600b

      (2) Lamb, J. R., Mestre, M. C., Lancaster, M. & Manton, J. D. Direct-view oblique plane microscopy. Optica 12, 469-472 (2025). https://doi.org/10.1364/OPTICA.558420

      (3) Liu, T. L. et al. Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms. Science 360 (2018). https://doi.org/10.1126/science.aaq1392

      (4) Sapoznik, E. et al. A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics. eLife 9 (2020). https://doi.org/10.7554/eLife.57681

      (5) Huisken, J. & Stainier, D. Y. Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM). Opt Lett 32, 2608-2610 (2007). https://doi.org/10.1364/ol.32.002608

      (6) Ricci, P. et al. Removing striping artifacts in light-sheet fluorescence microscopy: a review. Prog Biophys Mol Biol 168, 52-65 (2022). https://doi.org/10.1016/j.pbiomolbio.2021.07.003

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Mollá-Albaladejo et al. investigate the neurons downstream of GR64f and Gr66a, called G2Ns. They identify downstream neurons using trans-Tango labeling with RFP and then perform bulk RNA-seq on the RFP-sorted cells. Gene expression is up- or downregulated between the cell populations and between fed and starved states. They specifically identify Leukocinin as a neuropeptide that is upregulated in starved Gr66a cells. Leucokinin cells, identified by a GAL4 line indeed show higher expression when starved, especially in the SEZ. Furthermore, Leucokinin cells colocalize with the transTango signal from downstream neurons of both GRs. This connection is confirmed with GRASP. According to EM data, Leucokinin cells in the SEZ receive a lot of input and connect to many downstream neurons. In behavior experiments performed with flies lacking Leucokinin neurons, flies show reduced responsiveness to sugar and bitter mixtures when starved. The authors suggest that Leucokinin neurons integrate bitter and sugar tastes and that their output is modified by a hunger state.

      Strengths:

      The authors use a multitude of tools to identify SELK neurons downstream of taste sensory neurons and as starvation-sensitive cells. This study provides an example of how combining genetic labeling, RNA-seq, and EM analysis can be combined to investigate neural circuits.

      Weaknesses:

      The authors do not show a functional connection between sensory neurons and SELK neurons. Additionally, data from RNA seq, anatomical studies, and EM analysis are sometimes contradictory in terms of connectivity. GRASP signal is not foolproof that cells are synaptically connected.

      We appreciate the reviewer’s comments. Unfortunately, we have not successfully demonstrated a functional response of SELK neurons using in vivo calcium imaging with UAS-GCaMP7 (we tried f, m, and s versions), primarily due to challenges in obtaining stable signals. We stimulated GRNs using sucrose, caffeine, or a mixture of both, and maybe even if the concentrations were high, they were not enough to induce a response.

      Regarding GRASP, we acknowledge its limitations as a standalone technique for establishing genuine synaptic connections between neurons, as some signals may reflect false positives resulting from the mere proximity of the candidate neurons. To strengthen our findings, we complemented these results by demonstrating the positive colocalization of the Leucokinin antibody signal over the Gr66aGal4>trans-TANGO and Gr64f-Gal4>trans-TANGO (Figure 4), confirming that Leucokinin neurons are indeed postsynaptic to both sweet and bitter GRNs. Moreover, we incorporated BacTrace data to highlight the direct connectivity between sweet and bitter GRNs (now Figure 5E).

      In the revised manuscript, we have introduced the active-GRASP technique (Macpherson et al., 2015). In this version of GRASP, the presynaptic half of GFP (GFP 1-10) is fused to synaptobrevin, which becomes accessible in the membrane of the presynaptic neuron within the synaptic cleft upon presynaptic stimulation (in our case, by stimulating with sucrose sweet Gr64f<sup>GRNs</sup> and with caffeine the bitter Gr66a<sup>GRNs</sup>). Utilizing this technique, we successfully demonstrated (see new Figure 5B and 5D) that when presented with water, no signal was detected in the Gr66a-LexA, Lk-Gal4 > active-GRASP, or Gr64f-LexA, Lk-Gal4 > active-GRASP transgene flies. However, in the presence of caffeine, Gr66aLexA, Lk-Gal4 > active-GRASP transgene flies exhibited a clear signal in the SEZ, and similarly, sucrose presentation to Gr64f-LexA, Lk-Gal4 > active-GRASP transgene flies yielded a detectable signal. The results obtained from active-GRASP provide additional evidence supporting the connectivity between SELK neurons and both Gr64f<sup>GRNs</sup> and Gr66a<sup>GRNs</sup>, further indicating the functional connectivity of the GRNs and SELK neurons.

      The authors describe a behavioral phenotype when flies are starved, however, they do not use a specific driver for the described cell type, thus they should also tone down their claims.

      We agree with the reviewer that the Lk-Gal4 driver line used labels SELK, LHLK, and ABLK neurons. The behavior examined in this paper, the Proboscis Extension Response (PER), measures the initiation of feeding. Although the neural circuit involved in this behavior is primarily confined to the SEZ where SELK neurons are located, we cannot rule out the possibility that other Lk neurons may also play a role in the process. To restrict expression of the Tetanus Toxin, we have utilized the tsh-Gal80 (Clyne et al., 2008) transgene in combination with the Lk-Gal4>UAS-TNT and Lk-Gal4>UAS-TNT<sup>imp</sup> constructs to prevent the expression of the Tetanus Toxin in ABLK neurons, thereby restricting its expression to the SELK and LHLK neurons in the central brain. The new results (Sup Figure 7A) indicate that ABLK neurons do not play a role in integrating sweet and bitter information. However, we acknowledge the reviewer's point that we are still silencing LHLK neurons, so we have adjusted our claims to align more closely with our data

      Generally, the authors do not provide a big advancement to the field and some of the results are contradictory with previous publications.

      We believe our work does not contradict previous findings, nor does it invalidate the role of ABLK neurons in water homeostasis or the role of LHLK neurons in regulating sleep via starvation. We provide additional information on the possible role of SELK neurons in integrating gustatory information. The location of SELK neurons in the SEZ suggests that they may play a role in feeding behavior, and we have demonstrated that these neurons are indeed involved in integrating gustatory information to influence feeding decisions. We consider we have contributed by highlighting a new role for the Leucokinin neuropeptide in feeding behavior.

      Reviewer #2 (Public review):

      Summary:

      A core task of the brain is processing sensory cues from the environment. The neural mechanisms of how sensory information is transmitted from peripheral sense organs to subsequent being processing in defined brain centers remain an important topic in neuroscience. The taste system hereby assesses the palatability of food by evaluating the chemical composition and nutrient content while integrating the current need for energy by assessing the satiation level of the organism. The current manuscript provides insights into the early circuits of gustatory coding using the fruit fly as a model. By combining trans-tango and FACS- based bulk RNAseq to assess the target neurons of sweet sensing (using Gr64fGal4) and bitter sensing (using Gr66a-Gal4) in a first set of experiments the authors investigate genes that are differentially expressed or co-expressed in normal and starved conditions. With a focus on neuropeptides and neurotransmitters, different expressions in the different conditions were assessed resulting in the identification of Leucokinin as a potentially interesting gene. The notion is further supported by RNAseq of Lk- Gal4>mCD8:GFP sorted cells and immunostainings. GRASP and BacTrace experiments further support that the two Lk- expressing cells in the SEZ should indeed be postsynaptic to both types of sensories. Using EM-based connectomics data (based on a previous publication by Engert et al.), the authors also look for downstream targets of the bitter versus sweet gustatory neurons to identify the Lk-neurons. Based on the morphology they identify candidates and further depict the potential downstream neurons in the connectome, which appears largely in agreement with GRASP experiments. Finally silencing the Lk- neurons shows an increased PER response in starved flies (when combined with bitter compounds) as well as increased feeding neurons shows an increased PER response in starved flies (when combined with bitter compounds) as well as increased feeding in a FlyPad assay. Strengths:

      Overall this is an intriguing manuscript, which provides insight into the organization of 2nd order gustatory neurons. It specifically provides strong evidence for the Lk-neurons as a target of sweet and bitter GRNs and provides evidence for their role in regulating sweet vs bitter-based behavioral responses. Particularly the integration of different techniques and datasets in an elegant fashion is a strong side of the manuscript. Moreover to put the known LK-neurons into the context of 2nd order gustatory signalling is strengthening the knowledge about this pathway.

      Weaknesses:

      I do not see any major weakness in the current manuscript. Novelty is to some degree lessened by the fact, that the RNAseq approach did not identify new neurons but rather put the known LK-neurons as major findings. Similarly, the final behavioral section is not very deep and to some degree corroborates the previous publication by the Keene and Nässel labs - that said, the model they propose is indeed novel (but lacks depth in analyses; e.g. there is no physiology that would support the modulation of Lk neurons by either type of GRN). The connectomic section appears a bit out of place and after reading it it's not really clear what one should make of the potential downstream neurons (particularly since the Lk-receptor expression has been previously analyzed); here it might have been interesting to address if/how Lk-neurons may signal directly via a classical neurotransmitter (an information that might be found easily in the adult brain single-cell data).

      We thank the reviewer for the comment. Indeed, we attempted in vivo Ca imaging but were unsuccessful. We have rewritten the connectomic section to better integrate it with the rest of the text and have reanalyzed the data obtained. We considered gathering data from the single-cell adult dataset, but this dataset includes the entire adult fly brain, encompassing SELK and LHLK neurons, making it impossible to differentiate between the two types of Lk neurons. Any further analysis will require transcriptomic analysis of SELK via scRNAseq under the different metabolic conditions tested in this study work.

      Reviewer #3 (Public review):

      Summary:

      To make feeding decisions, animals need to process three types of information: positive cues like sweetness, negative cues like bitterness, and internal states such as hunger or satiety. This study aims to identify where the information is integrated into the fruit fly brain. The authors applied RNA sequencing on second-order gustatory neurons responsible for sweet and bitter processing, under fed and starved conditions. The sequencing data reveal significant changes in gene expression across sweet vs. bitter pathways and fed vs. starved states. The authors focus on the neuropeptide Leucokinin (Lk), whose expression is dependent on the starvation state. They identify a pair of neurons, named SELK neurons, which express Lk and receive direct input from both sweet and bitter gustatory neurons. These SELK neurons are ideal candidates to integrate gustatory and internal state information. Behavioral experiments show that blocking these neurons in starved flies alters their tolerance to bitter substances during feeding.

      Strengths:

      (1) The study employs a well-designed approach, targeting specific neuronal populations, which is more efficient and precise compared to traditional large-scale genetic screening methods.

      (2) The RNAseq results provide valuable data that can be utilized in future studies to explore other molecules beyond Lk.

      (3) The identification of SELK neurons offers a promising avenue for future research into how these neurons integrate conflicting gustatory signals and internal state information.

      Weaknesses:

      (1) Unfortunately, due to technical challenges, the authors were unable to directly image the functional activity of SELK neurons.

      (2) In the behavioral experiments, tetanus toxin was used to block SELK neurons. Since these neurons may release multiple neurotransmitters or neuropeptides, the results do not specifically demonstrate that Leucokinin (Lk) is the critical factor, as suggested in Figure 8. To address this, I recommend using RNAi to inhibit Lk expression in SELK neurons and comparing the outcomes to wild-type controls via the PER assay.

      We appreciate the author's comments and suggestions. As noted, Tetanus Toxin silences the neuron’s activity, affecting the functioning of various neurotransmitters and neuropeptides released by the targeted neuron. In response to the reviewer's recommendation, we employed an RNAi line specifically designed to silence Leucokinin production in Lk-expressing neurons.

      The results presented in Supplementary Figure 7B demonstrate that knocking down Leucokinin in Lk neurons significantly reduces the flies' tolerance to caffeine in sweet food.

      It is crucial to highlight that the sucrose concentration used in Figure 7C was 50mM, whereas in Supplementary Figure 7B, it was increased to 100mM. This adjustment was necessary because the Lk-Gal4, UAS-RNAi, and Lk-Gal4>UAS-RNAi transgenic lines exhibited reduced sensitivity to sucrose compared to the Lk-Gal4>UAS-TNT or Lk-Gal4>UAS-TNT<sup>imp</sup> lines. We aimed to establish a sucrose concentration that would elicit a 50% Proboscis Extension Response (PER) without adding any other compound, thereby allowing us to evaluate the additional effect of caffeine in the food.

      However, according to the data derived from the connectome, SELK neurons might be cholinergic, and this neurotransmitter might be involved in controlling also the behavior of the flies.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      To get more evidence for connections between sensory cells and SELK neurons, could the authors also analyze a second available EM data set? Would setting a different threshold (>5 synapses) reveal connections to both sensories? Comparisons between SELK in- and outputs from EM data and Tango labeling also seem to differ quite a lot based on provided images - can the authors count cell bodies in the stainings? Further proof would be to provide functional imaging data that shows that SELK neurons respond to sugar and bitter compounds.

      In this study, we utilized the recently published EM dataset for the Drosophila central brain connectome (Dorkenwald et al., 2024; Flywire.ai). Changing the number of synapses affects the counts of pre- and postsynaptic neurons. We set a threshold of more than five synapses, as recommended by Flywire, to avoid false positives (Dorkenwald et al., 2024). This threshold has been widely used in recent papers (Engert et al., 2022; Shiu et al., 2022; Walker et al., 2025).

      The neuron counts in the connectomic data differ from those in the trans- and retro-TANGO experiments. In our initial trans-TANGO experiment, which labeled postsynaptic neurons in the Gr64fGal4 and Gr66a-Gal4 transgenic lines, we counted the labeled neurons (see Supplementary Figure 1C) and observed considerable variability between different brains. Due to anticipated variability, we did not count the labeled neurons from trans-TANGO and retro-TANGO techniques in the Leucokinin neurons. Furthermore, neither technique labels all postsynaptic or presynaptic neurons, respectively. A recent study on the retro-TANGO technique (Sorkac et al., 2023) found a minimum threshold: the presynaptic neuron must form a certain number of synapses with the neuron of interest to be adequately labeled. According to this paper, the established threshold is 17 synapses. It is likely that the trans-TANGO technique also has a threshold relating to the number of labeled neurons, contingent on the synapse count. This would explain the discrepancy between the two results.

      Unfortunately, we have not been able to provide functional data pointing to the activation of SELK neurons by sucrose or caffeine. However, our active-GRASP data indicates that the connectivity between Gr64f<sup>GRNs</sup> and Gr66a<sup>GRNs</sup> with SELK neurons is present and functional.

      How many Leucokinin-positive cells are in the SEZ? Does the RNA-seq data provide further information about the SELK neurons? Potential receptor candidates for how they integrate hunger signals? AMPKa was described to be required in LHLK neurons.

      There are two SELK neurons in the SEZ. Due to the nature of our bulk RNA sequencing (RNAseq), we cannot link any additional gene expressions detected in our transcriptomic analysis specifically to the SELK neurons regarding the integration of various signaling processes. Furthermore, the single-cell RNA sequencing (scRNAseq) data available from the Drosophila brain, as reported by Li et al. (2022), does not allow accurate differentiation between SELK and LHLK neurons. To understand how these neurons integrate both metabolic and sensory information, it is crucial to conduct a focused RNAseq study specifically on the SELK neurons to understand how these neurons integrate both metabolic and sensory information. This targeted analysis would provide the necessary insights to elucidate their functional roles better. However, according to the data derived from the connectome, SELK neurons might be cholinergic, and this neurotransmitter might be involved in controlling also the behavior of the flies.

      According to previous studies (Yurgel et al., 2019), the Lk-GAL4 line is also expressed in the VNC, thus the authors could make use of the tsh-GAL80 tool to clean up the line. This study also performed GCaMP imaging in fed and 24h starved animals in SELK and couldn't find a difference, can the authors explain this discrepancy?

      We thank the reviewer for this suggestion. We have now added a new piece of data using the tsh-Gal80 transgene in our PER experiments (Supplementary Figure 7A). Blocking the expression of TNT in the ABLK neurons does not affect the main conclusion of the behavioral results. As stated previously, we were unable to obtain in vivo Ca imaging responses in SELK neurons upon exposure to sucrose, caffeine, or mixtures of sucrose and caffeine. We do not believe this is a discrepancy with previous works like Yurgel et al., 2019. It is likely that we faced technical issues regarding expression stability and that the stimulation was possibly too weak to detect changes in GFP levels

      Reviewer #2 (Recommendations for the authors):

      As mentioned above I do not have any major comments on the manuscript, but there are a few points that I feel should be considered:

      (1) The identification of the Lk-candidate neurons in the connectome remains a bit mysterious. In the method sections, this reads as follows "manual and visual criteria were applied to identify the neurons of interest ". a) What precisely was done to get to the candidates?b) Are there alternative candidates that may be Lk-neurons? c) How would another neuron affect the conclusion of the downstream analysis?

      We thank the reviewer for this comment. We have now modified and added new information in the connectomic section, reinforcing our conclusions and correcting the results obtained.

      Our GRASP, BacTRace, and immunohistochemistry experiments pointed to SELK neurons as postsynaptic to both Gr64f<sup>GRNs</sup> (sweet) and Gr66a<sup>GRNs</sup> (bitter). To identify which neurons in the connectome could be the SELK neurons, we utilized a previously described set of GRNs already identified in the connectome (Shiu et al., 2022). We extracted all postsynaptic neurons to the sweet and bitter GRNs identified and intersected both datasets, retaining only those candidate hits receiving simultaneous input from sweet and bitter GRNs. This process yielded a total of 333 hits. Through visual inspection, we discarded all hits that were merely neuronal fragments or neurons that clearly were not our candidates. We narrowed the list down to a final set of 17 candidate neurons whose arborization was located in the SEZ. We reduced the candidates to two final entries from this list: ID 720575940623529610 (GNG.276) and ID 720575940630808827 (GNG.685). The GNG.276 neuron had a counterpart in the SEZ identified as GNG.246. Both of these neurons were annotated as DNg70 in the Flywire database. GNG.685 had a counterpart identified as GNG.595, and these two neurons were classified as DNg68. In both cases, the neuronal candidates, DNg70 and DNg68, were classified as descending neurons, a characteristic of previously described SELK neurons (Nässel et al., 2021). In our initial analysis published in bioRxiv and sent for revision, we identified DNg70 as potentially the SELK neurons based solely on the morphology of the neurons via visual inspection. However, we employed a better method to determine which candidate is more likely to be the SELK neurons, concluding that DNg68, rather than DNg70, represents the SELK neurons. Briefly, we performed an immunohistochemistry for GFP in the Lk-Gal4>UAS-CD8:GFP flies. We aligned the resulting image in a Drosophila reference brain (JRC2018 U) using the CMTK Registration plugin in ImageJ. The resulting image was skeletonized using the Single Neurite Tracer plugin in ImageJ and later uploaded to the Flywire Gateway platform to compare the structure of the aligned and skeletonized SELK neurons to our candidates. This comparison clearly indicated that the DNg68 neurons are the best candidates for representing the SELK neurons, rather than DNg70. We have updated the text and Figures 6 and Supplementary Figure 6 to reflect the new results. These new results do not alter the conclusions of the paper.

      (2) In the transcriptomic experiments It seems that the raw transcripts are reporters, rather than normalised data. Why?

      All transcriptomic data is normalized. In Figure 1 the differential expression was calculated using Deseq2 normalized counts. In Figure 2, Transcripts Per Million (TPM) were calculated using the Salmon package and normalized for the gene length.

      (3) The expression of nAChRbeta1 in the transcriptomic data is rather striking. However, this remains currently not addressed: is this expression real?

      We have not confirmed the upregulation or downregulation in gene expression for other but for Leucokinin, which is our main interest. We found the presence of nAChRbeta1 interesting, as GRNs are cholinergic (Jaeger et al., 2018), suggesting that it would make sense to find cholinergic receptors in G2Ns. However, it is possible that these receptors are expressed in all G2Ns and serve as a common means of communication.

      (4) The description of the behavioural experiments in the results section is rather brief. I had a hard time following it since the genotypes are not repeated nor is it stated what is different in the experimental group vs control (but instead simply what changes in the experimental group, in a rather discussion-like fashion).

      We thank the reviewer for the comment, we have rewritten this section to improve its clarity.

      (5) If I understand the genetics for the behavioural experiments correctly it addresses the entire Lk-Gal4 expressing population, thus it is not possible to describe the role of the two SEZ neurons, but rather LkGal4 neurons. This should be clarified.

      We thank the reviewer for this comment. Indeed, the Lk-Gal4 driver we used drives expression in all Leucokinin neurons, making it impossible to distinguish between the SELK, LHLK, or ABLK neurons. We have added a new piece of behavioral data by using the tsh-Gal80 transgene to prevent the expression of TNT in the ABLK neurons (Supplementary Figure 7A), but still we cannot distinguish between SELK and LHLK. We have rewritten the text to clarify this fact.

      Reviewer #3 (Recommendations for the authors):

      Overall, the manuscript is well-written, I only have one minor suggestion for improvement. In Figure 8C, please clarify the use of TNT to block Lk release.

      We thank the reviewer for the comment, we have clarified the use of TNT in the text.

      References Clyne, J. D. & Miesenböck, G. Sex-Specific Control and Tuning of the Pattern Generator for Courtship Song in Drosophila. Cell 133, 354–363 (2008).

      Dorkenwald, S. et al. Neuronal wiring diagram of an adult brain. Nature 634, 124–138 (2024).

      Engert, S., Sterne, G. R., Bock, D. D. & Scott, K. Drosophila gustatory projections are segregated by taste modality and connectivity. Elife 11, e78110 (2022).

      Jaeger, A. H. et al. A complex peripheral code for salt taste in Drosophila. Elife 7, e37167 (2018).

      Macpherson, L. J. et al. Dynamic labelling of neural connections in multiple colours by trans-synaptic fluorescence complementation. Nat Commun 6, 10024 (2015).

      Nässel, D. R. Leucokinin and Associated Neuropeptides Regulate Multiple Aspects of Physiology and Behavior in Drosophila. Int J Mol Sci 22, 1940 (2021).

      Shiu, P. K., Sterne, G. R., Engert, S., Dickson, B. J. & Scott, K. Taste quality and hunger interactions in a feeding sensorimotor circuit. eLife 11, e79887 (2022).

      Walker, S. R., Peña-Garcia, M. & Devineni, A. V. Connectomic analysis of taste circuits in Drosophila. Sci. Rep. 15, 5278 (2025).

    1. Author response:

      Reviewer #1:

      As this code was developed for use with a 4096 electrode array, it is important to be aware of double-counting neurons across the many electrodes. I understand that there are ways within the code to ensure that this does not happen, but care must be taken in two key areas. Firstly, action potentials traveling down axons will exhibit a triphasic waveform that is different from the biphasic waveform that appears near the cell body, but these two signals will still be from the same neuron (for example, see Litke et al., 2004 "What does the eye tell the brain: Development of a System for the Large-Scale Recording of Retinal Output Activity"; figure 14). I did not see anything that would directly address this situation, so it might be something for you to consider in updated versions of the code.

      We thank the reviewer for this insightful comment. We agree that signals from the same neuron may be collected by adjacent channels. To address this concern in our software, we plan to add a routine to SpikeMAP that allows users to discard nearby channels where spike count correlations exceed a pre-determined threshold. Because there is no ground truth to map individual cells to specific channels on the hd-MEA, a statistical approach is warranted.

      Secondly, spike shapes are known to change when firing rates are high, like in bursting neurons (Harris, K.D., Hirase, H., Leinekugel, X., Henze, D.A. & Buzsáki, G. Temporal interaction between single spikes and complex spike bursts in hippocampal pyramidal cells. Neuron 32, 141-149 (2001)). I did not see this addressed in the present version of the manuscript.

      This is a valid concern. To ensure that firing rates are relatively constant over the duration of a recording, we will plot average spike rates using rolling windows of a fixed duration. We expect that population firing rates will remain relatively stable across the duration of recordings.

      Another area for possible improvement would be to build on the excellent validation experiments you have already conducted with parvalbumin interneurons. Although it would take more work, similar experiments could be conducted for somatostatin and vasoactive intestinal peptide neurons against a background of excitatory neurons. These may have different spike profiles, but your success in distinguishing them can only be known if you validate against ground truth, like you did for the PV interneurons.

      We agree that further cycles of experiments could be performed with SOM, VIP, and other neuronal subtypes, and we hope that researchers will take advantage of SpikeMAP too. We will clarify this possibility in the Discussion section of the manuscript.

      Reviewer #2:

      Summary:

      While I find that the paper is nicely written and easy to follow, I find that the algorithmic part of the paper is not really new and should have been more carefully compared to existing solutions. While the GT recordings to assess the possibilities of a spike sorting tool to distinguish properly between excitatory and inhibitory neurons are interesting, spikeMAP does not seem to bring anything new to state-of-the-art solutions, and/or, at least, it would deserve to be properly benchmarked. I would suggest that the authors perform a more intensive comparison with existing spike sorters.

      We thank the reviewer for this comment. As detailed in Table 1, SpikeMAP is the only method that performs E/I sorting on large-scale multielectrodes, hence a comparison to competing methods is not currently possible. That being said, many of the pre-processing steps of SpikeMAP (Figure 1) involve methods that are already well-established in the literature and available under different packages. To highlight the contribution of our work and facilitate the adoption of SpikeMAP, we plan to provide a “modular” portion of SpikeMAP that is specialized in performing E/I sorting and can be added to the pipeline of other packages such as KiloSort more clearly.  This modularized version of the code will be shared freely along with the more complete version already available.

      Weaknesses:

      (1) The global workflow of spikeMAP, described in Figure 1, seems to be very similar to that of Hilgen et al. 2020 (10.1016/j.celrep.2017.02.038). Therefore, the first question is what is the rationale of reinventing the wheel, and not using tools that are doing something very similar (as mentioned by the authors themselves). I have a hard time, in general, believing that spikeMAP has something particularly special, given its Methods, compared to state-of-the-art spike sorters.

      We agree with the reviewers that there are indeed similarities between our work and the Hilgen et al. paper. However, while the latter employs optogenetics to stimulate neurons on a large-scale array, their technique does not specifically target inhibitory (e.g., PV) neurons as described in our work. We will clarify our paper accordingly.

      This is why, at the very least, the title of the paper is misleading, because it lets the reader think that the core of the paper will be about a new spike sorting pipeline. If this is the main message the authors want to convey, then I think that numerous validations/benchmarks are missing to assess first how good spikeMAP is, with reference to spike sorting in general, before deciding if this is indeed the right tool to discriminate excitatory vs inhibitory cells. The GT validation, while interesting, is not enough to entirely validate the paper. The details are a bit too scarce for me, or would deserve to be better explained (see other comments after).

      The title of our work will be edited to make it clear that while elements of the pipeline are well-established and available from other packages, we are the first to extend this pipeline to E/I sorting on large-scale arrays.

      (2) Regarding the putative location of the spikes, it has been shown that the center of mass, while easy to compute, is not the most accurate solution [Scopin et al, 2024, 10.1016/j.jneumeth.2024.110297]. For example, it has an intrinsic bias for finding positions within the boundaries of the electrodes, while some other methods, such as monopolar triangulation or grid-based convolution, might have better performances. Can the authors comment on the choice of the Center of Mass as a unique way to triangulate the sources?

      We agree with the reviewer and will point out limits of the center-of-mass algorithm based on the article of Scopin et al (2024). Further, we will augment the existing code library to include monopolar triangulation or grid-based convolution as options available to end-users.

      (3) Still in Figure 1, I am not sure I really see the point of Spline Interpolation. I see the point of such a smoothing, but the authors should demonstrate that it has a key impact on the distinction of Excitatory vs. Inhibitory cells. What is special about the value of 90kHz for a signal recorded at 18kHz? What is the gain with spline enhancement compared to without? Does such a value depend on the sampling rate, or is it a global optimum found by the authors?

      We will clarify these points. Specifically, the value of 90kHz was chosen because it provided a reasonable temporal characterization of spikes; this value, however, can be adjusted within the software based on user preference.

      (4) Figure 2 is not really clear, especially panel B. The choice of the time scale for the B panel might not be the most appropriate, and the legend filtered/unfiltered with a dot is not clear to me in Bii.

      We will re-check Fig.2B which seems to have error in rendering, likely due to conversion from its original format.

      In panel E, the authors are making two clusters with PCA projections on single waveforms. Does this mean that the PCA is only applied to the main waveforms, i.e. the ones obtained where the amplitudes are peaking the most? This is not really clear from the methods, but if this is the case, then this approach is a bit simplistic and does not really match state-of-the-art solutions. Spike waveforms are quite often, especially with such high-density arrays, covering multiple channels at once, and thus the extracellular patterns triggered by the single units on the MEA are spatio-temporal motifs occurring on several channels. This is why, in modern spike sorters, the information in a local neighbourhood is often kept to be projected, via PCA, on the lower-dimensional space before clustering. Information on a single channel only might not be informative enough to disambiguate sources. Can the authors comment on that, and what is the exact spatial resolution of the 3Brain device? The way the authors are performing the SVD should be clarified in the methods section. Is it on a single channel, and/or on multiple channels in a local neighbourhood?

      Here, the reviewer is suggesting that it may be better to perform PCA on several channels at once, since spikes can occur at several channels at the same time. To address this concern, small routine will be written allowing users to choose how many nearby channels to be selected for PCA.

      (5) About the isolation of the single units, here again, I think the manuscript lacks some technical details. The authors are saying that they are using a k-means cluster analysis with k=2. This means that the authors are explicitly looking for 2 clusters per electrode? If so, this is a really strong assumption that should not be held in the context of spike sorting, because, since it is a blind source separation technique, one cannot pre-determine in advance how many sources are present in the vicinity of a given electrode. While the illustration in Figure 2E is ok, there is no guarantee that one cannot find more clusters, so why this choice of k=2? Again, this is why most modern spike sorting pipelines do not rely on k-means, to avoid any hard-coded number of clusters. Can the authors comment on that?

      It is true that k=2 is a pre-determined choice in our software. In practice, we found that k>2 leads to poorly defined clusters. However, we will ensure that this parameter can be adjusted in the software. Furthermore, if the user chooses not to pre-define this value, we will provide the option to use a Calinski-Harabasz criterion to select k.

      (6) I'm surprised by the linear decay of the maximal amplitude as a function of the distance from the soma, as shown in Figure 2H. Is it really what should be expected? Based on the properties of the extracellular media, shouldn't we expect a power law for the decay of the amplitude? This is strange that up to 100um away from the soma, the max amplitude only dropped from 260 to 240 uV. Can the authors comment on that? It would be interesting to plot that for all neurons recorded, in a normed manner V/max(V) as function of distances, to see what the curve looks like.

      We share the reviewer’s concern and will add results that include a population of neurons to assess the robustness of this phenomenon.

      (7) In Figure 3A, it seems that the total number of cells is rather low for such a large number of electrodes. What are the quality criteria that are used to keep these cells? Did the authors exclude some cells from the analysis, and if yes, what are the quality criteria that are used to keep cells? If no criteria are used (because none are mentioned in the Methods), then how come so few cells are detected, and can the authors convince us that these neurons are indeed "clean" units (RPVs, SNRs, ...)?

      We applied stringent criteria to exclude cells, and we will revise the main text to be clear about these criteria, which include a minimum spike rate and the use of LDA to separate out PCA clusters. For the cells that were retained, we will include SNR estimates.

      (8) Still in Figure 3A, it looks like there is a bias to find inhibitory cells at the borders, since they do not appear to be uniformly distributed over the MEA. Can the authors comment on that? What would be the explanation for such a behaviour? It would be interesting to see some macroscopic quantities on Excitatory/Inhibitory cells, such as mean firing rates, averaged SNRs... Because again, in Figure 3C, it is not clear to me that the firing rates of inhibitory cells are higher than Excitatory ones, whilst they should be in theory.       

      We will include a comparison of firing rates for E and I neurons. It is possible that I cells are located at the border of the MEA due to the site of injections of the viral vector, and not because of an anatomical clustering of I cells per se. We will clarify the text accordingly.

      (9) For Figure 3 in general, I would have performed an exhaustive comparison of putative cells found by spikeMAP and other sorters. More precisely, I think that to prove the point that spikeMAP is indeed bringing something new to the field of spike sorting, the authors should have compared the performances of various spike sorters to discriminate Exc vs Inh cells based on their ground truth recordings. For example, either using Kilosort [Pachitariu et al, 2024, 10.1038/s41592-024-02232-7], or some other sorters that might be working with such large high-density data [Yger et al, 2018, 10.7554/eLife.34518].

      As mentioned previously, Kilosort and related approaches do not address the problem of E/I identification (see Table 1). However, they do have pre-processing steps in common with SpikeMAP. We will add some specific comparison points – for instance, the use of k-means and PCA (which is more common across packages) and the use of cubic spline interpolation (which is less common). Further, we will provide a stand-alone E/I sorting module that can be added to the pipeline of other packages, so that users can use this functionality without having to migrate their entire analysis.

      (10) Figure 4 has a big issue, and I guess the panels A and B should be redrawn. I don't understand what the red rectangle is displaying.

      We apologize for this issue. It seems there was a rendering problem when converting the figure from its original format. We will address this issue in the revised version of the manuscript.

      (11) I understand that Figure 4 is only one example, but I have a hard time understanding from the manuscript how many slices/mice were used to obtain the GT data? I guess the manuscript could be enhanced by turning the data into an open-access dataset, but then some clarification is needed. How many flashes/animals/slices are we talking about? Maybe this should be illustrated in Figure 4, if this figure is devoted to the introduction of the GT data.

      We will mention how many flashes/animals/slices were employed in the GT data and provide open access to these data.

      (12) While there is no doubt that GT data as the ones recorded here by the authors are the most interesting data from a validation point of view, the pretty low yield of such experiments should not discourage the use of artificially generated recordings such as the ones made in [Buccino et al, 2020, 10.1007/s12021-020-09467-7] or even recently in [Laquitaine et al, 2024, 10.1101/2024.12.04.626805v1]. In these papers, the authors have putative waveforms/firing rate patterns for excitatory and inhibitory cells, and thus, the authors could test how good they are in discriminating the two subtypes.

      We thank the reviewer for the suggestion that SpikeMAP could be tested on artificially generated spike trains and will add the citation of the two papers mentioned. We hope future efforts will employ SpikeMAP on both synthetic and experimental data to explore the neural dynamics of E and I neurons in healthy and pathological circuits of the brain.

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The Authors investigated the anatomical features of the excitatory synaptic boutons in layer 1 of the human temporal neocortex. They examined the size of the synapse, the macular or the perforated appearance and the size of the synaptic active zone, the number and volume of the mitochondria, the number of the synaptic and the dense core vesicles, also differentiating between the readily releasable, the recycling and the resting pool of synaptic vesicles. The coverage of the synapse by astrocytic processes was also assessed, and all the above parameters were compared to other layers of the human temporal neocortex. The Authors conclude that the subcellular morphology of the layer 1 synapses is suitable for the functions of the neocortical layer, i.e. the synaptic integration within the cortical column. The low glial coverage of the synapses might allow the glutamate spillover from the synapses enhancing synaptic crosstalk within this cortical layer.

      Strengths:

      The strengths of this paper are the abundant and very precious data about the fine structure of the human neocortical layer 1. Quantitative electron microscopy data (especially that derived from the human brain) are very valuable, since this is a highly time- and energy consuming work. The techniques used to obtain the data, as well as the analyses and the statistics performed by the Authors are all solid, strengthen this manuscript, and support the conclusions drawn in the discussion.

      Comments on latest version:

      The third version of this paper has been substantially improved. The English is significantly better, there are only few paragraphs and sentences which are hard to understand (see my comments and suggestions below). Almost all of my suggestions were incorporated.

      We would like to thank the reviewer for the comments and incorporated the suggestions within the latest version of the manuscript.

      Remaining minor concerns:

      About epileptic and non-epileptic (non-affected) tissue. I am aware that temporal lobe neocortical tissue derived from epileptic patients is regarded as non-affected by many groups, and they are quite similar to the cortex of non-epileptic (tumour) patients in their electrophysiological properties and synaptic physiology. But please, note, that one paper you cited did not use samples from epileptic patients, but only tissue from non-epileptic tumor patients (Molnár et al. PLOS 2008).

      When you look deeper, and make thorough comparison of tissues derived from epileptic and non-epileptic patients, there are differences in the fine structure, as well as in several electrophysiological features. See for example Tóth et al., J Physiol, 2018, where higher density of excitatory synapses were found in L2 of neocortical samples derived from epileptic patients compared to non-epileptic (tumor) patients. Furthermore, the appearance of population bursts is similar, but their occurrence is more frequent and their amplitude is higher in tissue from epileptic compared to non-epileptic patients. So, I still cannot agree, that temporal neocortex of epileptic patients with the seizure focus in the hippocampus would be non-affected. Therefore I suggested to use the term biopsy tissue.

      We are thankful for this comment on using non-epileptic tissue also by others. We are also aware that Molnár et al. 2008 worked with tumor tissue.

      It is still not emphasized in the first paragraph of the Discussion, that only excitatory axon terminals were investigated.

      We now mentioned in the first paragraph of the discussion that only excitatory synaptic boutons were investigated.

      The text in the Results and the Discussion are somewhat inconsistent.

      The last two paragraphs of the Results section ends with several sentences which should be part of the discussion, such as line 328: This finding strongly supports multivesicular release... or line 344: --- pointing towards a layer-specific regulation of the putative RRP. Moreover, the results suggest that... and line 370: ... it is most likely... Please, correct this.

      We disagree with the reviewer on these points because these sentences summarizes the findings.

      The first paragraph of the Discussion summarizes the work of the quantitative EM work and gives one conclusion about the astrocytic coverage. This last sentence is inconsistent with the other parts of the paragraph. I would either write that "astrocytic coverage was also investigated" (or something similar), or move this sentence to the paragraph which discusses the astrocytic coverage.

      Results line 180-183. "Special connections" between astrocytic processes and synaptic boutons are mentioned, but not shown. Either show these (but then prove with staining!), or leave out this paragraph.

      We deleted this paragraph as suggested.

      Reviewer #2 (Public review):

      Summary:

      The study of Rollenhagen et al examines the ultrastructural features of Layer 1 of human temporal cortex. The tissue was derived from drug-resistant epileptic patients undergoing surgery, and was selected as further from the epilepsy focus, and as such considered to be non-epileptic. The analyses has included 4 patients with different age, sex, medication and onset of epilepsy. The manuscript is a follow-on study with 3 previous publications from the same authors on different layers of the temporal cortex:

      Layer 4 - Yakoubi et al 2019 eLife

      Layer 5 - Yakoubi et al 2019 Cerebral Cortex,

      Layer 6 - Schmuhl-Giesen et al 2022 Cerebral Cortex

      They find, the L1 synaptic boutons mainly have single active zone a very large pool of synaptic vesicles and are mostly devoid of astrocytic coverage.

      Strengths:

      The MS is well written easy to read. Result section gives a detailed set of figures showing many morphological parameters of synaptic boutons and surrounding glial elements. The authors provide comparative data of all the layers examined by them so far in the Discussion. Given that anatomical data in human brain are still very limited, the current MS has substantial relevance. The work appears to be generally well done, the EM and EM tomography images are of very good quality. The analyses is clear and precise.

      Weaknesses:

      The authors made all the corrections required and answered all of my concerns, included additional data sets, and clarified statements where needed.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Minor suggestions:

      Synaptic density, lines 189-193. If you say "comparatively" high, then compare to something (cite your own work for the other layers, and tell the approximative values for the other layers). Same in line 194 comparably high to what? Other option: say "relatively high".

      We corrected the sentences as suggested by the reviewer.

      Line 206: When present, mitochondria (comma missing)

      Corrected as suggested by the reviewer.

      Line 265: Dot is missing at the end of the sentence (after Shapira et al. 2003)

      Corrected as suggested by the reviewer.

      Lines 300-301: Check the English for this sentence: significant difference BETWEEN TWO sublaminae and not significant difference for both sublaminae.

      Corrected as suggested by the reviewer.

      Lines 304-305: Check the sentence, please, it is not understandable without the text in parenthesis.

      Corrected as suggested by the reviewer.

      Line 354 Dot missing at the end of the sentence (after Figure 6A, B)

      Corrected as suggested by the reviewer.

      Line 354-358: Please rephrase this sentence (too complicated, not understandable). I do not understand why results of the L4, L5, L6 are described here. What does it mean "Astrocytes and their fine processes formed a relatively dense, but a comparably loose network within the neuropil in L1"? Dense or loose?

      In the experiment measuring the volume fraction of astrocytic processes (Figure 6C), all six cortical layers were analyzed, thus we compared the values obtained for L1 with the results for L4, L5 and L6. For more clarity, we rephrased the sentence: “Astrocytes and their fine processes formed a relatively dense network in L4 and L5, but a comparably loose one within the neuropil in L1…” We also rephrased other sentences in this paragraph (as also suggested below).

      Lines 359-369: Please rephrase this paragraph. The sentences are too complicated, have too many parentheses, and are not understandable. I suggest to write first how many synapses were examined in L1 and L4, then how many of them were on spine and on dendrites (either n or %). Then give the values how many (n or %) of them were "tripartite synapses", out of spine synapses and of dendritic synapses in both layers. How many of them were partially covered in both layers. Please, write the data in a systematic way. The best would be to give the values in a table as well. This way it will be more understandable (now, it is chaotic, hard to follow).

      We rephrased the paragraph and added a new table (3).

      Line 383: Dot missing from the end of the sentence.

      Corrected as suggested by the reviewer.

      Line 436: Reconsider "comparably low compared to". The comparably means what in this case? The whole paragraph is hard to understand, please, check and review for improvements to the use of English or use chatGPT to check it.

      We corrected the sentence according to the reviewer’s suggestion.

      Line 487: Same thing again: "The comparably largest size of the RP in L1 when compared..." What would you like to say with "comparably"? Check the meaning of this word in a dictionary, please. I have the feeling that you are using this word instead of "relatively".

      Corrected as suggested by the reviewer.

      Line 488 "and TO that found fot L4 and L5 in rodents..."

      Corrected as suggested by the reviewer.

      Line 493-495: Same again, comparably when compared, correct, please.

      Corrected as suggested by the reviewer.

      Supplemental figures: Now I do understand why Hu-01 and Hu-02 are twice, and I think, 3 patients were examined for L1a and three for L1b. But which side is which on the subfigures? Left side (Hu-01, 02 03) was used for L1a, or L1b? Could you write this in the legend, or mark on the figure (at least at one subfigure), please?

      We implemented a comment for clarity.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public reviews:

      Concerning the grounding in experimental phenomenology, it would be beneficial to identify specific experiments to strengthen the model. In particular, what evidence supports reversible beta cell inactivation? This could potentially be tested in mice, for instance, by using an inducible beta cell reporter, treating the animals with high glucose levels, and then measuring the phenotype of the marked cells. Such experiments, if they exist, would make the motivation for the model more compelling.

      There is some direct evidence of reversible beta cell inactivation in rodent / in vitro models. We had already mentioned this in the discussion, but we have added some text emphasizing / clarifying the role of this evidence (lines 359–362).

      Others have also argued that some analyses of insulin treatment in conventional T2D, which has a stronger effect in patients with higher glucose before treatment, provides indirect evidence of reversal of glucotoxicity. We have also mentioned this in the revised paper (lines 284–285).

      For quantitative experiments, the authors should be more specific about the features of beta cell dysfunction in KPD. Does the dysfunction manifest in fasting glucose, glycemic responses, or both? Is there a ”pre-KPD” condition? What is known about the disease’s timescale?

      The answers to some of these questions are not entirely clear—patients present with very high glucose, and thus must be treated immediately. Due to a lack of antecedent data it is not entirely clear what the pre-KPD condition is, but there is some evidence that KPD is at least not preceded by diabetes symptoms. This point is already noted in the introduction of the paper and Table 1. However, we have added a small note clarifying that this does not rule out mild hyperglycemia, as in prediabetes (and indeed, as our model might predict) (lines 76–77). Similarly, due to the necessity of immediate insulin treatment, it is not clear from existing data whether the disorder manifests more strongly in fasting glucose or glucose response, although it is likely in both. (We might infer this since continuous insulin treatment does not produce fasting hypoglycemia, and the complete lack of insulin response to glucose shortly after presentation should produce a strong effect in glycemic response.) We believe our existing description of KPD lists all of the relevant timescales, however we have also slightly clarified this description in response to the first referee’s comments (lines 66–73, 83)

      The authors should also consider whether their model could apply to other conditions besides KPD. For example, the phenomenology seems similar to the ”honeymoon” phase of T1D. Making a strong case for the model in this scenario would be fascinating.

      This is an excellent idea, which had not occurred to us. We have briefly discussed this possibility in the remission (lines 281–291), but plan to analyze it in more detail in a future manuscript.

      Reviewer #1 (Recommendations for the author):

      Whenever simulation results are presented, parameter values should be specified right there in the figure captions.

      We have added the values of glucotoxicity parameters to the caption of Figure 2. In other figures, we have explicitly mentioned which panel of Figure 2 the parameters are taken from. Description of the non-glucotoxicity parameters is a bit cumbersome (there are a lot of them, but our model of fast dynamics is slightly different from Topp et al. so it does not suffice to simply say we took their parameters) so we have referred the reader to the Materials and Methods for those.

      I was confused by the language in Figure 4. Could the authors clarify whether they argue that: (1) the observed KPD behaviour is the result of the system switching from one stable state to another when perturbed with high glucose intake? (2) the observed KPD behaviour is the result of one of the steady states disappearing with high glucose intake?

      What we mean to say is that during a period of high sugar intake or exogeneous insulin treatment, one of the fixed points is temporarily removed—it is still a fixed point of the “normal” dynamics, but not a fixed point of the dynamics with the external condition added. Since when glucose (insulin) intake is high enough, only the low (high)-β fixed point is present, under one of these conditions the dynamics flow toward that fixed point. When the external influx of glucose/insulin is turned off, both fixed points are present again—but if the dynamics have moved sufficiently far during the external forcing, the fixed point they end up in will have switched from one fixed point to the other. We have edited the text to make this clearer (lines 153–185). Do note, however, that in response to both referee’s comments (see below), Figures 3 and 4 have been replaced with more illuminating ones. This specific point is now addressed by the new Figure 3.

      The adaptation of the prefactor ’c’ was confusing to me. I think I understood it in the end, but it sounded like, ”here’s a complication, but we don’t explain it because it doesn’t really matter”. I think the authors can explain this better (or potentially leave out the complication with ’c’ altogether?).

      Indeed, the existence of an adaptation mechanism is important for our overall picture of diabetes pathogenesis, but not for many of our analyses, which assume prediabetes. Nonetheless, we agree that the current explanation of it’s role is confusing because of its vagueness. We have elaborated the explanation of the type of dynamics we assume for c, adding an equation for its dynamics to the “Model” section of the Materials and methods, explained in lines 456–465. We have also amended Figure 1 to note this compensation.

      I expect the main impact of this work will be to get clinical practitioners and biomedical researchers interested in the intermediate timescale dynamics of β-cells and take seriously the possibility that reversible inactive states might exist. But this impact will only be achieved when the results are clearly and easily understandable by an audience that is not familiar with mathematical modelling. I personally found it difficult to understand what I was supposed to see in the figures at first glance. Yes, the subtle points are indeed explained in the figure captions, but it might be advantageous to make the points visually so clear that a caption is barely needed. For example, when claiming that a change in parameters leads to bistability, why not plot the steady state values as a function of that parameter instead of showing curves from which one has to infer a steady state?

      I would advise the authors to reconsider their visual presentation by, e.g., presenting the figures to clinical practitioners or biomedical researchers with just a caption title to test whether such an audience can decipher the point of the figure! This is of course merely a personal suggestion that the authors may decide to ignore. I am making this suggestion only because I believe in the quality of this work and that improving the clarity of the figures and the ease with which one can understand the main points would potentially lead to a much larger impact on the presented results.

      This is a very good point. We have made several changes. Firstly, we have added smaller panels showing the dynamics of β to Figure 2; previously, the reader had to infer what was happening to β from G(t). Secondly, we have completely replaced the two figures showing dβ/dt, and requiring the reader to infer the fixed points of β, with bifurcation diagrams that simply show the fixed points of G and β. The new figures show through bifurcation diagrams how there are multiple fixed points in KPD, how glucose or insulin treatment force the switching of fixed points, and how the presence of bistability depends on the rate of glucotoxicity. (These new figures are Fig. 3–5 in the revised manuscript.)

      Could the authors explicitly point out what could be learned from their work for the clinic? At the moment treatment consists of giving insulin to patients. If I understand correctly, nothing about the current treatment would change if the model is correct. Is there maybe something more subtle that could be relevant to devising an optimal treatment for KPD patients?

      This is another very good point. We have added a new figure (Fig. 7) in our results section showing how this model, or one like it, can be analyzed to suggest an insulin treatment schedule (once parameters for an individual patient can be measured), and added some discussion of this point (lines 224–240) as well as lifestyle changes our model might suggest for KPD patients to the discussion (lines 413–425).

      Similarly, could the authors explicitly point out how their model could be experimentally tested? For example, are the functions f(G) and g(G) experimentally accessible? Related to that, presumably the shape of those functions matters to reproduce the observed behaviour. Could the authors comment on that / analyze how reproducing the observed behaviour puts constraints on the shape of the used functions and chosen parameter values?

      g(G) has not been carefully measured in cellular data, however it could be in more quantative versions of existing experiments. Further, our model indeed requires some general features for the forms of f(G) and g(G) to produce KPD-like phenomena. We have added some comment on this to the discussion section of the revised manuscript (lines 367–372).

      Could the authors explicitly spell out which parameters they think differ between individual KPD patients, and which parameters differ between KPD patients and ’regular’ type 2 diabetics?

      In general we expect all parameters should vary both among KPD patients and between KPD / “conventional” T2D. The primary parameter determining whether KPD and conventional T2D, is seen, however, is the ratio kIN/kRE. We have elaborated on both these points in the revised mansuscript. (Lines 186–192, 250–257.)

      I was confused about the timescale of remission. At one point the authors write “KPD patients can often achieve partial remission: after a few weeks or months of treatment with insulin” but later the authors state that “the duration of the remission varies from 6 months to 10 years”.

      The former timescale is the typical timescale achieve remission. After remission is reached, however, it may or may not last—patients may experience a relapse, where their condition worsens and they again require insulin. We have edited the text to clarify this distinction (lines 66–73).

      When the authors talk about intermediate timescales in the main text could they specify an actual unit of time, such as days, weeks, or months as it would relate to the rate constants in their model for those transitions?

      We have done so (lines 86–87, figure 1 caption, figure 2 caption). Getting KPD-like behavior requires (at high glucose) the deactivation process to be somewhat faster than the reactivation process, so the relevant scales are between weeks (reactivation) and days (deactivation at high G).

      The authors state ”Our simple model of β-cell adaptation also neglects the known hyperglycemiainduced leftward shift in the insulin secretion curve f(G) in Eq. (2)) ”. This seems an important consideration. Could the authors comment on why they did not model this shift, and/or explicitly discuss how including it is expected to change the model dynamics?

      We agree that this process seems potentially relevant, as it seems to happen on a relatively fast timescale compared to glucose-induced β-cell death. It is, however, not so well characterized quantitatively that including it is a simple matter of putting in known values—we would be making assumptions that would complicate the interpretation of our results.

      It is clear that this effect will need to be considered when quanitatively modelling real patient data. However, it is also straightforward to argue that this effect by itself cannot produce KPD-like symptoms, and will only tend to reduce the rate of glucotoxocity necessary to produce bibstability. We have added a discussion of this in the revisions (lines 307–315). We have also, in general, expanded the discussion of the effects that each neglected detail we have mentioned is expected to have (lines 292–315).

      The authors end with a statement that their results may “contribute to explanation of other observations that involve rapid onset or remission of diabetes-like phenomena, such as during pregnancy or for patients on very low calorie diets.” Could the authors spell out exactly how their model potentially relates to these phenomena?

      Our thinking is that, even when another direct cause, such as loss of insulin resistance, is implicated in reversal of diabetes, some portion of the effect may be explained by reversal of glucotoxicity. This is indeed at this point just a hypothesis, but we have expanded on it briefly in the revision. (Lines 281–291.)

      Minor typos:

      In Figure 2.D the last zero of 200 on the axis was cut off.

      Line 359 - there is a missing word ”in the analysis”.

      We have fixed these typos, thanks.

      Reviewer #2 (Recommendations for the author):

      The manuscript could be significantly improved in two key areas: the presentation of the analysis, and the relation with experimental phenomenology.

      Regarding the analysis presentation, the figures could be substantially enhanced with minimal effort from the authors. At present, they are sparse, lack legends, and offer only basic analysis. The authors should consider presenting, for example, a bifurcation diagram for beta cell mass and fasting glucose levels as a function of kIN, and how insulin sensitivity and average meal intake modulate this relationship. The goal should be to present clear, testable predictions in an intuitive manner. Currently, the specific testable predictions of the model are unclear.

      The response to this question is copied from the reponses to related questions from the first referee.

      This is a very good point. We have made several changes. Firstly, we have added smaller panels showing the dynamics of β to Figure 2; previously, the reader thad to infer what was happening to β from G(t). Secondly, we have completely replaced the two figures showing dβ/dt, and requiring the reader to infer the fixed points of β, with bifurcation diagrams that simply show the fixed points of G and β. The new figures show through bifurcation diagrams how there are multiple fixed points in KPD, how glucose or insulin treatment force the switching of fixed points, and how the presence of bistability depends on the rate of glucotoxicity. We have also supplemented our phase diagram that shows the effects of SI and the total beta cell population with bifurcation diagrams showing β as SI and βTOT are varied. (These new figures are Fig. 3–5 in the present manuscript.) Finally, we have added another figure analyzing the model’s predictions for the optimal insulin treatment and the resulting time needed to achieve remission (Fig. 7)

    1. Author response:

      The following is the authors’ response to the previous reviews.

      Reviewer 1:

      The authors frequently refer to their predictions and theory as being causal, both in the manuscript and in their response to reviewers. However, causal inference requires careful experimental design, not just statistical prediction. For example, the claim that "algorithmic differences between those with BPD and matched healthy controls" are "causal" in my opinion is not warranted by the data, as the study does not employ experimental manipulations or interventions which might predictably affect parameter values. Even if model parameters can be seen as valid proxies to latent mechanisms, this does not automatically mean that such mechanisms cause the clinical distinction between BPD and CON, they could plausibly also refer to the effects of therapy or medication. I recommend that such causal language, also implicit to expressions like "parameter influences on explicit intentional attributions", is toned down throughout the manuscript.

      Thankyou for this chance to be clearer in the language. Our models and paradigm introduce a from of temporal causality, given that latent parameter distributions are directly influenced by latent parameter estimates at a previous point in time (self-uncertainty and other uncertainty directly governs social contagion). Nevertheless, we appreciate the reviewers perspective and have now toned down the language to reflect this.

      Abstract:

      ‘Our model makes clear predictions about the mechanisms of social information generalisation concerning both joint and individual reward.’

      Discussion:

      ‘We can simulate this by modelling a framework that incorporates priors based on both self and a strong memory impression of a notional other (Figure S3).’

      ‘We note a strength of this work is the use of model comparison to understand algorithmic differences between those with BPD and matched healthy controls.’

      Although the authors have now much clearer outlined the stuy's aims, there still is a lack of clarity with respect to the authors' specific hypotheses. I understand that their primary predictions about disruptions to self-other generalisation processes underlying BPD are embedded in the four main models that are tested, but it is still unclear what specific hypotheses the authors had about group differences with respect to the tested models. I recommend the authors specify this in the introduction rather than refering to prior work where the same hypotheses may have been mentioned.

      Thankyou for this further critique which has enabled us to more cleary refine our introduction. We have now edited our introduction to be more direct about our hypotheses, that these hypotheses are instantiated into formal models, and what our predictions were. We have also included a small section on how previous predictions from other computational assessments of BPD link to our exploratory work, and highlighted this throughout the manuscript.

      ‘This paper seeks to address this gap by testing explicitly how disruptions in self-other generalization processes may underpin interpersonal disruptions observed in BPD. Specifically, our hypotheses were: (i) healthy controls will demonstrate evidence for both self-insertion and social contagion, integrating self and other information during interpersonal learning; and (ii) individuals with BPD will exhibit diminished self-other integration, reflected in stronger evidence for observations that assume distinct self-other representations.

      We tested these hypotheses by designing a dynamic, sequential, three-phase Social Value Orientation (Murphy & Ackerman, 2014) paradigm—the Intentions Game—that would provide behavioural signatures assessing whether BPD differed from healthy controls in these generalization processes (Figure 1A). We coupled this paradigm with a lattice of models (M1-M4) that distinguish between self-insertion and social contagion (Figure 1B), and performed model comparison:

      M1. Both self-to-other (self-insertion) and other-to-self (social contagion) occur before and after learning M2. Self-to-other transfer only occurs M3. Other-to-self transfer only occurs M4. Neither transfer process, suggesting distinct self-other representations

      We additionally ran exploratory analysis of parameter differences and model predictions between groups following from prior work demonstrating changes in prosociality (Hula et al., 2018), social concern (Henco et al., 2020), belief stability (Story et al., 2024a), and belief updating (Story, 2024b) in BPD to understand whether discrepancies in self-other generalisation influences observational learning. By clearly articulating our hypotheses, we aim to clarify the theoretical contribution of our findings to existing literature on social learning, BPD, and computational psychiatry.’

      Caveats should also be added about the exploratory nature of the many parameter group comparisons. If there are any predictions about group differences that can be made based on prior literature, the authors should make such links clear.

      Thank you for this. We have now included caveats in the text to highlight the exploratory nature of these group comparisons, and added direct links to relevant literature where able:

      Introduction

      ‘We additionally ran exploratory analysis of parameter differences and model predictions between groups following from prior work demonstrating changes in prosociality (Hula et al., 2018), social concern (Henco et al., 2020), belief stability (Story et al., 2024a), and belief updating (Story, 2024b) in BPD to understand whether discrepancies in self-other generalisation influences observational learning. By clearly articulating our hypotheses, we aim to clarify the theoretical contribution of our findings to existing literature on social learning, BPD, and computational psychiatry.’

      Model Comparison

      ‘We found that CON participants were best fit at the group level by M1 (Frequency = 0.59, Exceedance Probability = 0.98), whereas BPD participants were best fit by M4 (Frequency = 0.54, Exceedance Probability = 0.86; Figure 2A). This suggests CON participants are best fit by a model that fully integrates self and other when learning, whereas those with BPD are best explained as holding disintegrated and separate representations of self and other that do not transfer information back and forth.

      We first explore parameters between separate fits (see Methods). Later, in order to assuage concerns about drawing inferences from different models, we examined the relationships between the relevant parameters when we forced all participants to be fit to each of the models (in a hierarchical manner, separated by group). In sum, our model comparison is supported by convergence in parameter values when comparisons are meaningful (see Supplementary Materials). We refer to both types of analysis below.’

      Phase 2 analysis

      ‘Prior work predicts those with BPD should focus more intently on public social information, rather than private information that only concerns one party (Henco et al., 2020). In BPD participants, only new beliefs about the relative reward preferences – mutual outcomes for both player - of partners differed (see Fig 2E): new median priors were larger than median preferences in phase 1 (mean = -0.47; = -6.10, 95%HDI: -7.60, -4.60).’

      ‘Models of moral preference learning (Story et al., 2024) predicts that BPD vs non-BPD participants have more rigid beliefs about their partners. We found that BPD participants were equally flexible around their prior beliefs about a partner’s relative reward preferences (= -1.60, 95%HDI: -3.42, 0.23), and were less flexible around their beliefs about a partner’s absolute reward preferences (=-4.09, 95%HDI: -5.37, -2.80), versus CON (Figure 2B).’

      Phase 3 analysis

      ‘Prior work predicts that human economic preferences are shaped by observation (Panizza, et al., 2021; Suzuki et al. 2016; Yu et al, 2021), although little-to-no work has examined whether contagion differs for relative vs. absolute preferences. Associative models predict that social contagion may be exaggerated in BPD (Ereira et al., 2018).… As a whole, humans are more susceptible to changing relative preferences more than selfish, absolute reward preferences, and this is disrupted in BPD.’

      Psychometric and Intentional Attribution analysis

      ‘Childhood trauma, persecution, and poor mentalising in BPD are all predicted to disrupt one’s ability to change (Fonagy & Luyten, 2009).’

      ‘Prior work has also predicted that partner-participant preference disparity influences mental state attributions (Barnby et al., 2022; Panizza et al., 2021).’

      I'm not sure I understand why the authors, after adding multiple comparison correction, now list two kinds of p-values. To me, this is misleading and precludes the point of multiple comparison corrections, I therefore recommend they report the FDR-adjusted p-values only. Likewise, if a corrected p-value is greater than 0.05 this should not be interpreted as a result.

      We have now adjusted the exploratory results to include only the FDR corrected values in the text.

      ‘We assessed conditional psychometric associations with social contagion under the assumption of M3 for all participants. We conducted partial correlation analyses to estimate relationships conditional on all other associations and retained all that survived bootstrapping (5000 reps), permutation testing (5000 reps), and subsequent FDR correction. When not controlled for group status, RGPTSB and CTQ scores were both moderately associated with MZQ scores (RGPTSB r = 0.41, 95%CI: 0.23, 0.60, p[fdr]=0.043; CTQ r = 0.354 95%CI: 0.13, 0.56, p[fdr]=0.02). This was not affected by group correction. CTQ scores were moderately and negatively associated with shifts in individualistic reward preferences (; r = -0.25, 95%CI: -0.46, -0.04, p[fdr]=0.03). This was not affected by group correction. MZQ scores were in turn moderately and negatively associated with shifts in prosocial-competitive preferences () between phase 1 and 3 (r = -0.26, 95%CI: -0.46, -0.06, p[fdr]=0.03). This was diminished when controlled for group status (r = 0.13, 95%CI: -0.34, 0.08, p[fdr]=0.20). Together this provides some evidence that self-reported trauma and self-reported mentalising influence social contagion (Fig S11). Social contagion under M3 was highly correlated with contagion under M1 demonstrating parsimony of outcomes across models (Fig S12).

      Prior work has predicted that partner-participant preference disparity influences mental state attributions (Barnby et al., 2022; Panizza et al., 2021). We tested parameter influences on explicit intentional attributions in Phase 2 while controlling for group status. Attributions included the degree to which they believed their partner was motived by harmful intent (HI) and self-interest (SI). According with prior work (Barnby et al., 2022), greater disparity of absolute preferences before learning was associated on a trend level with reduced attributions of SI (<= -0.23, p[fdr]=0.08), and greater disparity of relative preferences before learning exaggerated attributions of HI = 0.21, p[fdr]=0.08), but did not survive correction (Figure S4B). This is likely due to partners being significantly less individualistic and prosocial on average compared to participants (= -5.50, 95%HDI: -7.60, -3.60; = 12, 95%HDI: 9.70, 14.00); partners are recognised as less selfish and more competitive.’

      Can the authors please elaborate why the algorithm proposed to be employed by BPD is more 'entropic', especially given both their self-priors and posteriors about partners' preferences tended to be more precise than the ones used by CON? As far as I understand, there's nothing in the data to suggest BPD predictions should be more uncertain. In fact, this leads me to wonder, similarly to what another reviewer has already suggested, whether BPD participants generate self-referential priors over others in the same way CON participants do, they are just less favourable (i.e., in relation to oneself, but always less prosocial) - I think there is currently no model that would incorporate this possibility? It should at least be possible to explore this by checking if there is any statistical relationship between the estimated θ_ppt^m and 〖p(θ〗_par |D^0).

      Thank you for this opportunity to be clearer in our wording. We belief the reviewer is referring to this line in the discussion: ‘In either case, the algorithm underlying the computational goal for BPD participants is far higher in entropy and emphasises a less stable or reliable process of inference.’

      We note in the revised Figure 2 panel E and in the results that those with BPD under M4 show insertion along absolute reward (they still expect diminished selfishness in others), but neutral priors over relative reward (around 0, suggesting expectations of neither prosocial or competitive tendencies of others). Thus, θ_ppt^m (self preference) and θ_par^m (other preference) are tightly associated for absolute, but not relative reward.

      In our wording, we meant that whether under model M4 or M1, those with BPD either show a neutral prior over relative reward (M4) or a prior with large variance over relative reward (M1), showing expectations of difference between themselves and their partner. In both cases, expectation about a partner’s absolute reward preferences is diminished vs. CON participants. We have strengthened our language in the discussion to clarify this:

      ‘In either case, the algorithm underlying the computational goal for BPD participants is far higher in uncertainty, whether through a neutral central tendency (M4) or large variance (M1) prior over relative reward in phase 2, and emphasises a less certain and reliable expectation about others.’

      To note, social contagion under M3 was highly correlated with contagion under M1 (see Fig S11). This provides some preliminary evidence that trauma impacts beliefs about individualism directly, whereas trauma and persecutory beliefs impact beliefs about prosociality through impaired trait mentalising" - I don't understand what the authors mean by this, can they please elaborate and add some explanation to the main text?

      We have now clarified this in the text:

      ‘Together this provides some evidence that self-reported trauma and self-reported mentalising influence social contagion (Fig S11). Social contagion under M3 was highly correlated with contagion under M1 demonstrating parsimony of outcomes across models (Fig S12).’

      I noted that at least some of the newly added references have not been added to the bibliography (e.g., Hitchcock et al. 2022).

      Thankyou for noticing this omission. We have now ensured all cited works are in the reference list.

      Reviewer 2:

      The paper is not based on specific empirical hypotheses formulated at the outset, but, rather, it uses an exploratory approach. Indeed, the task is not chosen in order to tackle specific empirical hypotheses. This, in my view, is a limitation since the introduction reads a bit vague and it is not always clear which gaps in the literature the paper aims to fill. As a further consequence, it is not always clear how the findings speak to previous theories on the topic.’

      As I wrote in the public review, however, I believe that an important limitation of this work is that it was not based on testing specific empirical hypotheses formulated at the outset, and on selecting the experimental paradigm accordingly. This is a limitation because it is not always clear which gaps in the literature the paper aims to fill. As a consequence, although it has improved substantially compared to the previous version, the introduction remains a bit vague. As a further consequence, it is not always clear how the findings speak to previous theories on the topic. Still, despite this limitation, the paper has many strengths, and I believe it is now ready for publication

      Thank you for this further critique. We appreciate your appraisal that the work has improved substantially and is ready for publication. We nevertheless have opted to clarify our introduction and aprior predictions throughout the manuscript (please see response to Reviewer 1).

      Reviewer 3:

      Although the authors note that their approach makes "clear and transparent a priori predictions," the paper could be improved by providing a clear and consolidated statement of these predictions so that the results could be interpreted vis-a-vis any a priori hypotheses.

      In line with comments from both Reviewer 1 and 2, we have clarified our introduction to make it clear what our aprior predictions and hypotheses are about our core aims and exploratory analyses (see response to Reviewer 1).

      The approach of using a partial correlation network with bootstrapping (and permutation) was interesting, but the logic of the analysis was not clearly stated. In particular, there are large group (Table 1: CON vs. BPD) differences in the measures introduced into this network. As a result, it is hard to understand whether any partial correlations are driven primarily by mean differences in severity (correlations tend to be inflated in extreme groups designs due to the absence of observation in middle of scales forming each bivariate distribution). I would have found these exploratory analyses more revealing if group membership was controlled for.

      Thank you for this chance to be clearer in our methods. We have now written a more direct exposition of this exploratory method:

      ‘Exploratory Network Analysis

      To understand the individual differences of trait attributes (MZQ, RGPTSB, CTQ) with other-to-self information transfer () across the entire sample we performed a network analysis (Borsboom, 2021). Network analysis allows for conditional associations between variables to be estimated; each association is controlled for by all other associations in the network. It also allows for visual inspection of the conditional relationships to get an intuition for how variables are interrelated as a whole (see Fig S11). We implemented network analysis with the bootNet package in r using the ‘estimateNetwork’ function with partial correlations (Epskamp, Borsboom & Fried, 2018). To assess the stability of the partial correlations we further implemented bootstrap resampling with 5000 repetitions using the ‘bootnet’ function. We then additionally shuffled the data and refitted the network 5000 times to determine a p<sub>permuted</sub> value; this indicates the probability that a conditional relationship in the original network was within the null distribution of each conditional relationship. We then performed False Discovery Rate correction on the resulting p-values. We additionally controlled for group status for all variables in a supplementary analysis (Table S4).’

      We have also further corrected for group status and reported these results as a supplementary table, and also within the main text alongside the main results. We have opted to relegate Figure 4 into a supplementary figure to make the text clearer.

      ‘We explored conditional psychometric associations with social contagion under the assumption of M3 for all participants (where everyone is able to be influenced by their partner). We conducted partial correlation analyses to estimate relationships conditional on all other associations and retained all that survived bootstrapping (5000 reps), permutation testing (5000 reps), and subsequent FDR correction. When not controlled for group status, RGPTSB and CTQ scores were both moderately associated with MZQ scores (RGPTSB r = 0.41, 95%CI: 0.23, 0.60, p[fdr]=0.043; CTQ r = 0.354 95%CI: 0.13, 0.56, p[fdr]=0.02). This was not affected by group correction. CTQ scores were moderately and negatively associated with shifts in individualistic reward preferences (; r = -0.25, 95%CI: -0.46, -0.04, p[fdr]=0.03). This was not affected by group correction. MZQ scores were in turn moderately and negatively associated with shifts in prosocial-competitive preferences () between phase 1 and 3 (r = -0.26, 95%CI: -0.46, -0.06, p[fdr]=0.03). This was diminished when controlled for group status (r = 0.13, 95%CI: -0.34, 0.08, p[fdr]=0.20). Together this provides some evidence that self-reported trauma and self-reported mentalising influence social contagion (Fig S11). Social contagion under M3 was highly correlated with contagion under M1 demonstrating parsimony of outcomes across models (Fig S12).’

      Discussion first para: "effected -> affected"

      Thanks for spotting this. We have now changed it.

      Add "s" to "participant: "Notably, despite differing strategies, those with BPD achieved similar accuracy to CON participant."

      We have now changed this.

    1. Author response:

      Reviewer #1 (Public review):

      Summary:

      Argunşah et al. describe and investigate the mechanisms underlying the differential response dynamics of barrel vs septa domains of the whisker-related primary somatosensory cortex (S1). Upon repeated stimulation, the authors report that the response ratio between multi- and single-whisker stimulation increases in layer (L) 4 neurons of the septal domain, while remaining constant in barrel L4 neurons. This difference is attributed to the short-term plasticity properties of interneurons, particularly somatostatin-expressing (SST+) neurons. This claim is supported by the increased density of SST+ neurons found in L4 of the septa compared to barrels, along with a stronger response of (L2/3) SST+ neurons to repeated multi- vs single-whisker stimulation. The role of the synaptic protein Elfn1 is then examined. Elfn1 KO mice exhibited little to no functional domain separation between barrel and septa, with no significant difference in single- versus multi-whisker response ratios across barrel and septal domains. Consistently, a decoder trained on WT data fails to generalize to Elfn1 KO responses. Finally, the authors report a relative enrichment of S2- and M1-projecting cell densities in L4 of the septal domain compared to the barrel domain.

      Strengths:

      This paper describes and aims to study a circuit underlying differential response between barrel columns and septal domains of the primary somatosensory cortex. This work supports the view that barrel and septal domains contribute differently to processing single versus multi-whisker inputs, suggesting that the barrel cortex multiplexes sensory information coming from the whiskers in different domains.

      We thank the reviewer for the very neat summary of our findings that barrel cortex multiplexes converging information in separate domains.

      Weaknesses:

      While the observed divergence in responses to repeated SWS vs MWS between the barrel and septal domains is intriguing, the presented evidence falls short of demonstrating that short-term plasticity in SST+ neurons critically underpins this difference. The absence of a mechanistic explanation for this observation limits the work's significance. The measurement of SST neurons' response is not specific to a particular domain, and the Elfn1 manipulation does not seem to be specific to either stimulus type or a particular domain.

      We appreciate the reviewer’s perspective. Although further research is needed to understand the circuit mechanisms underlying the observed phenomenon, we believe our data suggest that altering the short-term dynamics of excitatory inputs onto SST neurons reduces the divergent spiking dynamics in barrels versus septa during repetitive single- and multi-whisker stimulation. Future work could examine how SST neurons, whose somata reside in barrels and septa, respond to different whisker stimuli and the circuits in which they are embedded. At this time, however, the authors believe there is no alternative way to test how the short-term dynamics of excitatory inputs onto SST neurons, as a whole, contribute to the temporal aspects of barrel versus septa spiking.

      The study's reach is further constrained by the fact that results were obtained in anesthetized animals, which may not generalize to awake states.

      We appreciate the reviewer’s concern regarding the generalizability of our findings from anesthetized animals to awake states. Anesthesia was employed to ensure precise individual whisker stimulation (and multi-whisker in the same animal), which is challenging in awake rodents due to active whisking. While anesthesia may alter higher-order processing, core mechanisms, such as short and long term plasticity in the barrel cortex, are preserved under anesthesia (Martin-Cortecero et al., 2014; Mégevand et al., 2009).

      The statistical analysis appears inappropriate, with the use of repeated independent tests, dramatically boosting the false positive error rate.

      Thank you for your feedback on our analysis using independent rank-based tests for each time point in wild-type (WT) animals. To address concerns regarding multiple comparisons and temporal dependencies (for Figure 1F and 4D for now but we will add more in our revision), we performed a repeated measures ANOVA for WT animals (13 Barrel, 8 Septa, 20 time points), which revealed a significant main effect of Condition (F(1,19) = 16.33, p < 0.001) and a significant Condition-Time interaction (F(19,361) = 2.37, p = 0.001). Post-hoc tests confirmed significant differences between Barrel and Septa at multiple time points (e.g., p < 0.0025 at times 3, 4, 6, 7, 8, 10, 11, 12, 16, 19 after Bonferroni posthoc correction), supporting a differential multi-whisker vs. single-whisker ratio response in WT animals. In contrast, a repeated measures ANOVA for knock-out (KO) animals (11 Barrel, 7 Septa, 20 time points) showed no significant main effect of Condition (F(1,14) = 0.17, p = 0.684) or Condition-Time interaction (F(19,266) = 0.73, p = 0.791), indicating that the Barrel-Septa difference observed in WT animals is absent in KO animals.

      Furthermore, the manuscript suffers from imprecision; its conclusions are occasionally vague or overstated. The authors suggest a role for SST+ neurons in the observed divergence in SWS/MWS responses between barrel and septal domains. However, this remains speculative, and some findings appear inconsistent. For instance, the increased response of SST+ neurons to MWS versus SWS is not confined to a specific domain. Why, then, would preferential recruitment of SST+ neurons lead to divergent dynamics between barrel and septal regions? The higher density of SST+ neurons in septal versus barrel L4 is not a sufficient explanation, particularly since the SWS/MWS response divergence is also observed in layers 2/3, where no difference in SST+ neuron density is found.

      Moreover, SST+ neuron-mediated inhibition is not necessarily restricted to the layer in which the cell body resides. It remains unclear through which differential microcircuits (barrel vs septum) the enhanced recruitment of SST+ neurons could account for the divergent responses to repeated SWS versus MWS stimulation.

      We fully appreciate the reviewer’s comment. We currently do not provide any evidence on the contribution of SST neurons in the barrels versus septa in layer 4 on the response divergence of spiking observed in SWS versus MWS. We only show that these neurons differentially distribute in the two domains in this layer. It is certainly known that there is molecular and circuit-based diversity of SST-positive neurons in different layers of the cortex, so it is plausible that this includes cells located in the two domains of vS1, something which has not been examined so far. Our data on their distribution are one piece of information that SST neurons may have a differential role in inhibiting barrel stellate cells versus septa ones. Morphological reconstructions of SST neurons in L4 of the somatosensory barrel cortex has shown that their dendrites and axons project locally and may confine to individual domains, even though not specifically examined (Fig. 3 of Scala F et al., 2019). The same study also showed that L4 SST cells receive excitatory input from local stellate cells) and is known that they are also directly excited by thalamocortical fibers (Beierlein et al., 2003; Tan et al., 2008), both of which facilitate.

      As shown in our supplementary figure, the divergence is also observed in L2/3 where, as the reviewer also points out, where we do not have a differential distribution of SST cells, at least based on a columnar analysis extending from L4. There are multiple scenarios that could explain this “discrepancy” that one would need to examine further in future studies. One straightforward one is that the divergence in spiking in L2/3 domains may be inherited from L4 domains, where L4 SST act on. Another is that even though L2/3 SST neurons are not biased in their distribution their input-output function is, something which one would need to examine by detailed in vitro electrophysiological and perhaps optogenetic approaches in S1. Despite the distinctive differences that have been found between the L4 circuitry in S1 and V1 (Scala F et al., 2019), recent observations indicate that small but regular patches of V1 marked by the absence of muscarinic receptor 2 (M2) have high temporal acuity (Ji et al., 2015), and selectively receive input from SST interneurons (Meier et al., 2025). Regions lacking M2 have distinct input and output connectivity patterns from those that express M2 (Meier et al., 2021; Burkhalter et al., 2023). These findings, together with ours, suggest that SST cells preferentially innervate and regulate specific domains -columns- in sensory cortices.

      Regardless of the mechanism, the Elfn1 knock-out mouse line almost exclusively affects the incoming excitability onto SST neurons (see also reply to comment below), hence what can be supported by our data is that changing the incoming short-term synaptic plasticity onto these neurons brings the spiking dynamics between barrels and septa closer together.

      The Elfn1 KO mouse model seems too unspecific to suggest the role of the short-term plasticity in SST+ neurons in the differential response to repeated SWS vs MWS stimulation across domains. Why would Elfn1-dependent short-term plasticity in SST+ neurons be specific to a pathway, or a stimulation type (SWS vs MWS)? Moreover, the authors report that Elfn1 knockout alters synapses onto VIP+ as well as SST+ neurons (Stachniak et al., 2021; previous version of this paper)-so why attribute the phenotype solely to SST+ circuitry? In fact, the functional distinctions between barrel and septal domains appear largely abolished in the Elfn1 KO.

      Previous work by others and us has shown that globally removing Elfn1 selectively removes a synaptic process from the brain without altering brain anatomy or structure. This allows us to study how the temporal dynamics of inhibition shape activity, as opposed to inhibition from particular cell types. We will nevertheless update the text to discuss more global implications for SST interneuron dynamics and include a reference to VIP interneurons that contain Elfn1.

      When comparing SWS to MWS, we find that MWS replaces the neighboring excitation which would normally be preferentially removed by short-term plasticity in SST interneurons, thus providing a stable control comparison across animals and genotypes. On average, VIP interneurons failed to show modulation by MWS. We were unable to measure a substantial contribution of VIP cells to this process and also note that the Elfn1 expressing multipolar neurons comprise only ~5% of VIP neurons (Connor and Peters, 1984; Stachniak et al., 2021), a fraction that may be lost when averaging from 138 VIP cells. Moreover, the effect of Elfn1 loss on VIP neurons is quite different and marginal compared to that of SST cells, suggesting that the primary impact of Elfn1 knockout is mediated through SST+ interneuron circuitry. Therefore, even if we cannot rule out that these 5% of VIP neurons contribute to barrel domain segregation, we are of the opinion that their influence would be very limited if any.

      Reviewer #2 (Public review):

      Summary:

      Argunsah and colleagues demonstrate that SST-expressing interneurons are concentrated in the mouse septa and differentially respond to repetitive multi-whisker inputs. Identifying how a specific neuronal phenotype impacts responses is an advance.

      Strengths:

      (1) Careful physiological and imaging studies.

      (2) Novel result showing the role of SST+ neurons in shaping responses.

      (3) Good use of a knockout animal to further the main hypothesis.

      (4) Clear analytical techniques.

      We thank the reviewer for their appreciation of the study.

      Weaknesses:

      No major weaknesses were identified by this reviewer. Overall, I appreciated the paper but feel it overlooked a few issues and had some recommendations on how additional clarifications could strengthen the paper. These include:

      (1) Significant work from Jerry Chen on how S1 neurons that project to M1 versus S2 respond in a variety of behavioral tasks should be included (e.g. PMID: 26098757). Similarly, work from Barry Connor's lab on intracortical versus thalamocortical inputs to SST neurons, as well as excitatory inputs onto these neurons (e.g. PMID: 12815025) should be included.

      We thank the reviewer for these valuable resources that we overlooked. We will include Chen et al. (2015), Cruikshank et al. (2007) and Gibson et al. (1999) to contextualize S1 projections and SST+ inputs, strengthening the study’s foundation as well as Beierlein et al. (2003) which nicely show both local and thalamocortical facilitation of excitatory inputs onto L4 SST neurons, in contrast to PV cells. The paper also shows the gradual recruitment of SST neurons by thalamocortical inputs to provide feed-forward inhibition onto stellate cells (regular spiking) of the barrel cortex L4 in rat.

      (2) Using Layer 2/3 as a proxy to what is happening in layer 4 (~line 234). Given that layer 2/3 cells integrate information from multiple barrels, as well as receiving direct VPm thalamocortical input, and given the time window that is being looked at can receive input from other cortical locations, it is not clear that layer 2/3 is a proxy for what is happening in layer 4.

      We agree with the reviewer that what we observe in L2/3 is not necessarily what is taking place in L4 SST-positive cells. The data on L2/3 was included to show that these cells, as a population, can show divergent responses when it comes to SWS vs MWS, which is not seen in L2/3 VIP neurons. Regardless of the mechanisms underlying it, our overall data support that SST-positive neurons can change their activation based on the type of whisker stimulus and when the excitatory input dynamics onto these neurons change due to the removal of Elfn1 the recruitment of barrels vs septa spiking changes at the temporal domain. Having said that, the data shown in Supplementary Figure 3 on the response properties of L2/3 neurons above the septa vs above the barrels (one would say in the respective columns) do show the same divergence as in L4. This suggests that a circuit motif may exist that is common to both layers, involving SST neurons that sit in L4, L5 or even L2/3. This implies that despite the differences in the distribution of SST neurons in septa vs barrels of L4 there is an unidentified input-output spatial connectivity motif that engages in both L2/3 and L4. Please also see our response to a similar point raised by reviewer 1.

      (3) Line 267, when discussing distinct temporal response, it is not well defined what this is referring to. Are the neurons no longer showing peaks to whisker stimulation, or are the responses lasting a longer time? It is unclear why PV+ interneurons which may not be impacted by the Elfn1 KO and receive strong thalamocortical inputs, are not constraining activity.

      We thank the reviewer for their comment and will clarify the statement.

      This convergence of response profiles was further clear in stimulus-aligned stacked images, where the emergent differences between barrels and septa under SWS were largely abolished in the KO (Figure 4B). A distinction between directly stimulated barrels and neighboring barrels persisted in the KO. In addition, the initial response continued to differ between barrel and septa and also septa and neighbor (Figure 4B). This initial stimulus selectivity potentially represents distinct feedforward thalamocortical activity, which includes PV+ interneuron recruitment that is not directly impacted by the Elfn1 KO (Sun et al., 2006; Tan et al., 2008). PV+ cells are strongly excited by thalamocortical inputs, but these exhibit short-term depression, as does their output, contrasting with the sustained facilitation observed in SST+ neurons. These findings suggest that in WT animals, activity spillover from principal barrels is normally constrained by the progressive engagement of SST+ interneurons in septal regions, driven by Elfn1-dependent facilitation at their excitatory synapses. In the absence of Elfn1, this local inhibitory mechanism is disrupted, leading to longer responses in barrels, delayed but stronger responses in septa, and persistently stronger responses in unstimulated neighbors, resulting in a loss of distinction between the responses of barrel and septa domains that normally diverge over time (see Author response image 1 below).

      Author response image 1.

      A) Barrel responses are longer following whisker stimulation in KO. B) Septal responses are slightly delayed but stronger in KO. C) Unstimulated neighbors show longer persistent responses in KO.

      (4) Line 585 "the earliest CSD sink was identified as layer 4..." were post-hoc measurements made to determine where the different shank leads were based on the post-hoc histology?

      Post hoc histology was performed on plane-aligned brain sections which would allow us to detect barrels and septa, so as to confirm the insertion domains of each recorded shank. Layer specificity of each electrode therefore could therefore not be confirmed by histology as we did not have coronal sections in which to measure electrode depth.

      (5) For the retrograde tracing studies, how were the M1 and S2 injections targeted (stereotaxically or physiologically)? How was it determined that the injections were in the whisker region (or not)?

      During the retrograde virus injection, the location of M1 and S2 injections was determined by stereotaxic coordinates (Yamashita et al., 2018). After acquiring the light-sheet images, we were able to post hoc examine the injection site in 3D and confirm that the injections were successful in targeting the regions intended. Although it would have been informative to do so, we did not functionally determine the whisker-related M1 and whisker-related S2 region in this experiment.

      (6) Were there any baseline differences in spontaneous activity in the septa versus barrel regions, and did this change in the KO animals?

      Thank you for this interesting question. Our previous study found that there was a reduction in baseline activity in L4 barrel cortex of KO animals at postnatal day (P)12, but no differences were found at P21 (Stachniak et al., 2023).

      Reviewer #3 (Public review):

      Summary:

      This study investigates the functional differences between barrel and septal columns in the mouse somatosensory cortex, focusing on how local inhibitory dynamics, particularly involving Elfn1-expressing SST⁺ interneurons, may mediate temporal integration of multi-whisker (MW) stimuli in septa. Using a combination of in vivo multi-unit recordings, calcium imaging, and anatomical tracing, the authors propose that septa integrate MW input in an Elfn1-dependent manner, enabling functional segregation from barrel columns.

      Strengths:

      The core hypothesis is interesting and potentially impactful. While barrels have been extensively characterized, septa remain less understood, especially in mice, and this study's focus on septal integration of MW stimuli offers valuable insights into this underexplored area. If septa indeed act as selective integrators of distributed sensory input, this would add a novel computational role to cortical microcircuits beyond what is currently attributed to barrels alone. The narrative of this paper is intellectually stimulating.

      We thank the reviewer for finding the study intellectually stimulating.

      Weaknesses:

      The methods used in the current study lack the spatial and cellular resolution needed to conclusively support the central claims. The main physiological findings are based on unsorted multi-unit activity (MUA) recorded via low-channel-count silicon probes. MUA inherently pools signals from multiple neurons across different distances and cell types, making it difficult to assign activity to specific columns (barrel vs. septa) or neuron classes (e.g., SST⁺ vs. excitatory).

      The recording radius (~50-100 µm or more) and the narrow width of septa (~50-100 µm or less) make it likely that MUA from "septal" electrodes includes spikes from adjacent barrel neurons.

      The authors do not provide spike sorting, unit isolation, or anatomical validation that would strengthen spatial attribution. Calcium imaging is restricted to SST⁺ and VIP⁺ interneurons in superficial layers (L2/3), while the main MUA recordings are from layer 4, creating a mismatch in laminar relevance.

      We thank the reviewer for pointing out the possibility of contamination in septal electrodes. Importantly, it may not have been highlighted, although reported in the methods, but we used an extremely high threshold (7.5 std, in methods, line 583) for spike detection in order to overcome the issue raised here, which restricts such spatial contaminations. Since the spike amplitude decays rapidly with distance, at high thresholds, only nearby neurons contribute to our analysis, potentially one or two. We believe that this approach provides a very close approximation of single unit activity (SUA) in our reported data. We will include a sentence earlier in the manuscript to make this explicit and prevent further confusion.

      Regarding the point on calcium imaging being performed on L2/3 SST and VIP cells instead of L4. Both reviewer 1 and 2 brought up the same issue and we responded as follows. As shown in our supplementary figure, the divergence is also observed in L2/3 where we do not have a differential distribution of SST cells, at least based on a columnar analysis extending from L4. There are multiple scenarios that could explain this “discrepancy” that one would need to examine further in future studies. One straightforward one is that the divergence in spiking in L2/3 domains may be inherited from L4 domains, where L4 SST act on. Another is that even though L2/3 SST neurons are not biased in their distribution their input-output function is, something which one would need to examine by detailed in vitro electrophysiological and perhaps optogenetic approaches in S1. Despite the distinctive differences that have been found between the L4 circuitry in S1 and V1 (Scala F et al., 2019), recent observations indicate that small but regular patches of V1 marked by the absence of muscarinic receptor 2 (M2) have high temporal acuity (Ji et al., 2015), and selectively receive input from SST interneurons (Meier et al., 2025). Regions lacking M2 have distinct input and output connectivity patterns from those that express M2 (Meier et al., 2021; Burkhalter et al., 2023). These findings, together with ours, suggest that SST cells preferentially innervate and regulate specific domains -columns- in sensory cortices.

      Furthermore, while the role of Elfn1 in mediating short-term facilitation is supported by prior studies, no new evidence is presented in this paper to confirm that this synaptic mechanism is indeed disrupted in the knockout mice used here.

      We thank Reviewer #3 for noting the absence of new evidence confirming Elfn1’s disruption of short-term facilitation in our knockout mice. We acknowledge that our study relies on previously strong published data demonstrating that Elfn1 mediates short-term synaptic facilitation of excitatory inputs onto SST+ interneurons (Sylwestrak and Ghosh, 2012; Tomioka et al., 2014; Stachniak et al., 2019, 2023). These studies consistently show that Elfn1 knockout abolishes facilitation in SST+ synapses, leading to altered temporal dynamics, which we hypothesize underlies the observed loss of barrel-septa response divergence in our Elfn1 KO mice (Figure 4). Nevertheless, to address the point raised, we will clarify in the revised manuscript (around lines 245-247 and 271-272) that our conclusions are based on these established findings, stating: “Building on prior evidence that Elfn1 knockout disrupts short-term facilitation in SST+ interneurons (Sylwestrak and Ghosh, 2012; Tomioka et al., 2014; Stachniak et al., 2019, 2023), we attribute the abolished barrel-septa divergence in Elfn1 KO mice to altered SST+ synaptic dynamics, though direct synaptic measurements were not performed here.”

      Additionally, since Elfn1 is constitutively knocked out from development, the possibility of altered circuit formation-including changes in barrel structure and interneuron distribution, cannot be excluded and is not addressed.

      We thank Reviewer #3 for raising the valid concern that constitutive Elfn1 knockout could potentially alter circuit formation, including barrel structure and interneuron distribution. To address this, we will clarify in the revised manuscript (around line ~271 and in the Discussion) that in our previous studies that included both whole-cell patch-clamp in acute brain slices ranging from postnatal day 11 to 22 (P11 - P21) and in vivo recordings from barrel cortex at P12 and P21, we saw no gross abnormalities in barrel structure, with Layer 4 barrels maintaining their characteristic size and organization, consistent with wild-type (WT) mice (Stachniak et al., 2019, 2023). While we cannot fully exclude subtle developmental changes, prior studies indicate that Elfn1 primarily modulates synaptic function rather than cortical cytoarchitecture (Tomioka et al., 2014). Elfn1 KO mice show no gross morphological or connectivity differences and the pattern and abundance of Elfn1 expressing cells (assessed by LacZ knock in) appears normal (Dolan and Mitchell, 2013).

      We will add the following to the Discussion: “Although Elfn1 is constitutively knocked out, we find here and in previous studies that barrel structure is preserved (Stachniak et al., 2019, 2023). Further, the distribution of Elfn1 expressing interneurons is not different in KO mice, suggesting minimal developmental disruption (Dolan and Mitchell, 2013). Nonetheless, we acknowledge that subtle circuit changes cannot be ruled out without the usage of time-depended conditional knockout of the gene.”

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      (16) Stachniak, T. J., Argunsah, A. Ö., Yang, J. W., Cai, L. & Karayannis, T. (2023). Presynaptic kainate receptors onto somatostatin interneurons are recruited by activity throughout development and contribute to cortical sensory adaptation. J. Neurosci. 43, 7101–7118.

      (17) Sun, Q.-Q., Huguenard, J. R. & Prince, D. A. (2006). Barrel cortex microcircuits: Thalamocortical feedforward inhibition in spiny stellate cells is mediated by a small number of fast-spiking interneurons. J. Neurosci. 26, 1219–1230.

      (18) Sylwestrak, E. L. & Ghosh, A. (2012). Elfn1 regulates target-specific release probability at CA1-interneuron synapses. Science 338, 536–540.

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      (21) Yamashita, T., Vavladeli, A., Pala, A., Galan, K., Crochet, S., Petersen, S. S. & Petersen, C. C. (2018). Diverse long-range axonal projections of excitatory layer 2/3 neurons in mouse barrel cortex. Front. Neuroanat. 12, 33.

    1. Author response:

      Reviewer #1 (Public review):

      The manuscript titled "The distinct role of human PIT in attention control" by Huang et al. investigates the role of the human posterior inferotemporal cortex (hPIT) in spatial attention. Using fMRI experiments and resting-state connectivity analyses, the authors present compelling evidence that hPIT is not merely an object-processing area, but also functions as an attentional priority map, integrating both top-down and bottom-up attentional processes. This challenges the traditional view that attentional control is localized primarily in frontoparietal networks.

      The manuscript is strong and of high potential interest to the cognitive neuroscience community. Below, I raise questions and suggestions to help with the reliability, methodology, and interpretation of the findings.

      Thank you for a nice summary of the key points of our study. Below you will find our responses to your questions.

      (1) The authors argue that hPIT satisfies the criteria for a priority map, but a clearer justification would strengthen this claim. For example, how does hPIT meet all four widely recognized criteria, such as spatial selectivity, attentional modulation, feature invariance, and input integration, when compared to classical regions such as LIP or FEF? A more systematic summary of how hPIT meets these benchmarks would be helpful. Additionally, to what extent are the observed attentional modulations in hPIT independent of general task difficulty or behavioral performance?

      Great suggestions! For the first suggestion, we will include a clearer justification in the revised manuscript. For the second one, all participants received task practice prior to scanning, and task accuracy exceeded 90% (we will explicitly report the accuracy rate in revision), suggesting the tasks were not overly demanding. Although ceiling effects limit the interpretability of behavioral-performance correlations, we argue that higher task demands would likely require greater attentional effort, leading to stronger modulation in hPIT, which aligns with our findings when we manipulated the attentional load.

      (2) The authors report that hPIT modulation is invariant to stimulus category, but there appear to be subtle category-related effects in the data. Were the face, scene, and scrambled images matched not only in terms of luminance and spatial frequency, but also in terms of factors such as semantic familiarity and emotional salience? This may influence attentional engagement and bias interpretation.

      The response of hPIT is generally insensitive to stimulus category, however, the reviewer is correct in noticing that attentional modulation in hPIT is slightly stronger to faces than scenes and scrambled images. Although faces used in the task had neutral expressions and the scene pictures were also neutral, it is indeed possible that potential semantic familiarity or emotional salience may contribute to the subtle category-related effects in the results of experiment 3. This point will be noted in the revised manuscript.

      (3) The result that attentional load modulates hPIT is important and adds depth to the main conclusions. However, some clarifications would help with the interpretation. For example, were there observable individual differences in the strength of attentional modulation? How consistent were these effects across participants?

      Yes, individual differences exist. In the revised manuscript, we will include individual subject data points in the figure 6B.

      (4) The resting-state data reveal strong connections between hPIT and both dorsal and ventral attention networks. However, the analysis is correlational. Are there any complementary insights from task-based functional connectivity or latency analyses that support a directional flow of information involving hPIT? In addition, do the authors interpret hPIT primarily as a convergence hub receiving input from both DAN and VAN, or as a potential control node capable of influencing activity in these networks? Also, were there any notable differences between hemispheres in either the connectivity patterns or attentional modulation?

      We agree that besides resting-state connection, task-based functional connectivity analyses would have the potential to provide additional information about whether hPIT serves as a convergence node or a control hub. While fMRI data are not the best to generate directional flow of information due to the low temporal resolution, we will conduct task-based functional connectivity analyses.

      We also observed modest hemispheric asymmetries in connectivity—for instance, both left and right hPIT showed stronger connectivity with right-hemisphere attention nodes. This will be described in the revised supplement.

      (5) A few additional questions arise regarding the anatomical characteristics of hPIT: How consistent were its location and size across participants? Were there any cases where hPIT could not be reliably defined? Given the proximity of hPIT to FFA and LOp, how was overlap avoided in ROI definition? Were the functional boundaries confirmed using independent contrasts?

      The size and location of hPIT are generally consistent across subjects, as shown in Supplementary Figure 1. The consistency is also supported by figure 4C. The hPIT is defined by conjunction maps across three tasks and then manually delineated avoiding overlapping voxels with FFA and LOp. The FFA was defined using an independent contrast (Exp3 contrast [face-scene]) and the Lop location was defined by anatomical parcellation (Glasser et al., 2016).

      Reviewer #2 (Public review):

      Summary

      This study investigates the role of the human posterior inferotemporal cortex (hPIT) in attentional control, proposing that hPIT serves as an attentional priority map that integrates both top-down (endogenous) and bottom-up (exogenous) attentional processes. The authors conducted three types of fMRI experiments and collected resting-state data from 15 participants. In Experiment 1, using three different spatial attention tasks, they identified the hPIT region and demonstrated that this area is modulated by attention across tasks. In Experiment 2, by manipulating the presence or absence of visual stimuli, they showed that hPIT exhibits strong attentional modulation in both conditions, suggesting its involvement in both bottom-up and top-down attention. Experiment 3 examined the sensitivity of hPIT to stimulus features and attentional load, revealing that hPIT is insensitive to stimulus category but responsive to task load - further supporting its role as an attentional priority map. Finally, resting-state functional connectivity analyses showed that hPIT is connected to both dorsal and ventral attention networks, suggesting its potential role as a bridge between the two systems. These findings extend prior work on monkey PITd and provide new insights into the integration of endogenous and exogenous attention.

      Strengths

      (1) The study is innovative in its use of specially designed spatial attention tasks to localize and validate hPIT, and in exploring the region's role in integrating both endogenous and exogenous attention, as prior works focus primarily on its involvement in endogenous attention.

      (2) The authors provided very comprehensive experiment designs with clear figures and detailed descriptions.

      (3) A broad range of analyses was conducted to support the hypothesis that hPIT functions as an attentional priority map -- including experiments of attentional modulation under both top-down and bottom-up conditions, sensitivity to stimulus features and task load, and resting-state functional connectivity. These analyses showed consistent results.

      (4) Multiple appropriate statistical analyses - including t-tests, ANOVAs, and post-hoc tests - were conducted, and the results are clearly reported.

      Thank you for a nice summary of the key points and strengths of our study.

      Weaknesses

      (1) The sample size is relatively small (n = 15), and inter-subject variability is big in Figures 5 and 6, as seen in the spread of individual data points and error bars. The analysis of attention-modulated voxel map intersections appears to be influenced by multiple outliers.

      We agree that the sample size (n = 15) is not ideal, and we acknowledge that some data points in Figures 5 and 6 appear to be potential outliers. However, according to conventional outlier detection criteria, all data points are within three standard deviations of the group mean and were therefore retained for analysis. Moreover, the attention-modulated voxel intersection map shown in Figure 4C is insensitive to outliers, because the intersection map plotted is based on the number of subjects.

      (2) The authors acknowledge important limitations, including the lack of exploration of feature-based attention and the temporal constraints inherent to fMRI.

      Yes, we hope to address these limitations in future studies.

      (3) Prior research has established that regions such as the prefrontal cortex (PFC) and posterior parietal cortex (PPC) are involved in both endogenous and exogenous attention and have been proposed as attentional priority maps. It remains unclear what is uniquely contributed by hPIT, how it functionally interacts with these classical attentional hubs, and whether its role is complementary or redundant. The study would benefit from more direct comparisons with these regions.

      In this study, we define the ROI base on intersection across three different types of spatial attention tasks, and the hPIT stands out in showing spatial attentional modulation across tasks. This could be due to the weak lateralized responses in PFC/PPC. To evaluate whether a region qualifies as a priority map, we applied four criteria (as mentioned in introduction). While dorsal and ventral attention network (DAN and VAN) regions can be considered important components of the priority map system, our findings suggest that among the regions tested, hPIT meets all four criteria. In Experiment 2, we included regions such as VFC (as part of PFC) and IPS (as part of PPC), and our findings suggest these areas are more involved in top-down attention. We agree with the reviewer’s suggestion and will perform additional analysis on PPC and PFC.

      (4) The functional connectivity analysis is only performed on resting-state data, and this approach does not capture context-dependent interactions. Task-based data analysis can provide stronger evidence.

      We acknowledge that resting-state FC is limited in assessing task-specific communication. To further investigate the role of hPIT, we plan to conduct task-based functional connectivity analyses.

      (5) The study does not report whether attentional modulation in hPIT is consistent across the two hemispheres. A comparison of hemispheric effects could provide important insight into lateralization and inter-individual variability, especially given the bilateral localization of hPIT.

      We thank the reviewer for this suggestion. hPIT was localized bilaterally using the same intersection-based method in Experiment 1. We have now performed additional analysis and found in Experiment 3, the difference in attentional modulation between high and low load conditions was significant in the right hPIT but not in the left. This result will be reported in the revised manuscript.

    1. Author response:

      Below, we will address point by point any and all concerns of the reviewers.

      Reviewer #1:

      There are no major concerns, but some material could be added for clarity and to make the work more accessible to a more general scientific audience.

      We will add text for clarity and to make the work more accessible to a general audience per this comment and similar suggestions of the other reviewers.

      (1.1) A figure clearly showing the habituation protocol and the use of the dishabituators would be a good addition, even if the procedure has been done before and is cited. There can always be readers who are seeing this for the first time.

      We do think this is a good idea as the time scales of the experiment will be clearly marked as well and we plan to generate one in the revised manuscript.

      (1.2) It would also be nice to comment on other ways dishabituation can happen (for example, when the stimulus is removed for a short time and returns) and what their time scales are.

      If the stimulus is withheld, spontaneous recovery occurs, a process distinct from dishabituation and worth exploring on its own. In a previous publication (Semelidou et al. eLife 2018;7:e39569), we have shown that in this habituation paradigm with 4 min exposure either to the aversive Octanol, or the attractive Ethyl Acetate, spontaneous recovery occurs on or after 6 minutes after the habituated stimulus is withheld. This contrasts the immediate effect of the single dishabituating stimulus, delivered for a few seconds at the end of exposure to the habituator. Granted that per Thomson (Neurobiol Learn Mem. 2009), spontaneous recovery is a characteristic of habituation, we will work this point in the text.

      (1.3) And more generally, the paper could perhaps improve by making a stronger case for why the results are important not just for flies but for neuroscience in general.

      Thank you for the encouragement. We will try to rationally generalize our findings.

      Reviewer #2:

      (2.1) However, the claim that this represents a fundamental difference between homosensory and heterosensory pathways for dishabituation is overstated.

      We had no intention of stating more than the fact that footshock and yeast odor dishabituators relay these stimuli to the mushroom bodies via distinct dopaminergic neurons, hence differentiating distinct dishabituating stimuli via the mechanosensory (footshock) and olfactory (yeast odor) modalities as they engage the mushroom bodies. As the reviewer suggests we will use more measured and specific language to state the above.

      (2.2) The introductory section does not adequately present current broad models for habituation and dishabituation.

      This was not done intentionally, but rather because we aimed at a less extended introductory section and ostensibly this resulted in brief and possibly inadequate presentation of current habituation models. We will present a much more detailed introduction and detail of habituation and dishabituation models in the revised manuscript (Also see reply to point 3.5 below).

      (2.3) There are many different time scales, even for Drosophila olfactory habituation. These, as well as potential underlying mechanistic differences, need to be acknowledged; any claim should be specifically qualified for the time scales being studied here.

      We understand and appreciate the point of the reviewer, as well as its significance and we will address this both in the revised text, but also by the paradigm figure we will add as stated above (point 1.1), where the time scales will be explicitly included and emphasized.

      (2.4) Additionally, there are several unclear, vague, and inaccurate sections and statements. A more careful, precise, and considered presentation of current views, as well as more measured claims of the impact of the findings, would substantially enhance my enthusiasm.

      We will address these concerns of course, though pointing out the specific offending parts would ascertain addressing them thoroughly. As stated above, we will incorporate current views in the introduction and when discussing our results and their impact.

      Reviewer #3:

      (3.1) The key issue is that the main concepts of this manuscript appear to be based on a misunderstanding/misinterpretation of the literature. As the authors set out to settle the debate "whether the novel dishabituating stimulus elicits sensitization of the habituated circuits, or it engages distinct neuronal routes to bypass habituation reinstating the naïve response", it seems that the authors based their investigation on the premise that "sensitization" is mediated by a facilitatory process within the S-R pathway, and "dishabituation" by a facilitatory process outside the S-R pathway. This is not the status quo in the field, particularly with the prevailing theory like the Dual-Process Theory.

      We appreciate the reviewer’s comment and the opportunity to clarify the conceptual framework of our work. Our intention was in fact to test the Groves and Thomson hypothesis (Neurobiol Learn Mem. 2009), in our olfactory habituation system. As such, dishabituation could have been the result of a facilitatory process within the S-R pathway, or from mechanisms outside of it. Our experimental design allowed to distinguish these possibilities and our results clearly show that dishabituation involves circuitry outside the S-R pathway. We do thank the reviewer for pointing out that we have not articulated clearly this intention and we will take care to communicate this effectively in the revised manuscript.

      (3.2) The original version of Dual-Process Theory (Groves and Thompson 1970, but also see Thompson 2008, Neurobiol Learn Mem) already hypothesized that habituation happens within the specific S-R pathway, and sensitization occurs separately in an "organism-wide" state system that modulates the output of all S-R pathways.

      As mentioned above, we are aware of the Dual-Process hypothesis. In fact, our data demonstrate that activity outside the olfactory S-R pathway, engaging novel neuronal circuits, mediates dishabituation. Unlike habituation, these circuits mediating dishabituation include at minimum, the mushroom bodies, the dopaminergic system and the APL neurons. In our view this does not support the “organism-wide state” system, but rather particular circuits that in agreement with the Groves and Thomson hypothesis, are outside the S-R pathway and modulate its behavioral output. We will work these concepts in the discussion section of the revised manuscript.

      (3.3) Dishabituation is recognized by the Dual-Process Theory as sensitization (organism-wide facilitation) manifested on top of existing habituation (depressed S-R pathway). This notion has been supported by a wide range of studies, including cat spinal cord reflex (e.g. Spencer et al. 1966) and work in Aplysia on heterosynaptic facilitation for both sensitization and dishabituation. Therefore, simply showing that the newly identified facilitatory pathways are outside the S-R habituation pathway is insufficient to demonstrate dishabituation.

      We respectfully disagree with the concluding sentence here. In all of our experiments, we observe a clear recovery of olfactory avoidance after exposure to the footshock, or yeast odor dishabituators. Moreover, the dishabituators are emulated by (photo)activation of particular neuronal circuits and the recovery of olfactory avoidance is blocked when these circuits are silenced. Regardless of whether this recovery is classified as dishabituation via sensitization or another facilitatory process, the key point is that the habituated response is reliably reinstated contingent upon the dishabituating stimulus. We believe this meets the established criteria for dishabituation.

      (3.4) As behavioral facilitation of a habituated response can be achieved by dishabituating (specific recovery of the S-R pathway) and/or superimposed sensitizing (organism-wide) processes, dishabituation and sensitization of this olfactory response must be first dissociated; however, the study provided no evidence for the dissociation. Without this piece of evidence, the claim of this paper that the newly identified pathways mediate dishabituation is not fully supported.

      We agree with the reviewer that we have not provided specific evidence dissociating dishabituation and sensitization of the particular olfactory response beyond the evidence implicating particular circuitry in the outcome of facilitation of the olfactory response.

      It should be noted that in photoactivation of the implicated circuitries in naïve flies, we do not observe enhanced octanol avoidance, suggesting that activation of these circuits alone does not induce sensitization. Moreover, our results show that neither footshock nor yeast odor drive an organism-wide sensitization, as silencing specific circuits was sufficient to block dishabituation—something that would not be expected if a global sensitization process was responsible of reinstating the olfactory response.

      Nonetheless, we will also attempt to dissociate sensitization from dishabituation using mutants previously reported deficient in sensitization (Duerr and Quinn, PNAS 1982), assuming these mutants retain normal olfactory habituation. We will also try sensitization protocols in the case of within-modal dishabituation to further clarify the underlying mechanisms. In principle, this includes using diluted Octanol as the habituating stimulus and attempt dishabituation with concentrated octanol.

      (3.5) The literature review of this manuscript has some discrepancies. In the introduction, the authors wrote "initial studies in Aplysia were consistent with the "dual-process theory" (Groves and Thompson 1979), where response recovery due to dishabituation appeared to result from sensitization superimposed on habituation, thus driving reversal of the attenuated response (Carew, Castellucci et al. 1971, Hochner, Klein et al. 1986, Marcus, Nolen et al. 1988, Ghirardi, Braha et al. 1992, Cohen, Kaplan et al. 1997, Antonov, Kandel et al. 1999, Hawkins, Cohen et al. 2006)." Hochner 1986 and Marcus 1988 in fact indicated otherwise. Hochner 1986 suggests that dishabituation and sensitization involve different molecular processes, while Marcus 1988 showed that dishabituation and sensitization have different behavioral characteristics. Therefore, the authors' statement is not supported by the cited literature.

      We are grateful to the reviewer for pointing out these significant discrepancies, consequent of multiple rounds of edits followed by our own oversight. These important publications for this manuscript will be referenced properly in the revised version of the manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary: 

      Beyond what is stated in the title of this paper, not much needs to be summarized. eIF2A in HeLa cells promotes translation initiation of neither the main ORFs nor short uORFs under any of the conditions tested. 

      Strengths: 

      Very comprehensive, in fact, given the huge amount of purely negative data, an admirably comprehensive and well-executed analysis of the factor of interest. 

      Weaknesses: 

      The study is limited to the HeLa cell line, focusing primarily on KO of eIF2A and neglecting the opposite scenario, higher eIF2A expression which could potentially result in an increase in non-canonical initiation events. 

      We thank the reviewer for the positive evaluation. As suggested by the reviewer in the detailed recommendations, we will clarify in the title, abstract and text that our conclusions are limited to HeLa cells. Furthermore, as suggested we will test the effect of eIF2A overexpression on the luciferase reporter constructs, and will upload a revised manuscript.

      Reviewer #2 (Public review):

      Summary 

      Roiuk et al describe a work in which they have investigated the role of eIF2A in translation initiation in mammals without much success. Thus, the manuscript focuses on negative results. Further, the results, while original, are generally not novel, but confirmatory, since related claims have been made before independently in different systems with Haikwad et al study recently published in eLife being the most relevant. 

      Despite this, we find this work highly important. This is because of a massive wealth of unreliable information and speculations regarding eIF2A role in translation arising from series of artifacts that began at the moment of eIF2A discovery. This, in combination with its misfortunate naming (eIF2A is often mixed up with alpha subunit of eIF2, eIF2S1) has generated a widespread confusion among researchers who are not experts in eukaryotic translation initiation. Given this, it is not only justifiable but critical to make independent efforts to clear up this confusion and I very much appreciate the authors' efforts in this regard.  

      Strengths 

      The experimental investigation described in this manuscript is thorough, appropriate and convincing. 

      Weaknesses 

      However, we are not entirely satisfied with the presentation of this work which we think should be improved. 

      We thank the reviewer for the positive evaluation. We will revise the manuscript according to the reviewer's suggestions made in the detailed recommendations.

      Reviewer #3 (Public review):

      Summary: 

      This is a valuable study providing solid evidence that the putative non-canonical initiation factor eIF2A has little or no role in the translation of any expressed mRNAs in cultured human (primarily HeLa) cells. Previous studies have implicated eIF2A in GTP-independent recruitment of initiator tRNA to the small (40S) ribosomal subunit, a function analogous to canonical initiation factor eIF2, and in supporting initiation on mRNAs that do not require scanning to select the AUG codon or that contain near-cognate start codons, especially upstream ORFs with non-AUG start codons, and may use the cognate elongator tRNA for initiation. Moreover, the detected functions for eIF2A were limited to, or enhanced by, stress conditions where canonical eIF2 is phosphorylated and inactivated, suggesting that eIF2A provides a back-up function for eIF2 in such stress conditions. CRISPR gene editing was used to construct two different knockout cell lines that were compared to the parental cell line in a large battery of assays for bulk or gene-specific translation in both unstressed conditions and when cells were treated with inhibitors that induce eIF2 phosphorylation. None of these assays identified any effects of eIF2A KO on translation in unstressed or stressed cells, indicating little or no role for eIF2A as a back-up to eIF2 and in translation initiation at near-cognate start codons, in these cultured cells. 

      The study is very thorough and generally well executed, examining bulk translation by puromycin labeling and polysome analysis and translational efficiencies of all expressed mRNAs by ribosome profiling, with extensive utilization of reporters equipped with the 5'UTRs of many different native transcripts to follow up on the limited number of genes whose transcripts showed significant differences in translational efficiencies (TEs) in the profiling experiments. They also looked for differences in translation of uORFs in the profiling data and examined reporters of uORF-containing mRNAs known to be translationally regulated by their uORFs in response to stress, going so far as to monitor peptide production from a uORF itself. The high precision and reproducibility of the replicate measurements instil strong confidence that the myriad of negative results they obtained reflects the lack of eIF2A function in these cells rather than data that would be too noisy to detect small effects on the eIF2A mutations. They also tested and found no evidence for a recent claim that eIF2A localizes to the cytoplasm in stress and exerts a global inhibition of translation. Given the numerous papers that have been published reporting functions of eIF2A in specific and general translational control, this study is important in providing abundant, high-quality data to the contrary, at least in these cultured cells. 

      Strengths: 

      The paper employed two CRISPR knock-out cell lines and subjected them to a combination of high-quality ribosome profiling experiments, interrogating both main coding sequences and uORFs throughout the translatome, which was complemented by extensive reporter analysis, and cell imaging in cells both unstressed and subjected to conditions of eIF2 phosphorylation, all in an effort to test previous conclusions about eIF2A functioning as an alternative to eIF2. 

      Weaknesses: 

      There is some question about whether their induction of eIF2 phosphorylation using tunicamycin was extensive enough to state forcefully that eIF2A has little or no role in the translatome when eIF2 function is strongly impaired. Also, similar conclusions regarding the minimal role of eIF2A were reached previously for a different human cell line from a study that also enlisted ribosome profiling under conditions of extensive eIF2 phosphorylation; although that study lacked the extensive use of reporters to confirm or refute the identification by ribosome profiling of a small group of mRNAs regulated by eIF2A during stress. 

      We thank the reviewer for the positive evaluation. We will revise the manuscript according to the recommendations made in the detailed recommendations. Regarding the two points mentioned here:

      (1) The reason eIF2alpha phosphorylation does not increase appreciably is because unfortunately the antibody is very poor. The fact that the Integrated Stress Response (ISR) is induced by our treatment can be seen, for instance, by the fact that ATF4 protein levels increase strongly (in the very same samples where eIF2alpha phosphorylation does not increase much, in Suppl. Fig. 5E). We will strengthen the conclusion that the ISR is indeed activated with additional experiments/data as suggested by the reviewer.

      (2) We agree that our results are in line with results from the previous study mentioned by the reviewer, so we will revise the manuscript to mention this other study more extensively in the discussion.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) I suggest to state (already in the abstract, but perhaps also even in the title, definitely in the rest of the paper) that this analysis is limited to the HeLa cell line. 

      As suggested, we have now specified in both the title and the abstract that the work is done in HeLa cells.

      (2) In my view, it is a pity that the authors - given the tools are available - did not check the impact of high eIF2A levels on expression of individual mRNAs under normal and stress conditions. I am not suggesting to repeat ribo-seq in this setup, it would be too much to ask for, but re-examining some of the many reporters the authors generated with eIF2A overexpressed may point to some function, e.g. increased number of non-canonical initiation events (non-AUG-initiated)? If anything, the use of HeLa and the primary focus on eIF2A KO neglecting the prospective impact of eIF2A overexpression should be mentioned as two main limitations of this study. 

      We thank the reviewer for the good suggestion to test our synthetic reporters with eIF2A overexpression. New Suppl. Fig. 4G now shows that overexpression of eIF2A does not affect translation of synthetic reporters carrying an ATG start codon in different initiation contexts, or carrying near-cognate start codons, in agreement with a lack of effect on translation which we previously observed with loss of eIF2A.

      (3) Ribo-seq with eIF2A. Did the authors focus on ORFs that are known, or whose isoforms are known, to be non-AUG initiated? Would the loss of eIF2A decrease FPs in their CDSes under at least some conditions?

      We have now assessed the read distribution on the eIF4G2 transcript in both the control and tunicamycin conditions ( Author response image 1). In our hands, eIF4G2 is one of the best examples of non-AUG initiation in human cells, since the main coding sequence starts with GTG and the CDS is well translated. Nonetheless, we do not observe any significant changes in read distribution (panels A-B) or overall translation efficiency of eIF4G2 upon eIF2A loss (panels C-D).

      Author response image 1.

      (A-B) Average reads occupancy on the eIF4G2 (ENST0000339995) transcript in DMSO treated (panel A, n=3) or tunicamycin treated samples (panel B, n=2) derived from either control (black) or eIF2A-KO (red) HeLa cells. Reads counts were normalized to sequencing depth and averaged between either 3 (DMSO-treated) or 2 (tunicamycin-treated) replicates. Graphs were then smoothened with a sliding window of 3 nt. (C-D) The total number of reads mapping to the eIF4G2 CDS, normalized to library sequencing depth per replica was quantified. No significant difference between control and eIF2A-KO cells was observed in either DMSO treated (panel C) or tunicamycin treated (panel D) cells. Significance by unpaired, two-sided, t-test. ns = not significant.

      Thank you for giving me the opportunity to review this article.

      Reviewer #2 (Recommendations for the authors):

      While some of our suggestions below may be considered subtle, in our opinion they are important and it would be good if the authors consider them for their revision, we also have a couple of technical suggestions. 

      (1) Abstract. 

      The authors failed to identify the role of eIF2A in translation initiation and have provided compelling evidence that eIF2A is not involved in recognition of non-AUG codons as start codons nor in recruitment of initiator tRNA during stress conditions which are two activities most commonly misattributed to eIF2A. However, they have not exhausted all possible potential functions of eIF2A, see below, it is also possible that eIF2A may have a role not yet suggested by anyone and it may function in translation initiation in special circumstances that have not been tested yet. The authors indeed discuss such possibility in the Discussion section. Given that there is genetic evidence (that is unaffected by biochemical impurities) linking eIF2A to other initiation factors (5B and 4E), we are not yet convinced that eIF2A does not have any role in translation initiation and therefore we find the last sentence of the abstract premature. We suggest to soften this statement into something like this: whether eIF2A has any role in translation remains unknown, it may even have a role in a different aspect of RNA Biology. 

      We agree with the reviewer. We changed the last sentence of the abstract to read as follows:

      “It is possible that eIF2A plays a role in translation regulation in specific conditions that we have not tested here, or that it plays a role in a different aspect of RNA biology.”

      (2) Recently eIF2A has been implicated in ribosomal frameshifting, see Wei et al 2023 DOI: 10.1016/j.celrep.2023.112987 

      Could authors look into PEG10 mRNA ribosome profile to see if there are detectable statistically significant changes in footprint density downstream of frameshift site between WT and eIF2A Kos? It is likely that the coverage will be insufficient to give a definitive answer, but it is worth checking, it would be a pity to miss it. 

      We thank the reviewer for this suggestion. We have now looked at the distribution of ribosome footprints on the PEG10 transcript variant that is expressed in HeLa cells (ENST00000482108) and indeed observe coverage downstream of the annotated stop codon, consistent with a frameshifting event that results in an extended protein isoform being translated. Visual assessment of the read distribution between the main ORF and the "ORF extension" does not show a substantial difference between control and eIF2A knock-out cells ( Author response image 2A-B). Additionally, we quantified the ratio of reads mapping to the PEG10 ORF upstream of the slippery site versus those mapping downstream, extending into the predicted longer protein. Nonetheless, we could not detect significant changes between control and eIF2A-KO cells in either tested condition ( Author response image 2C-D).

      Author response image 2.

      (A-B) Average reads occupancy on the PEG10 (ENST00000482108) transcript in DMSO treated (panel A, n=3) or tunicamycin treated samples (panel B, n=2) derived from either control (black) or eIF2A-KO (red) HeLa cells are shown. Reads counts were normalized to sequencing depth and averaged between either 3 (DMSO-treated) or 2 (tunicamycin-treated) replicates. Graphs were then smoothened with a sliding window of 3 nt. (C-D) The ratio of reads mapping to the ORF upstream of the slippery site to reads mapping to the predicted extended protein downstream to the slippery site is shown. Reads counts were normalized to the sequencing depth. Neither DMSO treated samples (panel C) nor tunicamycin treated samples (panel D) had a significant difference between control and eIF2A-KO cells. Significance by unpaired, two-sided, t-test. ns = not significant.

      (3) Introduction 

      Given the volume of unreliable claims regarding eIF2A in the literature and the overall confusion it is very difficult (may even be impossible) to write a clear coherent introduction into the topic. Nonetheless, there are few points that need to be taken into account. 

      The authors state that eIF2A is capable to recruit initiator tRNA citing Zoll et al 2002. This activity was later shown to be a biochemical artefact (which was most likely reproduced by Kim et al 2018), eIF2A fraction was contaminated with eIF2D which does bind tRNAs in GTP-independent manner. eIF2A purified from RRL separates from initiator tRNA binding activity, see Dmitriev et al 2010 DOI: 10.1074/jbc.M110.119693. This point is also relevant to the second paragraph of Discussion, it should be acknowledged that it has been shown previously that eIF2A does not bind the initiator tRNA.

      We appreciate the advice provided by the reviewer. We have modified both the introduction and the 2nd paragraph of the discussion to reflect that the tRNA-binding activity is due to contaminating eIF2D rather than eIF2A.

      In many cases the authors describe certain claims as facts even though they refute them themselves. For example 

      "Such eIF2A-driven non-AUG initiation events were shown to play a crucial role in different aspects of cell physiology and disease progression: cellular adaptation during the integrated stress response (Chen et al., 2019; Starck et al., 2016)"  While non-AUG initiation events do play crucial roles in different aspects of cell physiology (reviewed in Andreev et al 2023 doi: 10.1186/s13059-022-02674-2) eIF2A has nothing to do with it as the authors show themselves. Therefore different language should be used, e.g.. "eIF2A has been suggested (or proposed or reported) to be responsible for non-AUG initiation events that were shown to play ..." 

      The word "shown" is used in many other instances for the claims that the authors refute. "Shown" is only appropriate for strong evidence that leaves little doubt. 

      We agree with the reviewer and made the suggested changes in the text.

      (4) Supplementary Fig. 1. 

      Panel C is used to argue that eIF2A has a higher concentration than in the nucleus, perhaps it is worth explaining how this conclusion was drawn. If levels in cytoplasm are comparable to GAPDH and Tubulin but less than c-Myc in nucleus does it really mean that there is less eIF2A in the nucleus than in cytoplasm? This is not obvious to us. Also, presumably WCL stands for Whole Cell Lysate, it would be nice to introduce this abbreviation somewhere. 

      To compare levels of eIF2A in the nuclear and cytosolic fractions, we lysed the two fractions in equal volumes of buffer (i.e. the cytosolic fraction was extracted in 200 µl of hypotonic buffer, and the nuclear fraction was extracted in 200 µl of cell extraction buffer). This assures that per microliter of lysate we have the same number of "cytosols" or nuclei. Hence, equal intensity bands in the cytosolic and nuclear fractions would mean that half of the protein is in the nucleus and half is in the cytosol. We originally described this in the Methods section, but now also mention it in the Results and in the figure legend.

      We replaced WCL with "whole cell" in the figure. 

      (5) The differential translation analysis is described very briefly "To obtain values of translation efficiency, log2 fold changes, and adjusted p values the DESeq2 software package was used". Was TE calculated based on ribosome footprint to RNA-seq ratios? How exactly DESeq2 was used here? TE measured in this way spuriously correlates with RNA-seq values, see Larsson et al 2010 DOI: 10.1073/pnas.1006821107, perhaps it would be worse assessing differential translation with anota2seq (Oertlin et al 2019 doi: 10.1093/nar/gkz223.)? Anota2seq avoids calculating the ratios and enables comprehensive analysis of differential translation including detection of buffered translation which might be the case here while avoiding artefacts that may arise from varying RNA levels.  

      We now specified in more detail in the Methods section how we analyzed the data. Indeed, the DeSeq2 was used on translation efficiency values, which we calculated as the ratio of ribosome footprints to RNA-seq. 

      As suggested, we have now also performed the analysis using anota2seq (Suppl. Fig. 3C) and this analysis identified zero transcripts that are translationally regulated, in agreement with our analysis.

      (6) Section "eIF2a-inactivating stresses do not redirect tRNA delivery function to eIF2A." 

      The description of ISR mechanism is a bit inaccurate. Strictly speaking eIF2alpha phosphorylation does not inactivate it eIF2alpha. It results in formation of a very stable eIF2*GDP*eIF2B complex, thus severely depleting eIF2B which serves as a GEF for eIF2. This in turn reduces the ternary complex (eIF2*GTP*tRNAi) concentration since there is no free eIF2B to exchange GDP for GTP. Without getting into much detail, we think it would be more accurate to say that eIF2alpha phosphorylation leads to ternary complex depletion instead of saying that stress inactivates eIF2alpha. 

      We agree with the reviewer - we were trying to use simple, compact wording. We have now reworded the section title to "No detectable role for eIF2A in translation when eIF2 is inhibited" and rephrased the subsequent text to be correct.

      Also the subtitle uses eIF2a with small a that stands for alpha which potentially could lead to substantial confusion since in this case the difference between eIF2alpha and eIF2A is only in capitalisation of the last letter, many text-mining engines such as modern LLMs may not be able to pick the differences. Perhaps it would be better to refer to eIF2alpha by the HGNC approved name of its gene - eIF2S1 to avoid further confusions. For clarity it may be stated at the beginning that eIF2S1 is commonly known as eIF2alpha. 

      We thank the reviewer for this point. We have removed all instances of eIF2a (with lowercase a) from the manuscript to avoid this source of confusion. In the first instance of eIF2a we also added the official HGNC gene name. However, we prefer to use eIF2a instead of eIF2S1 because people outside the translation field tend to know the subunit as eIF2a, and we think it is important that also people outside the translation field read this manuscript, since some of the questionable papers on eIF2A come from labs working at the interface between translation and other fields.

      Minor 

      Introduction 

      (7) "uses the CAT anticodon" change CAT to CAU 

      We corrected CAT to CAU

      (8) "In the canonical initiation pathway", change "canonical" to "most common", canonical is somewhat a judgemental statement that originates in theology. Same applies to numerous occurrences of "canonical AUG", simply using "AUG" would be simpler and more accurate as you will avoid giving impression that there are "non-canonical AUGs".  

      Done.

      (9) "eIF2A was initially considered to be a functional analogue of prokaryotic IF2 (Merrick and Anderson, 1975), however later this role was reassigned to the above-mentioned heterotrimeric factor eIF2 (a,b,g) (Levin et al., 1973)." - there is a chronological contradiction within this sentence, the initial consideration is attributed to 1975 while its later reassignment to 1973. 

      We are grateful to the reviewer for spotting this mistake. There was a citation problem; we fixed it and now cite the correct paper for the initial discovery of eIF2A to PMID 5472357 (Shafritz et al 1970).

      (10) "On the other hand, studies on the role of eIF2A on viral IRES translation have arrived at conflicting results." Remove "On the other hand" since conflicting results have been mentioned above. In fact the entire sentence is somewhat redundant given prior "For example, eIF2A has been studied in the context of internal ribosome entry sites (IRES), where it was found to act both as a suppressor and an activator of IRESmediated initiation."  

      We have rewritten the paragraph to make it more coherent.

      (11) Fig. 1. C-D. is using CHX abbreviation for cycloheximide, this need to be mentioned on the legend or elsewhere in the text. Otherwise CHX may not be clear for a reader uninitiated in ribosome profiling. 

      We now mention in the figure legend that CHX stands for cycloheximide and indicate that it was used as a negative control to block translation. 

      (12) Page 7, section "Ribosome profiling reveals a few eIF2Adependent transcripts" 

      In this section you describe ribosome profiling experiments and identify few transcripts whose translation seems to be changing based on ribosome profiling data. Then you attempt to verify them using gene expression reporters and reasonably suggest that these are false positives. In essence this section argues that there are no eIF2A-dependent transcripts, therefore the title of this subsection is misleading, it makes sense to rename it so that it better reflects the content of this section. 

      We agree and have renamed the section to "Ribosome profiling identifies no eIF2Adependent transcripts"

      (13) Page 8, top. Rephrase "To do this, we performed ribosome profiling on control and eIF2AKO cells, which sequences the mRNA footprints protected by ribosomes."  

      Fixed.

      (14) Page 10, bottom. "Several studies have reported that eIF2A can delivery alternative initiator tRNAs to uORFs with nearcognate start codons". Change "delivery" to "deliver". 

      Thanks for spotting it. We corrected to “deliver”

      (15) Page 13 "This suggests that, as in non-stressed conditions, eIF2A has a minimal effect on global translation also when eIF2a activity is low." - rephrase to avoid impression that eIF2alpha activity is low in normal conditions, also please see comment #6 above. 

      We fixed this sentence to read: “This suggests that, as in non-stressed conditions, eIF2A has a minimal effect on global translation also when the integrated stress response is active.”

      Reviewer #3 (Recommendations for the authors):

      - The experimental data in Fig. S5E do not support the claim of increased eIF2 phosphorylation on TM treatment; although, comparing Fig. S5A with Fig. 1B supports a marked reduction in bulk translation and the reporter data in Fig. 4A show the expected induction of the uORF-containing reporters by TM. Because these are the conditions employed for ribosome profiling in stress conditions shown in Fig. 4B, it would be reassuring to document TM-induced translational efficiencies of ATF4 and the other known mRNAs resistant to eIF2 phosphorylation in the ribosome profiling data, including gene browser images of the replicate experiments. If the induction of TEs by TM for such mRNAs was not robust, it would be valuable to repeat the analysis using arsenite (SA) treatment, which produces a greater inhibition of bulk translation. 

      Unfortunately, the eIF2alpha antibody is not very good and also detects the nonphosphorylated protein, causing high background and poor apparent induction in response to tunicamycin. The fact that the ISR was activated is visible from the induction of ATF that was assessed by western blot in the Suppl. Fig. 5E. To ensure that our ribosome profiling libraries also recorded the activation of ISR we built single gene plots for ATF4 both in control and HeLa eIF2A-KO cell. As shown in  Author response image 3 A&B in both cell lines tunicamycin treatment led to the induction of ATF4. This can also be seen by the 4-fold induction in ATF4 translation efficiency in response to tunicamycin in both WT and eIF2A-KO cells ( Author response image 3C). Additionally, we checked that another marker induced by tunicamycin, HSPA5, is also translationally upregulated in both cell lines, as well as the downstream target of ATF4 – PPP1R15B. ( Author response image 3C). 

      Author response image 3.

      (A-B) Average read occupancy on the ATF4 (ENST00000674920) transcript in DMSO treated (n=3) or tunicamycin treated samples (n=2) derived from either control (panel A) or eIF2A-KO (panel B) HeLa cells are shown. Read counts were normalized to sequencing depth and averaged between either 3 (DMSO-treated) or 2 (tunicamycin-treated) replicates. Graphs were then smoothened with a sliding window of 3 nt. (C) Scatter plot of log2(fold change) of Translation Efficiency TM/DMSO for control cells on the xaxis versus eIF2AKO cells on the y-axis. The induction of ATF4 as well as the downstream target PPP1R15B are shown. The upregulation of HSP5A translation, the other hallmark of ER-stress induced by tunicamycin treatment is shown.

      - It should be pointed out in the text that in both published studies being cited here of cells lacking eIF2A, that by Gaikwad et al. on a yeast eIF2A deletion mutant, and that by Ichihara et al. on human HEK293 CRISPR KO cells, the analyses included stress conditions in which eIF2 phosphorylation is induced (amino acid starvation or SA treatment, respectively), as was conducted here.  

      Good point - we added this information into the introduction: 

      "Furthermore, loss of eIF2A in several systems did not recapitulate these effects on non-AUG initiation in either non-stressed or stress conditions (caused either by amino acid depletion or sodium arsenate treatment) (Gaikwad et al., 2024; Ichihara et al., 2021)."

      - The Ichihara et al. (2021) study just mentioned reached some of the same conclusions for HEK cells obtained here by conducting ribosome profiling in untreated and SA-treated cells, finding only 1 mRNA (untreated) or four mRNAs (SA-treated cells) that showed significantly reduced TEs in the eIF2A knockout vs. parental cells. It seems appropriate for the authors to expand their treatment of this prior work by summarizing its findings in some detail and also noting how their study goes beyond this previous one. 

      We have added a paragraph to the discussion pointing out that our data agree fully with Ichihara et al. (2021), and that Ichihara et al. (2021) also found only very few mRNAs that change in TE upon loss of eIF2A in either non-stressed or stressed conditions.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review):

      Summary:

      This manuscript describes the role of PRDM16 in modulating BMP response during choroid plexus (ChP) development. The authors combine PRDM16 knockout mice and cultured PRDM16 KO primary neural stem cells (NSCs) to determine the interactions between BMP signaling and PRDM16 in ChP differentiation.

      They show PRDM16 KO affects ChP development in vivo and BMP4 response in vitro. They determine genes regulated by BMP and PRDM16 by ChIP-seq or CUT&TAG for PRDM16, pSMAD1/5/8, and SMAD4. They then measure gene activity in primary NSCs through H3K4me3 and find more genes are co-repressed than co-activated by BMP signaling and PRDM16. They focus on the 31 genes found to be co-repressed by BMP and PRDM16. Wnt7b is in this set and the authors then provide evidence that PRDM16 and BMP signaling together repress Wnt activity in the developing choroid plexus.

      Strengths:

      Understanding context-dependent responses to cell signals during development is an important problem. The authors use a powerful combination of in vivo and in vitro systems to dissect how PRDM16 may modulate BMP response in early brain development.

      We thank the reviewer for the thoughtful summary and positive feedback. We appreciate the recognition of our integrative in vivo and in vitro approach. We're glad the reviewer found our findings on context-dependent gene regulation and developmental signaling valuable.

      Main weaknesses of the experimental setup:

      (1) Because the authors state that primary NSCs cultured in vitro lose endogenous Prdm16 expression, they drive expression by a constitutive promoter. However, this means the expression levels are very different from endogenous levels (as explicitly shown in Supplementary Figure 2B) and the effect of many transcription factors is strongly dose-dependent, likely creating differences between the PRDM16-dependent transcriptional response in the in vitro system and in vivo.

      We acknowledge that our in vitro experiments may not ideally replicate the in vivo situation, a common limitation of such experiments, our primary aim was to explore the molecular relationship between PRDM16 and BMP signaling in gene regulation. Such molecular investigations are challenging to conduct using in vivo tissues. In vitro NSCs treated with BMP4 has been used a model to investigate NSC proliferation and quiescence, drawing on previous studies (e.g., Helena Mira, 2010; Marlen Knobloch, 2017). Crucially, to ensure the relevance of our in vitro findings to the in vivo context, we confirmed that cultured cells could indeed be induced into quiescence by BMP4, and this induction necessitated the presence of PRDM16. Furthermore, upon identifying target genes co-regulated by PRDM16 and SMADs, we validated PRDM16's regulatory role on a subset of these genes in the developing Choroid Plexus (ChP) (Fig. 7 and Suppl.Fig7-8). Only by combining evidence from both in vitro and in vivo experiments could we confidently conclude that PRDM16 serves as an essential co-factor for BMP signaling in restricting NSC proliferation.

      (2) It seems that the authors compare Prdm16_KO cells to Prdm16 WT cells overexpressing flag_Prdm16. Aside from the possible expression of endogenous Prdm16, other cell differences may have arisen between these cell lines. A properly controlled experiment would compare Prdm16_KO ctrl (possibly infected with a control vector without Prdm16) to Prdm16_KO_E (i.e. the Prdm16_KO cells with and without Prdm16 overexpression.)

      We agree that Prdm16 KO cells carrying the Prdm16-expressing vector would be a good comparison with those with KO_vector. However, despite more than 10 attempts with various optimization conditions, we were unable to establish a viable cell line after infecting Prdm16 KO cells with the Prdm16-expressing vector. The overall survival rate for primary NSCs after viral infection is low, and we observed that KO cells were particularly sensitive to infection treatment when the viral vector was large (the Prdm16 ORF is more than 3kb).

      As an alternative oo assess vector effects, we instead included two other control cell lines, wt and KO cells infected with the 3xNLS_Flag-tag viral vector, and presented the results in supplementary Fig 2.  When we compared the responses of the four lines — wt, KO, wt infected with the Flag vector, KO infected with the Flag vector — to the addition and removal of BMP4, we confirmed that the viral infection itself has no significant impacts on the responses of these cells to these treatments regarding changes in cell proliferation and Ttr induction.

      Given that wt cells and the KO cells, with or without viral backbone infection behave quite similarly in terms of cell proliferation, we speculate that even if we were successful in obtaining a cell line with Prdm16-expressing vector in the KO cells, it may not exhibit substantial differences compared to wt cells infected with Prdm16-expressing vector.

      Other experimental weaknesses that make the evidence less convincing:

      (1) The authors show in Figure 2E that Ttr is not upregulated by BMP4 in PRDM16_KO NSCs. Does this appear inconsistent with the presence of Ttr expression in the PRDM16_KO brain in Figure1C?

      The reviwer’s point is that there was no significant increase in Ttr expression in Prdm16_KO cells after BMP4 treatment (Fig. 2E), but there remained residule Ttr mRNA signals in the Prdm16 mutant ChP (Fig. 1C). We think the difference lies in the measuable level of Ttr expression between that induced by BMP4 in NSC culture and that in the ChP. This is based on our immunostaining expreriment in which we tried to detect Ttr using a Ttr antibody. This antibody could not detect the Ttr protein in BMP4-treated Prdm16_expressing NSCs but clearly showed Ttr signal in the wt ChP. This means that although Ttr expression can be significantly increased by BMP4 in vitro to a level measurable by RT-qPCR, its absolute quantity even in the Prdm16_expressing condition is much lower compared to that in vivo. Our results in Fig 1C and Fig 2E, as well as Fig 7B, all consistently showed that Prdm16 depletion significantly reduced Ttr expression in in vitro and in vivo.

      (2) Figure 3: The authors use H3K4me3 to measure gene activity. This is however, very indirect, with bulk RNA-seq providing the most direct readout and polymerase binding (ChIP-seq) another more direct readout. Transcription can be regulated without expected changes in histone methylation, see e.g. papers from Josh Brickman. They verify their H3K4me3 predictions with qPCR for a select number of genes, all related to the kinetochore, but it is not clear why these genes were picked, and one could worry whether these are representative.

      H3K4me3 has widely been used as an indicator of active transcription and is a mark for cell identity genes. And it has been demonstrated that H3K4me3 has a direct function in regulating transciption at the step of RNApolII pausing release. As stated in the text, there are advantages and disadvantages of using H3K4me3 compared to using RNA-seq. RNA-seq profiles all gene products, which are affected by transcription and RNA stability and turnover. In contrast, H3K4me3 levels at gene promoter reflects transcriptional activity. In our case, we aimed to identify differential gene expression between proliferation and quiescence states. The transition between these two states is fast and dynamic. RNA-seq may not be able to identify functionally relevant genes but more likely produces false positive and negative results. Therefore, we chose H3K4me3 profiling.

      We agree that transcription may change without histone methylation changes. This may cause an under-estimation of the number of changed genes between the conditions. 

      We validated 7 out of 31 genes (Wnt7b, Id3, Mybl2, Spc24, Spc25, Ndc80 and Nuf2). We chose these genes based on two critira: 1) their function is implicated in cell proliferation and cell-cycle regulation based on gene ontology analysis; 2) their gene products are detectable in the developing ChP based on the scRNA-seq data. Three of these genes (Wnt7b, Id3, Mybl2) are not related to the kinetochore. We now clarify this description in the revised text.

      (3) Line 256: The overlap of 31 genes between 184 BMP-repressed genes and 240 PRDM16-repressed genes seems quite small.

      This result indicates that in addition to co-repressing cell-cycle genes, BMP and PRDM16 have independent fucntions. For example, it was reported that BMP regulates neuronal and astrocyte differentiation (Katada, S. 2021), while our previous work demonstrated that Prdm16 controls temporal identity of NSCs (He, L. 2021).

      (4) The Wnt7b H3K4me3 track in Fig. 3G is not discussed in the text but it shows H3K4me3 high in _KO and low in _E regardless of BMP4. This seems to contradict the heatmap of H3K4me3 in Figure 3E which shows H3K4me3 high in _E no BMP4 and low in _E BMP4 while omitting _KO no BMP4. Meanwhile CDKN1A, the other gene shown in 3G, is missing from 3E.

      The track in Fig 3G shows the absolute signal of H3K4me3 after mapping the sequencing reads to the genome and normaliz them to library size. Compare the signal in Prdm16_E with BMP4 and that in Prdm16_E without BMP4, the one with BMP4 has a lower peak. The same trend can be seen for the pair of Prdm16_KO cells with or without BMP4.  The heatmap in Fig. 3E shows the relative level of H3K4me3 in three conditions. The Prdm16_E cells with BMP4 has the lowest level, while the other two conditions (Prdm16_KO with BMP4 and Prdm16_E without BMP4) display higher levels. These two graphs show a consistent trend of H3K4me3 changes at the Wnt7b promoter across these conditions. Figure 3E only includes genes that are co-repressed by PRDM16 and BMP. CDKN1A’s H3K4me3 signals are consistent between the conditions, and thus it is not a PRDM16- or BMP-regulated gene. We use it as a negative control. 

      (5) The authors use PRDM16 CUT&TAG on dissected dorsal midline tissues to determine if their 31 identified PRDM16-BMP4 co-repressed genes are regulated directly by PRDM16 in vivo. By manual inspection, they find that "most" of these show a PRDM16 peak. How many is most? If using the same parameters for determining peaks, how many genes in an appropriately chosen negative control set of genes would show peaks? Can the authors rigorously establish the statistical significance of this observation? And why wasn't the same experiment performed on the NSCs in which the other experiments are done so one can directly compare the results? Instead, as far as I could tell, there is only ChIP-qPCR for two genes in NSCs in Supplementary Figure 4D.

      In our text, we indicated the genes containing PRDM16 binding peaks in the figures and described them as “Text in black in Fig. 6A and Supplementary Fig. 5A”. We will add the precise number “25 of these genes” in the main text to clarify it. We used BMP-only repressed 184-31 =153 genes (excluding PRDM16-BMP4 co-repressed) as a negative control set of genes. By computationally determine the nearest TSS to a PRDM16 peak, we identified 24/31 co-repressed genes and 84/153 BMP-only-repressed genes, containing PRDM16 peaks in the E12.5 ChP data. Fisher’s Exact Test comparing the proportions yields the P-value = 0.015.

      We are confused with the second part of the comment “And why wasn't the same experiment performed on the NSCs in which the other experiments are done so one can directly compare the results? Instead, as far as I could tell, there is only ChIP-qPCR for two genes in NSCs in Supplementary Figure 4D.” If the reviewer meant why we didn’t sequence the material from sequential-ChIP or validate more taget genes, the reason is the limitation of the material. Sequential ChIP requires a large quantity of the antibodies, and yields little material barely sufficient for a few qPCR after the second round of IP. This yielded amount was far below the minimum required for library construction. The PRDM16 antibody was a gift, and the quantity we have was very limited. We made a lot of efforts to optimize all available commercial antibodies in ChIP and Cut&Tag, but none of them worked in these assays.

      (6) In comparing RNA in situ between WT and PRDM16 KO in Figure 7, the authors state they use the Wnt2b signal to identify the border between CH and neocortex. However, the Wnt2b signal is shown in grey and it is impossible for this reviewer to see clear Wnt2b expression or where the boundaries are in Figure 7A. The authors also do not show where they placed the boundaries in their analysis. Furthermore, Figure 7B only shows insets for one of the regions being compared making it difficult to see differences from the other region. Finally, the authors do not show an example of their spot segmentation to judge whether their spot counting is reliable. Overall, this makes it difficult to judge whether the quantification in Figure 7C can be trusted.

      In the revised manuscript we have included an individal channel of Wnt2b and mark the boundaries. We also provide full-view images and examples of spot segmentation in the new supplementary figure 8. 

      (7) The correlation between mKi67 and Axin2 in Figure 7 is interesting but does not convincingly show that Wnt downstream of PRDM16 and BMP is responsible for the increased proliferation in PRDM16 mutants.

      We agree that this result (the correlation between mKi67 and Axin2) alone only suggests that Wnt signaling is related to the proliferation defect in the Prdm16 mutant, and does not necessarily mean that Wnt is downstream of PRDM16 and BMP. Our concolusion is backed up by two additional lines of evidences:  the Cut&Tag data in which PRDM16 binds to regulatory regions of Wnt7b and Wnt3a; BMP and PRDM16 co-repress Wnt7b in vitro.

      An ideal result is that down-regulating Wnt signaling in Prdm16 mutant can rescue Prdm16 mutant phenotype. Such an experiment is technically challenging. Wnt plays diverse and essential roles in NSC regulation, and one would need to use a celltype-and stage-specific tool to down-regulate Wnt in the background of Prdm16 mutation. Moreover, Wnt genes are not the only targets regulated by PRDM16 in these cells, and downregulating Wnt may not be sufficient to rescue the phenotype. 

      Weaknesses of the presentation:

      Overall, the manuscript is not easy to read. This can cause confusion.

      We have revised the text to improve clarity.

      Reviewer #1 (Recommendations for the authors):

      (1) Overall, the manuscript is not easy to read. Here are some causes of confusion for which the presentation could be cleaned up:

      We are grateful for the reviewer’s suggestion. In the revised manuscript, we have made efforts to improve the clarity of the text.

      (a) Part of the first section is confusing in that some statements seem contradictory, in particular:

      "there is no overall patterning defect of ChP and CH in the Prdm16 mutant" (line 125)

      "Prdm16 depletion disrupted the transition from neural progenitors into ChP epithelia" (line 144)

      It would be helpful if the authors could reformulate this more clearly.

      We modified the text to clarify that while the BMP-patterned domain is not affected, the transition of NSCs into ChP epithelial cells is compromised in the Prdm16 mutant.

      (b) Flag_PRDM16, PRDM16_expressing, PRDM16_E, PRDM16 OE all seem to refer to the same PRDM16 overexpressing cells, which is very confusing. The authors should use consistent naming. Moreover, it would be good if they renamed these all to PRDM16_OE to indicate expression is not endogenous but driven by a constitutive promoter.

      We appreciate the comment and agree that the use of multiple terms to refer to the same PRDM16-overexpressing condition was confusing. Our original intention in using Prdm16_E was to distinguish cells expressing PRDM16 from the two other groups: wild-type cells and Prdm16_KO cells, which both lack PRDM16 protein expression. However, we acknowledge that Prdm16_E could be misinterpreted as indicating expression from the endogenous Prdm16 promoter. To avoid this confusion and ensure consistency, we have now standardized the terminology and refer to this condition as Prdm16_OE, indicating Flag-tagged PRDM16 expression driven by a constitutive promoter.

      (c) Line 179 states "generated a cell line by infecting Prdm16_KO cells with the same viral vector, expressing 3xNSL_Flag". Do the authors mean 3xNLS_Flag_Prdm16, so these are the Prdm16_KO_E cells by the notation suggested above? Or is this a control vector with Flag only? The following paragraph refers to Supplementary Figure 2C-F where the same construct is called KO_CDH, suggesting this was an empty CDH vector, without Flag, or Prdm16. This is confusing.

      We appreciate the reviewer’s careful reading and helpful comment. We acknowledge the confusion caused by the inconsistent terminology. To clarify: in line 179, we intended to describe an attempt to generate a Prdm16_KO cell line expressing 3xNLS_Flag_Prdm16, not a control vector with Flag only. However, despite repeated attempts, we were unable to establish this line due to low viral efficiency and the vulnerability of Prdm16_KO cells to infection with the large construct. Therefore, these cells were not included in the subsequent analyses.

      The term KO_CDH refers to Prdm16_KO cells infected with the empty CDH control vector, which lacks both Flag and Prdm16. This is the line used in the experiments shown in Supplementary Fig. 2C–F. We have revised the text throughout the manuscript to ensure consistent use of terminology and to avoid this confusion.

      (2) The introductory statements on lines 53-54 could use more references.

      Thanks for the suggestion. We have now included more references.

      (3) It would be helpful if all structures described in the introduction and first section were annotated in Figure 1, or otherwise, if a cartoon were included. For example, the cortical hem, and fourth ventricle.

      Thanks for the suggestion. We have now indicated the structures, ChP, CH and the fourth ventricle, in the images in Figure 1 and Supplementary Figure 1.

      (4) In line 115, "as previously shown.." - to keep the paper self-contained a figure illustrating the genetics of the KO allele would be helpful.

      Thanks for the suggestion. We have now included an illustration of the Prdm16 cGT allele in Figure 1B.

      (5) In Figure 1D as costain for a ChP marker would be helpful because it is hard to identify morphologically in the Prdm16 KO.

      Appoligize for the unclarity. The KO allele contains a b-geo reporter driven by Prdm16 endogenous promoter. The samples were co-stained for EdU, b-Gal and DAPI. To distingquish the ChP domain from the CH, we used the presence of b b-Gal as a marker. We indicated this in the figure legend, but now have also clarified this in the revised text.

      (6) The details in Figure 1E are hard to see, a zoomed-in inset would help.

      A zoomed-in inset is now included in the figure.

      (7) Supplementary Figure 2A does not convincingly show that PRDM16 protein is undetectable since endogenous expression may be very low compared to the overexpression PRDM16_E cells so if the contrast is scaled together it could appear black like the KO.

      We appreciate the reviewer’s point and have carefully considered this concern. We concluded that PRDM16 protein is effectively undetectable in cultured wild-type NSCs based on direct comparison with brain tissue. Both cultured NSCs and brain sections were processed under similar immunostaining and imaging conditions. While PRDM16 showed robust and specific nuclear localization in embryonic brain sections (Fig. 1B and Supplementary Fig. 1A), only a small subset of cultured NSCs exhibited PRDM16 signal, primarily in the cytoplasm (middle panel of Fig. 2A). This stark contrast supports our conclusion that endogenous PRDM16 protein is either absent or significantly downregulated in vitro. Because of this limitation, we turned to over-expressing Prdm16 in NSC culture using a constitutive promoter. 

      (9) Line 182 "Following the washout step" - no such step had been described, maybe replace by "After washout of BMP".

      Yes, we have revised the text.

      (8) Line 214: "indicating a modest level" - what defines modest? Compared to what? Why is a few thousand moderate rather than low? Does it go to zero with inhibitors for pathways?

      Here a modest level means a lower level than to that after adding BMP4. To clarify this, we revised the description to “indicating endogenous levels of …”

      (9) The way qPCR data are displayed makes it difficult to appreciate the magnitude of changes, e.g. in Supplementary Figure 2B where a gap is introduced on the scale. Displaying log fold change / relative CT values would be more informative.

      We used a segmented Y-axis in Supplementary Figure 2B because the Prdm16 overexpression samples exhibited much higher experssion levels compared to other conditions. In response to this suggestion, we explored alternative ways to present the result, including ploting log-transformed values and log fold changes. However, these methods did not enhance the clarity of the differences – in fact, log scaling made the magnitude of change appear less apparent. To address this, we now present the overexpression samples in a separate graph, thereby eliminating the need for a broken Y-axis and improving the overall readability of the data.

      (10) Writing out "3 days" instead of 3D in Figure 2A would improve clarity. It would be good if the used time interval is repeated in other figures throughout the paper so it is still clear the comparison is between 0 and 3 days.

      We have changed “3D” to “3 days”. All BMP4 treatments in this study were 3 days.

      (11) Line 290: "we found that over 50% of SMAD4 and pSMAD1/5/8 binding peaks were consistent in Prdm16_E and Prdm16_KO cells, indicating that deletion of Prdm16 does not affect the general genomic binding ability of these proteins" - this only makes sense to state with appropriate controls because 50% seems like a big difference, what is the sample to sample variability for the same condition? Moreover, the next paragraph seems to contradict this, ending with "This result suggests that SMAD binding to these sites depends on PRDM16". The authors should probably clarify the writing.

      We appreciate the reviwer’s comment and agree that clarification was needed. Our point was that SMAD4 and pSMAD1/5/8 retain the ability to bind DNA broadly in the Prdm16 KO cells, with more than half of the original binding sites still occupied. This suggests that deletion of Prdm16 does not globally impair SMAD genomic binding. Howerever, our primary interest lies in the subset of sites that show differential by SMAD binding between wt and Prdm16 KO conditions, as thse are likely to be PRDM16-dependent. 

      In the following paragraph, we focused specifically on describing SMAD and PRDM16 co-bound sites. At these loci, SMAD4 and pSMAD1/5/8 showed reduced enrichment in the absence of PRDM16, suggesting PRDM16 facilitates SMAD binding at these particular regions. We have revised the text in the manuscript to more clearly distinguish between global SMAD binding and PRDM16-dependent sites.

      (12) Much more convincing than ChIP-qPCR for c-FOS for two loci in Figures 5F-G would be a global analysis of c-FOS ChIP-seq data.

      We agree that a global c-FOS ChIP-seq analysis would provide a more comprehensive view of c-FOS binding patterns. However, the primary focus of this study is the interaction between BMP signaling and PRDM16. The enrichment of AP-1 motifs at ectopic SMAD4 binding sites was an unexpected finding, which we validated using c-FOS ChIP-qPCR at selected loci. While a genome-wide analysis would be valuable, it falls beyond the current scope. We agree that future studies exploring the interplay among SMAD4/pSMAD, PRDM16, and AP-1 will be important and informative.

      (13) Figure 6A is hard to read. A heatmap would make it much easier to see differences in expression. Furthermore, if the point is to see the difference between ChP and CH, why not combine the different subclusters belonging to those structures? Finally, why are there 28 genes total when it is said the authors are evaluating a list of 31 genes and also displaying 6 genes that are not expressed (so the difference isn't that unexpressed genes are omitted)?

      For the scRNA-seq data, we chose violin plots because they display both gene expression levels and the number of cells that express each gene. However, we agree that the labels in Figure 6A were too small and difficult to read. We have revised the figure by increasing the font size and moved genes with low expression to  Supplementary Figure 5A. Figure 6A includes 17 more highly expressed genes together with three markers, and  Supplementary Figure 5A contains 13 lowly expressed genes. One gene Mrtfb is missing in the scRNA-seq data and thus not included. We have revised the description of the result in the main text and figure legends.

      Reviewer #2 (Public review):

      Summary:

      This article investigates the role of PRDM16 in regulating cell proliferation and differentiation during choroid plexus (ChP) development in mice. The study finds that PRDM16 acts as a corepressor in the BMP signaling pathway, which is crucial for ChP formation.

      The key findings of the study are:

      (1) PRDM16 promotes cell cycle exit in neural epithelial cells at the ChP primordium.

      (2) PRDM16 and BMP signaling work together to induce neural stem cell (NSC) quiescence in vitro.

      (3) BMP signaling and PRDM16 cooperatively repress proliferation genes.

      (4) PRDM16 assists genomic binding of SMAD4 and pSMAD1/5/8.

      (5) Genes co-regulated by SMADs and PRDM16 in NSCs are repressed in the developing ChP.

      (6) PRDM16 represses Wnt7b and Wnt activity in the developing ChP.

      (7) Levels of Wnt activity correlate with cell proliferation in the developing ChP and CH.

      In summary, this study identifies PRDM16 as a key regulator of the balance between BMP and Wnt signaling during ChP development. PRDM16 facilitates the repressive function of BMP signaling on cell proliferation while simultaneously suppressing Wnt signaling. This interplay between signaling pathways and PRDM16 is essential for the proper specification and differentiation of ChP epithelial cells. This study provides new insights into the molecular mechanisms governing ChP development and may have implications for understanding the pathogenesis of ChP tumors and other related diseases.

      Strengths:

      (1) Combining in vitro and in vivo experiments to provide a comprehensive understanding of PRDM16 function in ChP development.

      (2) Uses of a variety of techniques, including immunostaining, RNA in situ hybridization, RT-qPCR, CUT&Tag, ChIP-seq, and SCRINSHOT.

      (3) Identifying a novel role for PRDM16 in regulating the balance between BMP and Wnt signaling.

      (4) Providing a mechanistic explanation for how PRDM16 enhances the repressive function of BMP signaling. The identification of SMAD palindromic motifs as preferred binding sites for the SMAD/PRDM16 complex suggests a specific mechanism for PRDM16-mediated gene repression.

      (5) Highlighting the potential clinical relevance of PRDM16 in the context of ChP tumors and other related diseases. By demonstrating the crucial role of PRDM16 in controlling ChP development, the study suggests that dysregulation of PRDM16 may contribute to the pathogenesis of these conditions.

      We thank the reviewer for the thorough and thoughtful summary of our study. We’re glad the key findings and significance of our work were clearly conveyed, particularly regarding the role of PRDM16 in coordinating BMP and Wnt signaling during ChP development. We also appreciate the recognition of our integrated approach and the potential implications for understanding ChP-related diseases.

      Weaknesses:

      (1) Limited investigation of the mechanism controlling PRDM16 protein stability and nuclear localization in vivo. The study observed that PRDM16 protein became nearly undetectable in NSCs cultured in vitro, despite high mRNA levels. While the authors speculate that post-translational modifications might regulate PRDM16 in NSCs similar to brown adipocytes, further investigation is needed to confirm this and understand the precise mechanism controlling PRDM16 protein levels in vivo.

      While mechansims controlling PRDM16 protein stability and nuclear localization in the developing brain are interesting, the scope of this paper is revealing the function of PRDM16 in the choroid plexus and its interaction with BMP signaling. We will be happy to pursuit this direction in our next study.

      (2) Reliance on overexpression of PRDM16 in NSC cultures. To study PRDM16 function in vitro, the authors used a lentiviral construct to constitutively express PRDM16 in NSCs. While this approach allowed them to overcome the issue of low PRDM16 protein levels in vitro, it is important to consider that overexpressing PRDM16 may not fully recapitulate its physiological role in regulating gene expression and cell behavior.

      As stated above, we acknowledge that findings from cultured NSCs may not directly apply to ChP cells in vivo. We are cautious with our statements. The cell culture work was aimed to identify potential mechanisms by which PRDM16 and SMADs interact to regulate gene expression and target genes co-regulated by these factors. We expect that not all targets from cell culture are regulated by PRDM16 and SMADs in the ChP, so we validated expression changes of several target genes in the developing ChP and now included the new data in Fig. 7 and Supplementary Fig. 7. Out of the 31 genes identified from cultured cells, four cell cycle regulators including Wnt7b, Id3, Spc24/25/nuf2 and Mybl2, showed de-repression in Prdm16 mutant ChP. These genes can be relevant downstream genes in the ChP, and other target genes may be cortical NSC-specific or less dependent on Prdm16 in vivo.

      (3) Lack of direct evidence for AP1 as the co-factor responsible for SMAD relocation in the absence of PRDM16. While the study identified the AP1 motif as enriched in SMAD binding sites in Prdm16 knockout cells, they only provided ChIP-qPCR validation for c-FOS binding at two specific loci (Wnt7b and Id3). Further investigation is needed to confirm the direct interaction between AP1 and SMAD proteins in the absence of PRDM16 and to rule out other potential co-factors.

      We agree that the finding of the AP1 motif enriched at the PRDM16 and SMAD co-binding regions in Prdm16 KO cells can only indirectly suggest AP1 as a co-factor for SMAD relocation. That’s why we used ChIP-qPCR to examine the presence of C-fos at these sites. Although we only validated two targets, the result confirms that C-fos binds to the sites only in the Prdm16 KO cells but not Prdm16_expressing cells, suggesting AP1 is a co-factor.  Our results cannot rule out the presence of other co-factors.

      Reviewer #2 (Recommendations for the authors):

      Minor typo: [7, page 3] "sicne" should be "since".

      We appreciate the reviewer’s careful reading. We have now corrected the typo and revised some part of the text to improve clarity.

      Reviewer #3 (Public review):

      Summary:

      Bone morphogenetic protein (BMP) signaling instructs multiple processes during development including cell proliferation and differentiation. The authors set out to understand the role of PRDM16 in these various functions of BMP signaling. They find that PRDM16 and BMP co-operate to repress stem cell proliferation by regulating the genomic distribution of BMP pathway transcription factors. They additionally show that PRDM16 impacts choroid plexus epithelial cell specification. The authors provide evidence for a regulatory circuit (constituting of BMP, PRDM16, and Wnt) that influences stem cell proliferation/differentiation.

      Strengths:

      I find the topics studied by the authors in this study of general interest to the field, the experiments well-controlled and the analysis in the paper sound.

      We thank the reviewer for their positive feedback and thoughtful summary. We appreciate the recognition of our efforts to define the role of PRDM16 in BMP signaling and stem cell regulation, as well as the soundness of our experimental design and analysis.

      Weaknesses:

      I have no major scientific concerns. I have some minor recommendations that will help improve the paper (regarding the discussion).

      We have revised the discussion according to the suggestions.

      Reviewer #3 (Recommendations for the authors):

      Specific minor recommendations:

      Page 18. Line 526: In a footnote, the authors point out a recent report which in parallel was investigating the link between PRDM16 and SMAD4. There is substantial non-overlap between these two papers. To aid the reader, I would encourage the authors to discuss that paper in the discussion section of the manuscript itself, highlighting any similarities/differences in the topic/results.

      Thanks for the suggestion. We now included the comparison in the discussion. One conclusion between our study and this publication is consistent, that PRDM16 functions as a co-repressor of SMAD4. However, the mechanims are different. Our data suggests a model in which PRDM16 facilitates SMAD4/pSMAD binding to repress proliferation genes under high BMP conditions. However, the other report suggests that SMAD4 steadily binds to Prdm16 promoter and switches regulatory functions depending on the co-factors. Together with PRDM16, SMAD4 represses gene expression, while with SMAD3 in response to high levels of TGF-b1, it activates gene expression. These differences could be due to different signaling (BMP versus TGF-b), contexts (NSCs versus Pancreatic cancers) etc.

      Page 3. Line 65: typo 'since'

      We appreciate the reviewer’s careful reading. We have now corrected the typo and revised the text to improve clarity.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      This manuscript describes a series of experiments documenting trophic egg production in a species of harvester ant, Pogonomyrmex rugosus. In brief, queens are the primary trophic egg producers, there is seasonality and periodicity to trophic egg production, trophic eggs differ in many basic dimensions and contents relative to reproductive eggs, and diets supplemented with trophic eggs had an effect on the queen/worker ratio produced (increasing worker production).

      The manuscript is very well prepared and the methods are sufficient. The outcomes are interesting and help fill gaps in knowledge, both on ants as well as insects, more generally. More context could enrich the study and flow could be improved.

      We thank the reviewer for these comments. We agree that the paper would benefit from more context. We have therefore greatly extended the introduction.

      Reviewer #2 (Public Review):

      The manuscript by Genzoni et al. provides evidence that trophic eggs laid by the queen in the ant Pogonomyrmex rugosis have an inhibitory effect on queen development. The authors also compare a number of features of trophic eggs, including protein, DNA, RNA, and miRNA content, to reproductive eggs. To support their argument that trophic eggs have an inhibitory effect on queen development, the authors show that trophic eggs have a lower content of protein, triglycerides, glycogen, and glucose than reproductive eggs, and that their miRNA distributions are different relative to reproductive eggs. Although the finding of an inhibitory influence of trophic eggs on queen development is indeed arresting, the egg cross-fostering experiment that supports this finding can be effectively boiled down to a single figure (Figure 6). The rest of the data are supplementary and correlative in nature (and can be combined), especially the miRNA differences shown between trophic and reproductive eggs. This means that the authors have not yet identified the mechanism through which the inhibitory effect on queen development is occurring. To this reviewer, this finding is more appropriate as a short report and not a research article. A full research article would be warranted if the authors had identified the mechanism underlying the inhibitory effect on queen development. Furthermore, the article is written poorly and lacks much background information necessary for the general reader to properly evaluate the robustness of the conclusions and to appreciate the significance of the findings.

      We thank the reviewer for these comments. We agree that the paper would benefit by having more background information and more discussion. We have followed this advice in the revision.

      Reviewer #3 (Public Review):

      In "Trophic eggs affect caste determination in the ant Pogonomyrmex rugosus" Genzoni et al. probe a fundamental question in sociobiology, what are the molecular and developmental processes governing caste determination? In many social insect lineages, caste determination is a major ontogenetic milestone that establishes the discrete queen and worker life histories that make up the fundamental units of their colonies. Over the last century, mechanisms of caste determination, particularly regulators of caste during development, have remained relatively elusive. Here, Genzoni et al. discovered an unexpected role for trophic eggs in suppressing queen development - where bi-potential larvae fed trophic eggs become significantly more likely to develop into workers instead of gynes (new queens). These results are unexpected, and potentially paradigm-shifting, given that previously trophic eggs have been hypothesized to evolve to act as an additional intracolony resource for colonies in potentially competitive environments or during specific times in colony ontogeny (colony foundation), where additional food sources independent of foraging would be beneficial. While the evidence and methods used are compelling (e.g., the sequence of reproductive vs. trophic egg deposition by single queens, which highlights that the production of trophic eggs is tightly regulated), the connective tissue linking many experiments is missing and the downstream mechanism is speculative (e.g., whether miRNA, proteins, triglycerides, glycogen levels in trophic eggs is what suppresses queen development). Overall, this research elevates the importance of trophic eggs in regulating queen and worker development but how this is achieved remains unknown.

      We thank the reviewer for these comments and agree that future work should focus on identifying the substances in trophic eggs that are responsible for caste determination.  

      Recommendations For The Authors:

      Reviewer #1 (Recommendations For The Authors):

      Introduction:

      The context for this study is insufficiently developed in the introduction - it would be nice to have a more detailed survey of what is known about trophic eggs in insects, especially social insects. The end of the introduction nicely sets up the hypothesis through the prior work described by Helms Cahan et al. (2011) where they found JH supplementation increased trophic egg production and also increased worker size. I think that the introduction could give more context about egg production in Pogonomyrmex and other ants, including what is known about worker reproduction. For example, Suni et al. 2007 and Smith et al. 2007 both describe the absence of male production by workers in two different harvester ants. Workers tend to have underdeveloped ovaries when in the presence of the queen. Other species of ants are known to have worker reproduction seemingly for the purpose of nutrition (see Heinze and Hölldober 1995 and subsequent studies on Crematogaster smithi). Because some ants, including Pogonomyrmex, lack trophallaxis, it has been hypothesized that they distribute nutrients throughout the nest via trophic eggs as is seen in at least one other ant (Gobin and Ito 2000). Interestingly, Smith and Suarez (2009) speculated that the difference in nutrition of developing sexual versus worker larvae (as seen in their pupal stable isotope values) was due to trophic egg provisioning - they predicted the opposite as was found in this study, but their prediction was in line with that of Helms Cahan et al. (2011). This is all to say that there is a lot of context that could go into developing the ideas tested in this paper that is completely overlooked. The inclusion of more of what is known already would greatly enrich the introduction.

      We agree that it would be useful to provide a larger context to the study. We now provide more information on the life-history of ants and explained under what situations queens and workers may produce trophic eggs. We also mentioned that some ants such as Crematogaster smithi have a special caste of “large workers” which are morphologically intermediate between winged queens and small workers and appear to be specialized in the production of unfertilized eggs. We now also mention the study of Goby and Ito (200) where the authors show that trophic eggs may play an important role in food distribution withing the colony, in particular in species where trophallaxis is rare or absent.

      Methods:

      L49: What lineage is represented in the colonies used? The collection location is near where both dependent-lineage (genetic caste determining) P. rugosus and "H" lineage exist. This is important to know. Further, depending on what these are, the authors should note whether this has relevance to the study. Not mentioning genetic caste determination in a paper that examines caste determination is problematic.

      This is a good point. We have now provided information at the very beginning of the material and method section that the queens had been collected in populations known not to have dependentlineage (genetic caste determining) mechanisms of caste determination.

      L63 and throughout: It would be more efficient to have a paragraph that cites R (must be done) and RStudio once as the tool for all analyses. It also seems that most model construction and testing was done using lme4 - so just lay this out once instead of over and over.

      We agree and have updated the manuscript accordingly.

      L95: 'lenght' needs to be 'length' in the formula.

      Thanks, corrected.

      L151: A PCA was used but not described in the methods. This should be covered here. And while a Mantel test is used, I might consider a permANOVA as this more intuitively (for me, at least) goes along with the PCA.

      We added the PCA description in the Material and Method section.

      Results:

      I love Fig. 3! Super cool.

      Thanks for this positive comment.

      Discussion:

      It would be good to have more on egg cannibalism. This is reasonably well-studied and could be good extra context.

      We have added a paragraph in the discussion to mention that egg cannibalism is ubiquitous in ants.

      Supp Table 1: P. badius is missing and citations are incorrectly attributed to P. barbatus.

      P. badius was present in the Table but not with the other Pogonomyrmex species. For some genera the species were also not listed in alphabetic order. This has been corrected.

      Reviewer #2 (Recommendations For The Authors):

      Comments on introduction:

      The introduction is missing information about caste determination in ants generally and Pogonomyrmex rugosis specifically. This is important because some colonies of Pogonomyrmex rugosis have been shown to undergo genetic caste determination, in which case the main result would be rendered insignificant. What is the evidence that caste determination in the lineages/colonies used is largely environmentally influenced and in what contexts/environmental factors? All of this should be made clear.

      This is a good point. We have expanded the introduction to discuss previous work on caste determination in Pogonomyrmex species with environmental caste determination and now also provide evidence at the beginning of the Material and Method section that the two populations studied do not have a system of genetic caste determination.

      Line 32 and throughout the paper: What is meant exactly by 'reproductive eggs'? Are these eggs that develop specifically into reproductives (i.e., queens/males) or all eggs that are non-trophic? If the latter, then it is best to refer to these eggs as 'viable' in order to prevent confusion.

      We agree and have updated the manuscript accordingly.

      Figure 1/Supp Table 1: It is surprising how few species are known to lay trophic eggs. Do the authors think this is an informative representation of the distribution of trophic egg production across subfamilies, or due to lack of study? Furthermore, the branches show ant subfamilies, not families. What does the question mark indicate? Also, the information in the table next to the phylogeny is not easy to understand. Having in the branches that information, in categories, shown in color for example, could be better and more informative. Finally, having the 'none' column with only one entry is confusing - discuss that only one species has been shown to definitely not lay trophic eggs in the text, but it does not add much to the figure.

      Trophic eggs are probably very common in ants, but this has not been very well studied. We added a sentence in the manuscript to make this clear.

      Thanks for noticing the error family/subfamily error. This has been corrected in Figure 1 and Supplementary Table 1.

      The question mark indicates uncertainty about whether queens also contribute to the production of trophic eggs in one species (Lasius niger). We have now added information on that in the Figure legend.

      We agree with the reviewer that it would be easier to have the information on whether queens and workers produce trophic on the branches of the Tree. However, having the information on the branches would suggest that the “trait” evolved on this part of the tree. As we do not know when worker or queen production of trophic eggs exactly evolved, we prefer to keep the figure as it is.

      Finally, we have also removed the none in the figure as suggested by the reviewer and discussed in the manuscript the fact that the absence of trophic eggs has been reported in only one ant species (Amblyopone silvestrii: Masuko 2003_)._

      Comments on materials and methods:

      Why did they settle on three trophic eggs per larva for their experimental setup?

      We used three trophic eggs because under natural conditions 50-65% of the eggs are trophic. The ratio of trophic eggs to viable eggs (larvae) was thus similar natural condition.

      Line 50: In what kind of setup were the ants kept? Plaster nests? Plastic boxes? Tubes? Was the setup dry or moist? I think this information is important to know in the context of trophic eggs.

      We now explain that colonies were maintained in plastic boxes with water tubes.

      Line 60: Were all the 43 queens isolated only once, or multiple times?

      Each of the 43 queens were isolated for 8 hours every day for 2 weeks, once before and once after hibernation (so they were isolated multiple times). We have changed the text to make clear that this was done for each of the 43 queens.

      Could isolating the queen away from workers/brood have had an effect on the type of eggs laid?

      This cannot be completely ruled out. However, it is possible to reliably determine the proportion of viable and trophic eggs only by isolating queens. And importantly the main aim of these experiments was not to precisely determine the proportion viable and trophic eggs, but to show that this proportion changes before and after hibernation and that queens do not lay viable and trophic eggs in a random sequence.

      Since it was established that only queens lay trophic eggs why was the isolation necessary?

      Yes this was necessary because eggs are fragile and very difficult to collect in colonies with workers (as soon as eggs are laid they are piled up and as soon as we disturb the nest, a worker takes them all and runs away with them). Moreover, it is possible that workers preferentially eat one type of eggs thus requiring to remove eggs as soon as queens would have laid them. This would have been a huge disturbance for the colonies.

      Line 61: Is this hibernation natural or lab induced? What is the purpose of it? How long was the hibernation and at what temperature? Where are the references for the requirement of a diapause and its length?

      The hibernation was lab induced. We hibernated the queens because we previously showed that hibernation is important to trigger the production of gynes in P. rugosus colonies in the laboratory (Schwander et al 2008; Libbrecht et al 2013). Hibernation conditions were as described in Libbrecht et al (2013).  

      Line 73: If the queen is disturbed several times for three weeks, which effect does it have on its egg-laying rate and on the eggs laid? Were the eggs equally distributed in time in the recipient colonies with and without trophic eggs to avoid possible effects?

      It is difficult to respond what was the effect of disturbance on the number and type of eggs laid. But again our aim was not to precisely determine these values but determine whether there was an effect of hibernation on the proportion of trophic eggs. The recipient colonies with and without trophic eggs were formed in exactly the same way. No viable eggs were introduced in these colonies, but all first instar larvae have been introduced in the same way, at the same time, and with random assignment. We have clarified this in the Material and Method section.

      Line 77: Before placing the freshly hatched larvae in recipient colonies, how long were the recipient colonies kept without eggs and how long were they fed before giving the eggs? Were they kept long enough without the queen to avoid possible effects of trophic eggs, or too long so that their behavior changed?

      The recipient colonies were created 7 to 10 days before receiving the first larvae and were fed ad libitum with grass seeds, flies and honey water from the beginning. Trophic eggs that would have been left over from the source colony should have been eaten within the first few days after creating the recipient colonies. However, even if some trophic eggs would have remained, this would not influence our conclusion that trophic eggs influence caste fate, given the fully randomized nature of our treatments and the considerable number of independent replicates. The same applies to potential changes in worker behavior following their isolation from the queen.

      Line 77: Is it known at what stage caste determination occurs in this species? Here first instar larvae were given trophic eggs or not. Does caste-determination occur at the first instar stage? If not, what effect could providing trophic eggs at other stages have on caste-determination?

      A previous study showed that there is a maternal effect on caste determination in the focal species (Schwander et al 2008). The mechanism underlying this maternal effect was hypothesized to be differential maternal provisioning of viable eggs. However, as we detail in the discussion, the new data presented in our study suggests that the mechanism is in fact a different abundance of trophic eggs laid by queens. There is currently no information when exactly caste determination occurs during development

      Comments on results:

      Line 65: How does investigating the order of eggs laid help to "inform on the mechanisms of oogenesis"?

      We agree that the aim was not to study the mechanism of oogenesis. We have changed this sentence accordingly: “To assess whether viable and trophic eggs were laid in a random order, or whether eggs of a given type were laid in clusters, we isolated 11 queens for 10 hours, eight times over three weeks, and collected every hour the eggs laid”

      Figure 2: There is no description/discussion of data shown in panels B, C, E, and F in the main text.

      We have added information in the main text that while viable eggs showed embryonic development at 25 and 65 hours (Fig 12 B, C) there was no such development for trophic eggs (Fig. 2 E,F).

      Line 172: Please explain hibernation details and its significance on colony development/life cycle.

      We have added this information in the Material and Method section.

      Figure 6: How is B plotted? How could 0% of gynes have 100% survival?

      The survival is given for the larvae without considering caste. We have changed the de X axis of panel B and reworded the Figure legend to clarify this.

      Is reduced DNA content just an outcome of reduced cell number within trophic eggs, i.e., was this a difference in cell type or cell number? Or is it some other adaptive reason?

      It is likely to be due to a reduction in cell number (trophic eggs have maternal DNA in the chorion, while viable eggs have in addition the cells from the developing zygote) but we do not have data to make this point.

      Is there a logical sequence to the sequence of egg production? The authors showed that the sequence is non-random, but can they identify in what way? What would the biological significance be?

      We could not identify a logical sequence. Plausibly, the production of the two types of eggs implies some changes in the metabolic processes during egg production resulting in queens producing batches of either viable or trophic eggs. This would be an interesting question to study, but this is beyond the scope of this paper.

      Figure 6b is difficult to follow, and more generally, legends for all figures can be made clearer and more easy to follow.

      We agree. We have now improved the legends of Fig 6B and the other figures.

      Lines 172-174: "The percentage of eggs that were trophic was higher before hibernation...than after. This higher percentage was due to a reduced number of reproductive eggs, the number of trophic eggs laid remained stable" - are these data shown? It would be nice to see how the total egglaying rate changes after hibernation. Also, is the proportion of trophic eggs laid similar between individual queens?

      No the data were not shown and we do not have excellent data to make this point. We have therefore removed the sentence “This higher percentage was due to a reduced number of reproductive eggs, the number of trophic eggs laid remained stable” from the manuscript.

      Figure 6B: Do several colonies produce 100% gynes despite receiving trophic eggs? It would be interesting if the authors discussed why this might occur (e.g., the larvae are already fully determined to be queens and not responsive to whatever signal is in the trophic eggs).

      The reviewer is correct that 4 colonies produced 100% gynes despite receiving trophic eggs. However, the number of individuals produced in these four colonies was small (2,1,2,1, see supplementary Table 2). So, it is likely that it is just by chance that these colonies produced only gynes.

      Figure 5: Why a separation by "size distribution variation of miRNA"? What is the relevance of looking at size distributions as opposed to levels?

      We did that because there many different miRNA species, reflected by the fact that there is not just one size peak but multiple one. This is why we looked at size distribution

      Figure 2: The image of the viable embryo is not clear. If possible, redo the viable to show better quality images.

      Unfortunately, we do not anymore have colonies in the laboratory so this is not possible.

      Comments on discussion:

      Lines 236-247: Can an explanation be provided as to why the effect of trophic eggs in P. rugosus is the opposite of those observed by studies referenced in this section? Could P. rugosus have any life history traits that might explain this observation?

      In the two mentioned studies there were other factors that co-varied with variation in the quantity of trophic eggs. We mentioned that and suggested that it would be useful to conduct experimental manipulation of the quantity of trophic eggs in the Argentine ant and P. barbatus (the two species where an effect of trophic eggs had been suggested).

      The discussion should include implications and future research of the discovery.

      We made some suggestions of experiments that should be performed in the future

      The conclusion paragraph is too short and does not represent what was discussed.

      We added two sentences at the end of the paragraph to make suggestions of future studies that could be performed.

      Lines 231 to 247: Drastically reduce and move this whole part to the introduction to substantiate the assumption that trophic eggs play a nutritional role.

      We moved most of this paragraph to the introduction, as suggested by the reviewer.

      Reviewer #3 (Recommendations For The Authors):

      I would like to commend the authors on their study. The main findings of the paper are individually solid and provide novel insight into caste determination and the nature of trophic eggs. However, the inferences made from much of the data and connections between independent lines of evidence often extend too far and are unsubstantiated.

      We thank the reviewer for the positive comment. We made many changes in the manuscript to improve the discussion of our results.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      In the manuscript submission by Zhao et al. entitled, "Cardiac neurons expressing a glucagon-like receptor mediate cardiac arrhythmia induced by high-fat diet in Drosophila" the authors assert that cardiac arrhythmias in Drosophila on a high-fat diet are due in part to adipokinetic hormone (Akh) signaling activation. High-fat diet induces Akh secretion from activated endocrine neurons, which activate AkhR in posterior cardiac neurons. Silencing or deletion of Akh or AkhR blocks arrhythmia in Drosophila on a high-fat diet. Elimination of one of two AkhR-expressing cardiac neurons results in arrhythmia similar to a high-fat diet.

      Strengths:

      The authors propose a novel mechanism for high-fat diet-induced arrhythmia utilizing the Akh signaling pathway that signals to cardiac neurons.

      Weaknesses:

      Major comments:

      (1) The authors state, "Arrhythmic pathology is rooted in the cardiac conduction system." This assertion is incorrect as a blanket statement on arrhythmias. There are certain arrhythmias that have been attributable to the conduction system, such as bradycardic rhythms, heart block, sinus node reentry, inappropriate sinus tachycardia, AV nodal reentrant tachycardia, bundle branch reentry, fascicular ventricular tachycardia, or idiopathic ventricular fibrillation to name a few. However the etiological mechanism of many atrial and ventricular arrhythmias, such as atrial fibrillation or substrate-based ventricular tachycardia, are not rooted in the conduction system. The introduction should be revised to reflect a clear focus (away from?) on atrial fibrillation (AF). In addition, AF susceptibility is known to be modulated by autonomic tone, which is topically relevant (irrelevant?) to this manuscript.

      Thank you for the helpful comment. We rephrased the sentence as “Arrhythmic pathology is often rooted in the cardiac conduction system”.

      (2) The authors state that "HFD led to increased heartbeat and an irregular rhythm." In representative examples shown, HFD resulted in pauses, slower heart rate, and increased irregularity in rhythm but not consistently increased heart rate (Figures 1B, 3A, and 4C). Based on the cited work by Ocorr et al (https://doi.org/10.1073/pnas.0609278104), Drosophila heart rate is highly variable with periods of fast and slow rates, which the authors attributed to neuronal and hormonal inputs. Ocorr et al then describe the use of "semi-intact" flies to remove autonomic input to normalize heart rate. Were semi-intact flies used? If not, how was heart rate variability controlled? And how was heart rate "increase" quantified in high-fat diet compared to normal-fat diet? Lastly, how does one measure "arrhythmia" when there is so much heart rate variability in normal intact flies?

      We also observed that fly heart rate is highly variable with periods of fast and slow rates. To control heart rate variability, Ocorr et al. used semi-intact flies to record the heartbeat  (https://doi.org/10.1073/pnas.0609278104). We consider it a rigorous method to get highly consistent results with high quality videos/images. Since our work has a focus on the neuronal inputs to the heart, we did not use the semi-intact method. Our concern is that it is likely to disrupt the neuronal processes during the dissection. Using OCT, we recorded the heartbeat of intact flies in an 8 s time window, when the heartbeat was relatively stable. The different groups of flies, which were fed on a high-fat diet or a normal-fat diet, were recorded using the same method. Thus, we could compare the differences in heart rate.

      (3) The authors state, "to test whether the HFD-induced increase in Akh in the APC affects APC neuron activity, we used CaLexA (https://doi.org/10.3109/01677063.2011.642910)." According to the reference, CaLexA is a tool to map active neurons and would not indicate, as the authors state, whether Akh affects APC neuron activity specifically. It is equally possible that APC neurons may be activated by HFD and produce more Akh. Please clarify this language.

      Thank you for clarifying the calcium reporter, CaLexA. We rephrased this sentence to “to test whether HFD affects APC neuron activity, we used CaLexA”.

      (4) Are the AkhR+ neurons parasympathetic or sympathetic? Please provide additional experimentation that characterizes these neurons. The AkhR+ neurons appear to be anti-arrhythmic. Please expand the discussion to include a working hypothesis of the overall findings on Akh, AkhR, and AkhR+ neurons.

      Noyes et al. showed that Akh treatment increases heartbeat (Noyes, B. E., F. N. Katz, and M. H. Schaffer. 1995. “Identification and Expression of the Drosophila Adipokinetic Hormone Gene.” Molecular and Cellular Endocrinology 109 (2): 133–41.), suggesting that AkhR+ neurons are sympathetic. We showed that high-fat diet induced Akh expression and secretion, which led to stimulation of AkhR+ neuron and increased heart rate, supporting the sympathetic role of the AkhR+ neurons. Additional explanation on the sympathetic & anti-arrhythmic role of the Akh, AkhR, and AkhR+ neurons were added to the discussion.

      (5) The authors state, "Heart function is dependent on glucose as an energy source." However, the heart's main energy source is fatty acids with minimal use of glucose (doi: 10.1016/j.cbpa.2006.09.014). Glucose becomes more utilized by cardiomyocytes under heart failure conditions. Please amend/revise this statement.

      Thank you for pointing this out and providing the reference. We rephrased this sentence “Heart function is dependent on continuous ATP production. Cardiac ATP in Drosophila might come from fatty acids, glucose, and lactate (Kodde et al., 2007), as well as trehalose.”

      Reviewer #2 (Public Review):

      This manuscript explores mechanisms underlying heart contractility problems in metabolic disease using Drosophila as a model. They confirm, as others have demonstrated, that a high-fat diet (HFD) induces cardiac problems in flies. They showed that a high-fat diet increased Akh mRNA levels and calcium levels in the Akh-producing cells (APC), suggesting there is increased production and release of this hormone in a HFD context. When they knock down Akh production in the APCs using RNAi they see that cardiac contractility problems are abolished. They similarly show that levels of the Akh receptor (Akhr) are increased on a HFD and that loss of Akhr also rescues contractility problems on a HFD.

      One highlight of the paper was the identification of a pair of neurons that express a receptor for the metabolic hormone Akh, and showing initial data that these neurons innervate the cardiac muscle. They then overexpress cell death gene reaper (rpr) in all Akhr-positive cells with Akhr-GAL4 and see that cardiac contractility becomes abnormal.

      However, this paper contains several findings that have been reported elsewhere and it contains key flaws in both experimental design and data interpretation. There is some rationale for doing the experiments, and the data and images are of good quality. However, others have shown that HFD induces cardiac contractility problems (Birse 2010), that Akh mRNA levels are changed with HFD (Liao 2021) that Akh modulates cardiac rhythms (Noyes 1995), so Figures 1-4 are largely a confirmation of what is already known. This limits the overall magnitude of the advances presented in these figures. Overall, the stated concerns limit the impact of the manuscript in advancing our understanding of heart contractility.

      We thank the reviewer for the positive comments and appreciate the reviewer for the instructive suggestions. Birse 2010 (PMID: 21035763) was cited in our manuscript. Liao 2021 showed that Akh mRNA levels are changed with HFD. We added the reference to the revised manuscript and modified the text as: “In consistent with a previous work (Liao et al., 2020), we showed that the expression of Akh was significantly up-regulated in the flies fed a HFD, compared to NFD-fed flies (Figure 2B)”. Our qPCR verified Liao’s results. On top of this, we investigated the calcium levels in the Akh producing cells (APCs) and showed elevated calcium levels in the APC in HFD fed flies. In the revised version, we added more data to show that Akh protein levels were increased with HFD (Figure 2E-F). In line with Noyes' discovery, which showed that Akh injection caused cardioaccelation in prepupae, we showed that genetic manipulation of Akh expression affected heartbeat in the adults.   

      Reviewer #3 (Public Review):

      Zhao et al. provide new insights into the mechanism by which a high-fat diet (HFD) induces cardiac arrhythmia employing Drosophila as a model. HFD induces cardiac arrhythmia in both mammals and Drosophila. Both glucagon and its functional equivalent in Drosophila Akh are known to induce arrhythmia. The study demonstrates that Akh mRNA levels are increased by HFD and both Akh and its receptor are necessary for high-fat diet-induced cardiac arrhythmia, elucidating a novel link. Notably, Zhao et al. identify a pair of AKH receptor-expressing neurons located at the posterior of the heart tube. Interestingly, these neurons innervate the heart muscle and form synaptic connections, implying their roles in controlling the heart muscle. The study presented by Zhao et al. is intriguing, and the rigorous characterization of the AKH receptor-expressing neurons would significantly enhance our understanding of the molecular mechanism underlying HFD-induced cardiac arrhythmia.

      Many experiments presented in the manuscript are appropriate for supporting the conclusions while additional controls and precise quantifications should help strengthen the authors' augments. The key results obtained by loss of Akh (or AkhR) and genetic elimination of the identified AkhR-expressing cardiac neurons do not reconcile, complicating the overall interpretation.

      It is intriguing to see an increase in Akh mRNA levels in HFD-fed animals. This is a key result for linking HFD-induced arrhythmia to Akh. Thus, demonstrating that HFD also increases the Akh protein levels and Akh is secreted more should significantly strengthen the manuscript.

      Thank you for the positive comments and the instructive suggestions. We performed immunostaining to show that Akh protein levels increased, which is consistent with elevated Akh mRNA expression in HFD-fed flies. The data was added to Figure 2, panels E and F. Akh secretion from the APCs is regulated by APC activity (https://doi.org/10.1038/s41586-019-1675-4). We used a calcium reporter CaLexA (https://doi.org/10.3109/01677063.2011.642910) to monitor APC activity and showed that HFD increased APC activity (Figure 2, C-D).

      The experiments employing an AkhR null allele nicely demonstrate its requirement for HFD-induced cardiac arrhythmia. Depletion of Akh in Akh-expressing cells recapitulates the consequence of AkhR knockout, supporting that both Akh and its receptor are required for HFD-induced cardiac arrhythmia. Given that RNAi is associated with off-target effects and some RNAi reagents do not work, testing multiple independent RNAi lines is the standard procedure. It is also important to show the on-target effect of the RNAi reagents used in the study.

      Indeed, RNAi approaches can suffer from off-target effects. For Akh experiments, we used an RNAi line BL_34960, which was generated using artificial microRNAs shRNA (DOI: 10.1038/nmeth.1592). In comparison to long-hairpin constructs, shRNA constructs are expected to be advantageous, e.g., more efficient and minimized off-target. We performed immunostaining to determine Akh-Gal4>UAS-Akh-RNAi efficiency. We showed that anti-Akh fluorescence diminished in Akh-Gal4>UAS-Akh-RNAi APCs. The data was added to Figure 3-figure supplement 1.

      The most exciting result is the identification of AkhR-expressing neurons located at the posterior part of the heart tube (ACNs). The authors attempted to determine the function of ACNs by expressing rpr with AkhR-GAL4, which would induce cell death in all AkhR-expressing cells, including ACNs. The experiments presented in Figure 6 are not straightforward to interpret. Moreover, the conclusion contradicts the main hypothesis that elevated Akh is the basis of HFD-induced arrhythmia. The results suggest the importance of AkhR-expressing cells for normal heartbeat. However, elimination of Akh or AkhR restores normal rhythm in HFD-fed animals, suggesting that Akh and AkhR are not important for maintaining normal rhythms. If Akh signaling in ACNs is key for HFD-induced arrhythmia, genetic elimination of ACNs should unalter rhythm and rescue the HFD-induced arrhythmia. An important caveat is that the experiments do not test the specific role of ACNs. ACNs should be just a small part of the cells expressing AkhR. The experiments presented in Figure 6 cannot justify the authors' conclusion. Specific manipulation of ACNs will significantly improve the study. Moreover, the main hypothesis suggests that HFD may alter the activity of ACNs in a manner dependent on Akh and AkhR. Testing how HFD changes calcium, possibly by CaLexA (Figure 2) and/or GCaMP, in wild-type and AkhR mutants could be a way to connect ACNs to HFD-induced arrhythmia. Moreover, optogenetic manipulation of ACNs will allow for specific manipulation of ACNs, which is crucial for studying the specific role of ACNs in controlling cardiac rhythms.

      Thank you for the insightful comments. We have been trying to find a way to only target the AkhR neurons using split-Gal4. Up to now, it’s not successful. Akh/AkhR signaling shall play a key role in the ACNs, however, we cannot rule out the possibility that ACNs also receive signals other than Akh in the modulation of heartbeat.

      Interestingly, expressing rpr with AkhR-GAL4 was insufficient to eliminate both ACNs. It is not clear why it didn't eliminate both ACNs. Given the incomplete penetrance, appropriate quantifications should be helpful. Additionally, the impact on other AhkR-expressing cells should be assessed. Adding more copies of UAS-rpr, AkhR-GAL4, or both may eliminate all ACNs and other AkhR-expressing cells. The authors could also try UAS-hid instead of UAS-rpr.

      We added more data to show that AkhR+ neurons are positive in anti-Akh staining, indicating the AkhR+ neurons indeed receive Akh.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      Typo in line 765: "increased Akh section into the circulation." Section should be secretion.

      Thank you for finding the typo. We changed section to secretion.

      Reviewer #2 (Recommendations For The Authors):

      One interesting extension to our knowledge in Figures 3 & 4 is that loss of Akhr and loss of Akh both block the cardiac contractility defects that accompany a HFD. The main concern I have with the Akh finding is that the authors use only a GAL4 control and no UAS alone control. Metabolic phenotypes often show strain-specific effects, so to make conclusions it is essential that the authors include a UAS alone control alongside the other genotypes to be sure it does not rescue the cardiac contractility defects that accompany a HFD by itself.

      I am interested in the authors' identification of a pair of Akhr-positive neurons that innervate the cardiac muscle. I am not aware of any other studies identifying these neurons, or revealing their function. The contents of Figure 5 therefore represent the largest advance in the study. However, the characterization of these neurons is very superficial, and a lot more work to understand their regulation and function in a HFD context is needed to make conclusions about their role in any HFD-induced cardiac contractility problems. Or to determine how Akh influences the function of these specific neurons in an HFD context.

      The reason I say this is that the authors ablate all Akhr-positive cells in Figure 6 and show that this disturbs normal cardiac contractility. While studies on the one pair of Akhr-positive neurons would be really interesting, ablating all Akhr-positive cells, which includes the fat and many other cell types in the fly, is not a scientifically rigorous approach to answering this question. As a result, the authors are only able to make the claim that ablating many cell types throughout the animal disrupts cardiac contractility, which does not advance our understanding of mechanisms underlying heart contractility problems. In addition, because the experiments they designed did not test whether it was Akh binding to Akhr on those neurons that regulate cardiac contractility problems in a HFD context, their experiments do not support their model in Figure 7.

      The authors also make conclusions that are fairly speculative around Line 231 when describing their model in Figure 7. These claims are simply not supported by the data they present and must be removed. For example, the authors have not identified an endocrine-heart axis, they simply showed that changes in Akh can influence the heart, but this is not necessarily a direct effect on a specific cell type. They do not show data that Akh binds the newly identified Akhr-positive neuron pair to mediate the effects of HFD-induced contractility defects - they just ablate all Akhr-positive cells (fat, neurons, and other types) and show cardiac defects. If those neurons did mediate the abnormal cardiac rhythm promoted by Akh, then ablating those neurons (and not a large number of additional tissues) should rescue HFD-induced heart defects just like reducing Akhr or Akh did (but this is the opposite of what they see). Overall, concerns with experimental design, data interpretation, and relatively few findings that aren't reported elsewhere reduce the impact of this paper.

      We appreciate the positive comments and helpful suggestions. Indeed, it is important to get clean genetic access to the cardiac neurons. We intended to use split Gal4 system to target the AkhR cardiac neurons. We have tried to build a split Gal4 driver AkhR-p65.AD. Two rounds of injection were carried out. However, we did not recover a transgenic line.

      In the revised version, we performed immunostaining using Akh antibodies to show that anti-Akh fluorescence was observed in AkhR neurons (Figure 5-figure supplement 1), indicating an endocrine-heart axis.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      The manuscript by Duilio M. Potenza et al. explores the role of Arginase II in cardiac aging, majorly using whole-body arg-ii knock-out mice. In this work, the authors have found that Arg-II exerts non-cell-autonomous effects on aging cardiomyocytes, fibroblasts, and endothelial cells mediated by IL-1b from aging macrophages. The authors have used arg II KO mice and an in vitro culture system to study the role of Arg II. The authors have also reported the cell-autonomous effect of Arg-II through mitochondrial ROS in fibroblasts that contribute to cardiac aging. These findings are sufficiently novel in cardiac aging and provide interesting insights. While the phenotypic data seems strong, the mechanistic details are unclear. How Arg II regulates the IL-1b and modulates cardiac aging is still being determined. The authors still need to determine whether Arg II in fibroblasts and endothelial contributes to cardiac fibrosis and cell death. This study also lacks a comprehensive understanding of the pathways modulated by Arg II to regulate cardiac aging.

      We sincerely appreciate the valuable feedback provided by the reviewer. It's gratifying to hear that our work provided novel information on the role of arginase-II in cardiac aging which is a complex process involving various cell types and mechanisms. We have devoted considerable effort by performing new experiments to address the reviewer's comments and to delineate more detailed mechanisms of Arg-II in cardiac aging. Please, see below our specific answers to each point of the reviewers.

      Strengths:

      This study provides interesting information on the role of Arg II in cardiac aging.

      The phenotypic data in the arg II KO mice is convincing, and the authors have assessed most of the aging-related changes.

      The data is supported by an in vitro cell culture system.

      We appreciate this reviewer’s positive assessment on the strength of our study.

      Weaknesses:

      The manuscript needs more mechanistic details on how Arg II regulates IL-1b and modulates cardiac aging.

      We made great effort and have performed new experiments in human monocyte cell line (THP1) in which iNOS is not expressed and not inducible by LPS and arg-ii gene was knocked out by CRISPR technology. Moreover, murine bone-marrow derived macrophages in which inos gene was ablated, is also use for this purpose. We found that in the human THP1 monocytes in which Arg-II but not iNOS is induced by LPS (100 ng/mL for 24 hours) (Suppl. Fig. 6A), mRNA and protein levels of IL-1b precursor are markedly reduced in arg-ii knockout THP1<sup>arg-ii<sup>-/-</sup></sup> as compared to the THP1<sup>wt</sup> cells (Suppl. Fig. 6B and 6C), further confirming that Arg-II promotes IL-1b production as also shown in RAW264.7 macrophages (Suppl. Fig. 5A and 5C). Moreover, in the mouse bone-marrow-derived macrophages, LPS-induced IL-1b production is inhibited by inos deficiency (BMDM<sup>inos-/-</sup> vs BMDM<sup>wt</sup>) (Suppl. Fig. 6D and 6E), while Arg-II levels are slightly enhanced in the BMDM<sup>inos-/-</sup> cells (Suppl. Fig. 6D and 6F). All together, these results suggest that iNOS slightly reduces Arg-II expression. Arg-II and iNOS can be upregulated by LPS independently. Both Arg-II and iNOS are required for IL-1b production upon LPS stimulation as illustrated in Suppl. Fig. 6G. For detailed results and discussion, please see answers to the comments point 2 or point 6 raised by this reviewer.

      The authors used whole-body KO mice, and the role of macrophages in cardiac aging is not studied in this model. A macrophage-specific arg II Ko would be a better model.

      We fully agree with this comment of the reviewer. Unfortunately, this macrophage specific arg-ii knockout animal model is not available, yet. Future research shall develop the macrophage-specific arg-ii<sup>-/-</sup> mouse model to confirm this conclusion with aging animals. Since Arg-II is also expressed in fibroblasts and endothelial cells and exerts cell-autonomous and paracrine functions, aging mouse models with conditional arg-ii knockout in the specific cell types would be the next step to elucidate cell-specific function of Arg-II in cardiac aging. We have pointed out this aspect for future research on page 19, lines 2 to 6.

      Experiments need to validate the deficiency of Arg II in cardiomyocytes.

      As pointed out by this reviewer in the comment point 10, Arg-II was previously reported to be expressed in isolated cardiomyocytes from in rats (PMID: 16537391). Unfortunately, negative controls. i.e., arg-ii<sup>-/-</sup> samples were not included in the study to avoid any possible background signals. We made great effort to investigate whether Arg-II is present in the cardiomyocytes from different species including mice, rats and humans and have included old arg-ii<sup>-/-</sup> mouse samples as a negative control. This allows to validate the antibody specificity and background noises beyond any reasonable doubt. The new experiments in Suppl. Fig. 4 confirms the specificity of the antibody against Arg-II in old mouse kidney which is known to express Arg-II in the S3 proximal tubular cells (Huang J, et al. 2021). To exclude the possible species-specific different expression of Arg-II in the cardiomyocytes, aged mouse and rat heart tissues were used for cellular localization of Arg-II by confocal immunofluorescence staining. As shown in Suppl. Fig. 4B and 4C, both species show Arg-II expression only in non-cardiomyocytes (cells between striated cardiomyocytes) (red arrows) but not in striated cardiomyocytes. Even in the rat myocardial infarction tissues, Arg-II was not found in cardiomyocytes but in endocardium cells (Suppl. Fig. 4B). In isolated cardiomyocytes exposed to hypoxia, a well know strong stimulus for Arg-II protein levels, no Arg-II signals could be detected, while in fibroblasts from the same animals, an elevated Arg-II levels under hypoxia is demonstrated (Fig. 5B). Furthermore, even RT-qPCR could not detect arg-ii mRNA in cardiomyocytes but in non-cardiomyocytes (Fig. 5C). All together, these results demonstrate that Arg-II are not expressed or at negligible levels in cardiomyocytes but expressed in non-cardiomyocytes. This new experiments with rat heart are included in the method section on page 20, the 1st paragraph. The results are described on page 7, the 1st paragraph, and discussed on page 12, the 2nd paragraph. Legend to Suppl. Fig. 4 is included in the file “Suppl. figure legend_R”.

      The authors have never investigated the possibility of NO involvement in this mice model.

      As above mentioned, we made great effort and have performed new experiments in human monocyte cell line (THP1) in which iNOS is not expressed and not inducible by LPS and arg-ii gene was knocked out by CRISPR technology. Moreover, murine bone-marrow derived macrophages in which inos gene was ablated, is also use for this purpose. The results show that Arg-II and iNOS can be upregulated by LPS independent of each other and iNOS slightly reduces Arg-II expression. However, both Arg-II and iNOS are required for IL-1b production upon LPS stimulation. For detailed results and discussion, please see answers to the comments point 2 or point 6 raised by this reviewer.

      A co-culture system would be appropriate to understand the non-cell-autonomous functions of macrophages.

      We appreciate the suggestion by this reviewer regarding the co-culture system to test the non-cell autonomous role of Arg-II. We think that our current model, which involves treating cells with conditioned media, is a well-established and effective method for demonstrating the non-cell autonomous role of Arg-II. This approach allows us to observe the effects of Arg-II on surrounding cells through the factors present in the conditioned media released from macrophages. The co-culture system could be considered, if the released factor in the conditioned medium is not stable. This is however not the case. Therefore, we are confident that our experimental model with conditioned medium is sufficiently enough to demonstrate a paracrine effect of cell-cell interaction (please also see answers to the comment point 16.

      The Myocardial infarction data shown in the mice model may not be directly linked to cardiac aging.

      As we have introduced and discussed in the manuscript, aging is a predominant risk factor for cardiovascular disease (CVD). Studies in experimental animal models and in humans provide evidence demonstrating that aging heart is more vulnerable to stressors such as ischemia/reperfusion injury and myocardial infarction as compared to the heart of young individuals. Even in the heart of apparently healthy individuals of old age, chronic inflammation, cardiomyocyte senescence, cell apoptosis, interstitial/perivascular tissue fibrosis, endothelial dysfunction and endothelial-mesenchymal transition (EndMT), and cardiac dysfunction either with preserved or reduced ejection fraction rate are observed. Our study is aimed to investigate the role of Arg-II in cardiac aging phenotype and age-associated cardiac vulnerability to stressors. Therefore, cardiac functional changes and myocardial infarction in response to ischemia/reperfusion injury are suitable surrogate parameters for the purpose.

      Reviewer #2 (Public Review):

      Summary:

      The results from this study demonstrated a cell-specific role of mitochondrial enzyme arginase-II (Arg-II) in heart aging and revealed a non-cell-autonomous effect of Arg-II on cardiomyocytes, fibroblasts, and endothelial cells through the crosstalk with macrophages via inflammatory factors, such as by IL-1b, as well as a cell-autonomous effect of Arg-II through mtROS in fibroblasts contributing to cardiac aging phenotype. These findings highlight the significance of non-cardiomyocytes in the heart and bring new insights into the understanding of pathologies of cardiac aging. It also provides new evidence for the development of therapeutic strategies, such as targeting the ArgII activation in macrophages.

      We're grateful for the reviewer's positive feedback, acknowledging the significant findings of our study on the role of arginase-II (Arg-II) in cardiac aging. We appreciate this reviewer’s insight into the therapeutic potential of targeting Arg-II activation in macrophages and are excited about the implications for future interventions in age-related cardiac pathologies. Thank you for recognizing the importance of our work in advancing our understanding of cardiac aging and potential therapeutic strategies.

      Strengths:

      This study targets an important clinical challenge, and the results are interesting and innovative. The experimental design is rigorous, the results are solid, and the representation is clear. The conclusion is logical and justified.

      We thank this reviewer for the positive comment.

      Weaknesses:

      The discussion could be extended a little bit to improve the realm of the knowledge related to this study.

      We appreciate this comment and have added and revised our discussion on this aspect accordingly at the end of the discussion section on page 19.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      I have several critical concerns, specifically about the mechanism of how Arg-II plays a role in cardiac aging.

      My major concerns are:

      (1) The authors have shown non-cell-autonomous effects on aging cardiomyocytes, fibroblasts, and endothelial cells mediated by IL-1b from aging macrophages. A macrophage-specific Arg-II knock-out mouse model is a suitable and necessary control to establish claims.

      We fully agree with this comment of the reviewer. Unfortunately, this macrophage specific arg-ii knockout animal model is not available, yet. Future research shall develop the macrophage-specific arg-ii<sup>-/-</sup> mouse model to confirm this conclusion with aging animals. Since Arg-II is also expressed in fibroblasts and endothelial cells and exerts cell-autonomous and paracrine functions, aging mouse models with conditional arg-ii knockout in the specific cell types would be the next step to elucidate cell-specific function of Arg-II in cardiac aging. We have pointed out this aspect for future research on page 19, lines 2 to 6.

      (2) This study suggests that Arg-II exerts its effect through IL-1b in cardiac ageing. However, all experiments performed to demonstrate the link between ArgII and IL-1β are correlative at best. The underlying molecular mechanism, including transcription factors involved in the regulation of IL-1β by arg-ii, has not been demonstrated.

      We sincerely appreciate this reviewer’s comment on the aspect! To make it clear, a causal role of Arg-II in promoting IL-1β production in macrophages is evidenced by the experimental results showing that old arg-ii<sup>-/-</sup> mouse heart has lower IL-1β levels than the age-matched wt mouse heart (Fig. 6A to 6D). We further showed that the cellular IL-1β protein levels and release are reduced in old arg-ii<sup>-/-</sup> mouse splenic macrophages as compared to the wt cells (Fig. 7A, 7C, and 7D). This result is further confirmed with the mouse macrophage cell line RAW264.7 (Suppl. Fig. 5A and suppl. Fig. 5C), in which we demonstrate that silencing arg-ii reduces IL-1β levels stimulated with LPS.

      According to this reviewer’s comment (see comment point 6), we made further effort to investigate possible involvement of iNOS in Arg-II-regulated IL-1β production in macrophages stimulated with LPS. We performed new experiments in human monocyte cell line (THP1) in which iNOS is not expressed and not inducible by LPS and arg-ii gene was knocked out by CRISPR technology in the cells.

      Moreover, murine bone-marrow derived macrophages in which inos gene was ablated, is also use for this purpose. We found that in the human THP1 monocytes in which Arg-II but not iNOS is induced by LPS (100 ng/mL for 24 hours) (Suppl. Fig. 6A), mRNA and protein levels of IL-1b are markedly reduced in arg-ii knockout THP1<sup>arg-ii<sup>-/-</sup></sup> as compared to the THP1<sup>wt</sup> cells (Suppl. Fig. 6B and 6C), further confirming that Arg-II promotes IL-1b production as also shown in RAW264.7 macrophages (Suppl. Fig. 5A and 5C). The results suggest that Arg-II promotes IL-1b production independently of iNOS. Moreover, the role of iNOS in IL-1b production was also studied in the mouse bone-marrow-derived macrophages in which inos gene is ablated. The results demonstrate that LPS-induced IL-1b production is inhibited by inos deficiency (BMDM<sup>inos-/-</sup> vs BMDM<sup>wt</sup>) (Suppl. Fig. 6D and 6E), while Arg-II levels are slightly enhanced in the BMDM<sup>inos-/-</sup> cells (Suppl. Fig. 6D and 6F). Since arginase and iNOS share the same metabolic substrate L-arginine, <sup>inos-/-</sup> is expected to increase IL-1b production. This is however not the case. A strong inhibition of IL-1β production in <sup>inos-/-</sup> macrophages is observed. These results implicate that iNOS promotes IL-1β production independently of Arg-II and the inhibiting effect of IL-1β by inos deficiency is dominant and able to counteract Arg-II’s stimulating effect on IL-1β production. Hence, our results demonstrate that Arg-II promotes IL-1β production in macrophages independently of iNOS. All together, these results suggest that iNOS slightly reduces Arg-II expression. Arg-II and iNOS can be upregulated by LPS independently. Both Arg-II and iNOS are required for IL-1b production upon LPS stimulation (This concept is illustrated in the Suppl. Fig. 6G). The new results are described on page 8, the last paragraph and page 9, the 1st paragraph, presented in Suppl. Fig.6. The legend to Suppl. Fig. 6 is described in the file “Supplementary figure legend-R”. The related experimental methods are updated on page 23, the last two paragraphs and page 26 the last paragraph. The results are discussed o page 14, the last paragraph and page 15, the first two paragraphs.

      (3) Figure 2: The authors have not validated the whole-body Arg-II knock-out mice for arg-ii ablation.

      Thanks for pointing out this missing information! We have added the information regarding genotyping of the mice in the method section on page 20, first paragraph. Moreover, Fig. 5C also confirms the genotyping of the non-cardiomyocyte cells isolated from wt and arg-ii<sup>-/-</sup> animals.

      (4) It is unclear why the authors have chosen to focus on IL-1β specifically, among other pro-inflammatory cytokines that were also downregulated in Arg-II-/- mice as demonstrated in Fig. 2A-D.

      We appreciate the reviewer's question, which provides an opportunity to delve deeper into our findings. In our investigation, we observed that aging is accompanied by elevated levels of various proinflammatory markers. Intriguingly, our data revealed that tnf-α remained unaffected by the ablation of arg-ii during aging in the heart tissues, while Il-1β showed a significant reduction in arg-ii<sup>-/-</sup> animals compared to age-matched wild-type (wt) mice (Fig. 2). Mcp1 is however a chemoattractant for macrophages and F4-80 serves as a pan marker for macrophages. Moreover, our previous studies demonstrate a relationship between Arg-II and IL-1β in vascular disease and obesity and age-associated renal and pulmonary fibrosis. Finally, IL-1β has been shown to play a causal role in patients with coronary atherosclerotic heart disease as shown by CANTOS trials. Therefore, we have focused on IL-1β in this study. We have now explained and strengthened this aspect in the manuscript on page 7, the last two lines and page 8, the 1st paragraph as following:

      “Taking into account that our previous studies demonstrated a relationship of Arg-II and IL-1β in vascular disease and obesity (Ming et al., 2012) and in age-associated organ fibrosis such as renal and pulmonary fibrosis (Huang et al., 2021; Zhu et al., 2023), and IL-1β has been shown to play a causal role in patients with coronary atherosclerotic heart disease as shown by CANTOS trials (Ridker et al., 2017), we therefore focused on the role of IL-1β in crosstalk between macrophages and cardiac cells such as cardiomyocytes, fibroblasts and endothelial cells”.

      (5) Although macrophages are shown to be involved in cardiac ageing in the arg-ii mouse model, the authors have not estimated macrophage infiltration and expression of inflammatory or senescence markers in the hearts of these mice.

      Thank you very much for raising this important point! Taking the comments of the reviewer into account, we have performed new experiments, i.e., multiple immunofluorescent staining to analyze the infiltrated (CCR2<sup>+</sip>/F4-80<sup>+</sup>) and resident (LYVE1<sup>+</sup>/F4-80<sup>+</sup>) macrophage populations and to investigate to which extent that Arg-II affects the infiltrated and resident macrophage populations in the aging heart and whether this is regulated by arg-ii<sup>-/-</sup>. The results show an age-associated increase in the numbers of F4/80<sup>+</sup> cells in the wt mouse heart, which is reduced in the age-matched arg-ii<sup>-/-</sup> animals (Fig. 2G). This result is in accordance with the result of f4/80 gene expression shown in Fig. 2A, demonstrating that arg-ii gene ablation reduces macrophage accumulation in the aging heart. Interestingly, resident macrophages as characterized by LYVE1<sup>+</sup>/F4-80<sup>+</sup> cells (Fig. 2E and 2H) are predominant in the aging heart as compared to the infiltrated CCR2<sup>+</sup>/F4-80<sup>+</sup> cells (Fig. 2F and 2I). The increase in both LYVE1<sup>+</sup>/F4-80<sup>+</sup> and CCR2<sup>+</sup>/F4-80<sup>+</sup> macrophages in aging heart is reduced in arg-ii<sup>-/-</sup> mice (Fig. 2E, 2F, 2H, and 2I). These new results are described on page 6, the 1st paragraph, presented in Fig. 2E to 2I, and discussed on page 13, the 2nd, paragraph. The legend to Fig. 2 is revised. The method for this additional experiment is included on page 22, the 1st paragraph.

      Moreover, the aged-associated accumulation of the senescence cells as demonstrated by p16<sup>ink4</sup> positive cells is significantly reduced in arg-ii<sup>-/-</sup> animals. This new result is incorporated in the Fig. 1 as Fig. 1G and 1H and described / discussed on page 5, the 2nd paragraph and page 14, the 2nd last sentences of the 1st paragraph. The method of p16<sup>ink4</sup> staining is included in the method section on page 22, the 1st paragraph, line 7. The legend to Fig. 1 is revised accordingly.

      (6) Previously, Arg-II has been reported to serve a crucial role in ageing associated with reduced contractile function in rat hearts by regulating Nitric Oxide Synthase (PMID: 22160208). Elevated NO and superoxide have been shown to play crucial roles in the etiology of cardiovascular diseases (PMID: 24180388). Therefore, it is important to assess whether Nitric Oxide (NO) is involved in the aging-related phenotype in this mouse model.

      Following the reviewer's suggestion, we conducted new experiments to investigate the role of nitric oxide (NO) in the context of the effect of Arg-II-induced IL-1b production in macrophages. We have addressed this question in the response to the comment point 2.

      (7) Based on the results demonstrated in the study, ablation of Arg-II can be expected to cause a reduction in inflammation-associated phenotypes throughout the body at the multi-organ level. The observed improved cardiac phenotype could be an outcome of whole-body Arg-II ablation. It would be fruitful to develop a cardiac-specific Arg-II knockout mouse model to establish the role of Arg-II in the heart, independent of other organ systems.

      We agree with the comment of the reviewer on this point. Unfortunately, as explained above (see point 1), it is currently not possible for us to perform the requested experiments, due to lack of cardiac specific arg-ii-knockout mouse model. Moreover, such an approach is complicated by the absence of Arg-II in cardiomyocytes and the expression of Arg-II in multiple cells including endothelial cells, fibroblasts and macrophage of different origin (resident and monocyte-derived infiltrating cells). It’s thus difficult to generate a cardiac-specific gene knockout mouse. One shall investigate roles of cell-specific Arg-II in cardiac aging by generating cell-specific arg-ii<sup>-/-</sup> mice. We appreciate very this important aspect and have discussed issue on page 19, the lines 2 to 6.

      (8) Contrary to the findings in this paper, Arg-II has previously been reported to be essential for IL-10-mediated downregulation of pro-inflammatory cytokines, including IL-1β (PMID: 33674584).

      Thank you very much for mentioning this study! We have now discussed thoroughly the controversies as the following on page 15, the last paragraph and page 16, the 1st paragraph;

      “It is of note that a study reported that Arg-II is required for IL-10 mediated-inhibition of IL-1b in mouse BMDM upon LPS stimulation (Dowling et al., 2021), which suggests an anti-inflammatory function of Arg-II. The results of our present study, however, demonstrate that LPS enhances Arg-II and IL-1b levels in macrophages and knockout or silencing Arg-II reduces IL-1b production and release, demonstrating a pro-inflammatory effect of Arg-II. Our findings are supported by the study from another group, which shows decreased pro-inflammatory cytokine production including IL-6 and IL-1b in arg-ii<sup>-/-</sup> BMDM most likely through suppression of NFkB pathway, since arg-ii<sup>-/-</sup> BMDM reveals decreased activation of NFkB and IL-1b levels upon LPS stimulation (Uchida et al., 2023). Most importantly, our previous study also showed that re-introducing arg-ii gene back to the arg-ii<sup>-/-</sup> macrophages markedly enhances LPS-stimulated pro-inflammatory cytokine production (Ming et al., 2012), providing further evidence for a pro-inflammatory role of arg-ii under LPS stimulation. In support of this conclusion, chronic inflammatory diseases such as atherosclerosis and type 2 diabetes (Ming et al., 2012), inflammaging in lung (Zhu et al., 2023), kidney (Huang et al., 2021) and pancreas (Xiong, Yepuri, Necetin, et al., 2017) of aged animals or acute organ injury such as acute ischemic/reperfusion or cisplatin-induced renal injury are reduced in the arg-ii<sup>-/-</sup> mice (Uchida et al., 2023). The discrepant findings between these studies and that with IL-10 may implicate dichotomous functions of Arg-II in macrophages, depending on the experimental context or conditions. Nevertheless, our results strongly implicate a pro-inflammatory role of Arg-II in macrophages in the inflammaging in aging heart”.

      (9) The authors have only performed immunofluorescence-based experiments to show fibrotic and apoptotic phenotypes throughout this study. To verify these findings, we suggest that they additionally perform RT-PCR or western blotting analysis for fibrotic markers and apoptotic markers.

      The fibrotic aspect was analyzed not only by microscopy but also by using a quantitative biochemical assay such as hydroxyproline content assessment. Hydroxyproline is a major component of collagen and largely restricted to collagen. Therefore, the measurement of hydroxyproline levels can be used as an indicator of collagen content as previous investigated in the lung (Zhu et al., 2023). We have also measured collagen genes expression by RT-qPCR as suggested by the reviewer and found an age-related decline of collagen mRNA expression levels in both wt and arg-ii<sup>-/-</sup> mice, suggesting that the age-associated cardiac fibrosis and prevention in arg-ii<sup>-/-</sup> mice is due to alterations of translational and/or post-translational regulations, including collagen synthesis and/or degradation. The results are in accordance with that reported by other studies published in the literature. We have pointed out this aspect on page 5, the 2nd paragraph:

      “The increased cardiac fibrosis in aging is however, associated with decreased mRNA levels of collagen-Ia (col-Ia) and collagen-IIIa (col-IIIa), the major isoforms of pre-collagen in the heart (Suppl. Fig. 2A and 2B), which is a well-known phenomenon in cardiac fibrotic remodelling (Besse et al., 1994; Horn et al., 2016). The results demonstrate that age-associated cardiac fibrosis and prevention in arg-ii<sup>-/-</sup> mice is due to alterations of translational and/or post-translational regulations including collagen synthesis and/or degradation”.

      The results are presented in Suppl. Fig. 2, legend to Suppl. Fig. 2 is included in the file “Suppl. figure legend_R”. Suppl. table 2 for primers is revised accordingly.

      We did not use additional markers to perform apoptotic assays with whole heart, since Fig. 3 shows good evidence that the aging is associated with increased apoptotic cells in the heart and significantly reduced in the arg-ii<sup>-/-</sup> mice. The reduction of TUNEL positive (apoptotic) cells in aged arg-ii<sup>-/-</sup> mice is mainly due to decrease in apoptotic cardiomyocytes. With the histological analysis, the apoptotic cell types can be well analysed. Moreover, biochemical assay for apoptosis such as caspase-3 cleavage with whole heart tissues can not distinguish apoptotic cell types and may not be sensitive enough for aging heart, due to relatively low numbers of apoptotic cells in aging heart as compared to myocardial infarct model.  

      (10) Figure 4: arg-ii has previously been reported to be expressed in rat cardiomyocytes (PMID: 16537391). We strongly suggest the authors verify the expression of Arg-II via immunostaining in isolated cardiomyocytes (using published protocols), and by using multiple different cardiomyocyte-specific markers for colocalization studies to prove the lack of arg-ii expression beyond a reasonable doubt.

      As pointed out by this reviewer, Arg-II was previously reported to be expressed in isolated cardiomyocytes from in rats (PMID: 16537391). Unfortunately, negative controls. i.e., arg-ii<sup>-/-</sup> samples were not included in the study to avoid any possible background signals. We made great effort to investigate whether Arg-II is present in the cardiomyocytes from different species including mice, rats and humans and have included old arg-ii<sup>-/-</sup> mouse samples as a negative control. This allows to validate the antibody specificity and background noises beyond any reasonable doubt. The new experiments in Suppl. Fig. 4 confirms the specificity of the antibody against Arg-II in old mouse kidney which is known to express Arg-II in the S3 proximal tubular cells (Huang J, et al. 2021). To exclude the possible species-specific different expression of Arg-II in the cardiomyocytes, aged mouse and rat heart tissues were used for cellular localization of Arg-II by confocal immunofluorescence staining. As shown in Suppl. Fig. 4B and 4C, both species show Arg-II expression only in non-cardiomyocytes (cells between striated cardiomyocytes) (red arrows) but not in striated cardiomyocytes. Even in the rat myocardial infarction tissues, Arg-II was not found in cardiomyocytes but in endocardium cells (Suppl. Fig. 4B). In isolated cardiomyocytes exposed to hypoxia, a well know strong stimulus for Arg-II protein levels, no Arg-II signals could be detected, while in fibroblasts from the same animals, an elevated Arg-II levels under hypoxia is demonstrated (Fig. 5B). Furthermore, RT-qPCR could not detect arg-ii mRNA in cardiomyocytes but in non-cardiomyocytes (Fig. 5C). All together, these results demonstrate that Arg-II are not expressed or at negligible levels in cardiomyocytes but expressed in non-cardiomyocytes. This new experiments with rat heart are included in the method section on page 20, the 1st paragraph. The results are described on page 7, the 1st paragraph, and discussed on page 12, the 2nd paragraph. Legend to Suppl. Fig. 4 is included in the file “Suppl. figure legend_R”.

      (11) Figure 6G: It may be worthwhile to supplement arg-ii<sup>-/-</sup> old cells with IL-1beta to see if there is an increase in TUNEL-positive cells.

      IL-1b is a well known pro-inflammatory cytokine that causes apoptosis in various cell types including cardiomyocytes (Shen Y., et al., Tex Heart Inst J. 2015;42:109–116. doi: 10.14503/THIJ-14-4254; Liu Z. et. al., Cardiovasc Diabetol 2015;14,125. doi: 10.1186/s12933-015-0288-y; Li. Z., et al., Sci Adv 2020;6:eaay0589. doi: 10.1126/sciadv.aay0589). We appreciate very much the interesting idea of this reviewer to investigate the apoptotic responses of cardiomyocytes from arg-ii<sup>-/-</sup> mice to IL-1b. We agree that it is possible that cardiomyocytes from wt from arg-ii<sup>-/-</sup> mice react differently to IL-1b, although the cardiomyocytes do not express Arg-II as demonstrated in our present study. If this is true, it must be due to non-cell autonomous effects of different aging microenvironment in the heart or epigenetic modulations of the myocytes. We found that this is a very interesting aspect and requires further extensive investigation. Since our current study focused on the effect of wt and arg-ii<sup>-/-</sup> macrophages on cardiomyocytes and non-cardiomyocytes, we prefer not to include this suggested aspect in our manuscript and would like to explore it in the following study.

      (12) Figures 4-9: It would be interesting to see if the effect of ArgII in cardiac ageing is gender-specific. It is recommended to include experimental data with male mice in addition to the results demonstrated in female mice.

      As pointed out in the manuscript, we have focused on female mice, because an age-associated increase in arg-ii expression is more pronounced in females than in males (Fig. 1A). As suggested by this reviewer, we performed additional experiments investigating effects of arg-ii deficiency in male mice during aging, focusing on pathophysiological outcomes of ischemia/reperfusion injury in ex vivo experiments. The ex vivo functional analytic experiments with Langendorff system were performed in aged male mice (see Suppl. Fig. 9). Following ischemia/reperfusion injury, wt male mice display reduced left ventricular developed pressure (LVDP), as well as the inotropic and lusitropic states (expressed as dP/dt max and dP/dt min, respectively). As previously reported (Murphy et al., 2007), we also found that old male mice are more prone to I/R injury than age-matched female animals. Specifically, 15 minutes of ischemia are enough to significantly affect the left ventricle contractile function in the male mice (Suppl. Fig. 9). As opposite, age-matched old female mice are relatively resistant to I/R injury, and at least 20 min of ischemia are necessary to induce a significant impairment of the contractile function (Fig. 10). Similar to females, the post I/R recovery of cardiac function is also significantly improved in the male arg-ii<sup>-/-</sup> mice as compared to age-matched wt animals. In addition to functional recovery, triphenyl tetrazolium chloride (TTC) staining (myocardial infarction) upon I/R-injury in males is significantly reduced in the age-matched male arg-ii<sup>-/-</sup> animals (Suppl. Fig. 9C and 9D). All together, these results reveal a role for Arg-II in heart function impairment during aging in both genders with a higher vulnerability to stress in the males. These new results are presented in Suppl. Fig. 9, described on page 10, the last paragraph and page 11. The results are discussed on page 18, the 2nd paragraph as following:

      “The fact that aged females have higher Arg-II but are more resistant to I/R injury seems contradictory to the detrimental effect of Arg-II in I/R injury. It is presumable that cardiac vulnerability to injuries stressors depends on multiple factors/mechanisms in aging. Other factors/mechanisms associated with sex may prevail and determine the higher sensitivity of male heart to I/R injury, which requires further investigation. Nevertheless, the results of our study show that Arg-II plays a role in cardiac I/R injury also in males”.

      The information on the experimental methods in the male animals is included on page 20, the last paragraph and page 21, the 1st paragraph. Legend to Suppl. Fig. 9 is included in the file “Suppl. figure legend_R”.

      (13) Figure 6G: cardiomyocytes from wild-type mice, when treated with macrophages, show 0% TUNEL-positive cells. Since it is unlikely to obtain no TUNEL staining in a cell population, there may be an experimental or analytical error.

      Now it is Fig. 7F and 7G. This is due to our specific experimental procedure. After tissue digestion, cardiomyocytes were plated on laminin-coated dishes. Laminin promotes the adhesion of survived cells. Following plating, we conducted a deep washing process to remove damaged and partially adherent cells. This step ensures that only well-shaped, viable, and strongly adherent cells remain as bioassay cells. These “healthy” cells are then selected for the experiments. the apoptotic cells are removed by washing out, reflecting the high viability of the bioassay cells. We have added this detailed information in the method section on page 24, the 2nd paragraph.

      (14) Figure 7J: Please assess whether arg-ii depletion also affects the mtROS phenotype.

      According to the suggestion of this reviewer, we performed new experiments which show that human cardiac fibroblasts (HCFs) exposed to hypoxia (1% O<sub>2</sub>, 48 hours), a known physiological trigger of Arg-II up-regulation, exhibit increased mtROS generation, which involves Arg-II (new Fig. 8M to 8P). We found that Arg-II protein level as well as mtROS (assessed by mitoSOX staining) were both enhanced, accompanied by increased levels of HIF1α (Fig 8M). Moreover, mito-TEMPO pre-incubation reduces mtROS, confirming the mitochondrial origin of the ROS. Silencing of arg-ii with rAd-mediated shRNA, significantly reduces mtROS levels demonstrating a role of Arg-II in the production of mitochondrial ROS in cardiac fibroblasts (Fig 8M to 8P). We have included these results on page 9, the last paragraph and discussed the results on page 17, the 1st paragraph. The related method is described on page 26, the 2nd paragraph. Legend to Fig. 8 is updated on page 32.

      (15) Figure 8A-E: The authors have treated human-origin endothelial cells with mice-origin macrophage-conditioned media. It would be more suitable to treat the endothelial cells with human-origin macrophage-conditioned media.

      We acknowledge the concern regarding the use of mouse-origin macrophage-conditioned media on human-origin endothelial cells. It is to note, the biological cross-reactivity of cytokines from one species on cells from a different species has been reported in the literature. It was observed that there is quite a strict threshold of 60% amino acid identity, above which cytokines tend to cross-react and statistically, cytokines would tend to cross-react more often as their % amino acid identity increases (Scheerlinck JPY. Functional and structural comparison of cytokines in different species. Vet Immunol Immunopathol. 1999; 72:39-44. https://doi.org/10.1016/S0165-2427(99)00115-4). Taking IL-1b as an example, the 17.5 kDa mature mouse and human IL-1b share 92% aa sequence identity, suggesting a high cross-reactivity. Indeed, human IL-1b has shown biological cross-reactivity in mouse cells (Ledesma E., et al. Interleukin-1 beta (IL-1β) induces tumor necrosis factor alpha (TNF-α) expression on mouse myeloid multipotent cell line 32D cl3 and inhibits their proliferation. Cytokine. 2004; 26:66-72. https://doi.org/10.1016/j.cyto.2003.12.009). Moreover, our results also support the reported cross-reactivity between human and mouse IL-1b. The CM from mouse macrophage indeed showed biological function in human endothelial cells. The observed effects of the conditioned media from aged wild-type macrophages on endothelial cells were specifically mediated through IL-1β. This conclusion is supported by our data showing that the upregulation induced by the conditioned media was significantly reduced by the addition of an IL-1β receptor blocker.

      (16) The co-culture system would be more interesting to test the non-cell autonomous role of Arg II.

      We appreciate the suggestion by this reviewer regarding the co-culture system to test the non-cell autonomous role of Arg-II. We believe that our current model, which involves treating cells with conditioned media, is a well-established and effective method for demonstrating the non-cell autonomous role of Arg-II. This approach allows us to observe the effects of Arg-II on surrounding cells through the factors present in the conditioned media. The co-culture system could be considered, if the released factor in the conditioned medium is not stable. This is however not the case. So we are confident that our experimental model with conditioned medium is good enough to demonstrate a paracrine effect of cell-cell interaction.

      Reviewer #2 (Recommendations For The Authors):

      Some minor comments may be considered to improve the realm of the knowledge related to this study.

      We appreciate this comment and have added and revised our discussion on this aspect accordingly at the end of the discussion section on page 19, the last 6 lines.

      (1) The current study showed strong evidence demonstrating the key role of cardiac macrophages in pathologies of cardiac aging, particularly, the macrophages (MФ) from the circulating blood (hematogenous). It is known that the heart is among the minority of organs in which substantial numbers of yolk-sac MФ persist in adulthood and play a crucial role in maintaining cardiac function. Thus, the adult mammalian heart contains two separate and discrete cardiac MФ subgroups, i.e., the resident MФs originated from yolk sac-derived progenitors and the hematogenous MФs recruited from circulating blood monocytes. These two subtypes of MФs may play distinctive roles in the aging heart and the response to cardiac injury. The author could extend the discussion on the possibility of the resident MФs in aging hearts, which could be further investigated in the future.

      We appreciate the suggestion and agree that it provides valuable insight into the study. Taking the comments of the reviewer 1 into account, we have performed new experiments, i.e., co- immunostaining to analyze the infiltrated (CCR2<sup>+</sup>/F4-80<sup>+</sup>) and resident (LYVE1<sup>+</sup>/F4-80<sup>+</sup>) macrophage populations and to investigate to which extent that Arg-II affects infiltrated and resident macrophage populations in the aging heart. We found that in line with the gene expression of f4/80, immunofluorescence staining reveals an age-associated increase in the numbers of F4/80<sup>+</sup> cells in the wt mouse heart, which is reduced in the age-matched arg-ii<sup>-/-</sup> animals (Fig. 2E, F, G), demonstrating that arg-ii gene ablation reduces macrophage accumulation in the aging heart. Interestingly, resident macrophages as characterized by LYVE1<sup>+</sup>/F4-80<sup>+</sup> cells (Fig. 2E and 2H) are predominant in the aging heart as compared to the infiltrated CCR2<sup>+</sup>/F4-80<sup>+</sup> cells (Fig. 2F and 2I). The increase in both LYVE1<sup>+</sup>/F4-80<sup>+</sup> and CCR2<sup>+</sup>/F4-80<sup>+</sup> macrophages in aging heart is reduced in arg-ii<sup>-/-</sup> mice (Fig. 2E, 2F, 2H, and 2I). These new results are described on page 6, the 1st paragraph, presented in Fig. 2E to 2I, and discussed on page 13, the 2nd, paragraph. The legend to Fig. 2 is revised. The method for this additional experiment is included on page 22, the 1st paragraph.

      (2) It would be beneficial to the readers if the author could provide some explanation about why ArgII could not be detected in VSMCs in the mouse heart and the species difference between humans and mice. In addition, the author may provide an assumption on the possibility that there may also be a cross-talk between macrophages and VSMCs in the aging heart. A little bit more explanation in the Discussion will be helpful.

      We acknowledge and appreciate the suggestion and have discussed these points on page 19 as the following:

      “In this context, another interesting aspect is the cross-talk between macrophages and vascular SMC in the aging heart. In our present study, we could not detect Arg-II in vascular SMC of mouse heart but in that of human heart. This could be due to the difference in species-specific Arg-II expression in the heart or related to the disease conditions in human heart which is harvested from patients with cardiovascular diseases. Indeed, in the apoe<sup>-/-</sup> mouse atherosclerosis model, aortic SMCs do express Arg-II (Xiong et al., 2013). It is interesting to note that rodents hardly develop atherosclerosis as compared to humans. Whether this could be partly contributed by the different expression of Arg-II in vascular SMC between rodents and humans requires further investigation. In our present study, the aspect of the cross-talk between macrophages and vascular SMC is not studied. Since the crosstalk between macrophages and vascular SMC has been implicated in the context of atherogenesis as reviewed (Gong et al., 2025), further work shall investigate whether Arg-II expressing macrophages could interact with vascular SMC in the coronary arteries in the heart and contribute to the development of coronary artery disease and/or vascular remodelling and the underlying mechanisms“.

      (3) Please clarify the arrows in Figure 9C that indicate the infarct area in each splicing section from one heart.

      The arrows in Figure 9C (now Fig. 10C) are indeed utilized to indicate the sections displaying the infarcted area within each splicing section from one heart. We have explained the arrow in the figure legend (now Fig. 10 and also new Suppl. Fig. 9).

    1. Author response:

      Our response aims to address the following:

      The lack of pleiotropy is an unconfirmable assumption of MR, and the addition of those models is therefore quite important, as this is a primary weakness of the MR approach. Given that concern, I read the sensitivity analyses using pleiotropy-robust models as the main result, and in that case, they can't test their hypotheses as these models do not show a BMI instrumental variable association. The other weakness, which might be remedied, is that the power of the tests here is not described. When a hypothesis is tested with an under-powered model, the apparent lack of association could be due to inadequate sample size rather than a true null. Typically, when a statistically significant association is reported, power concerns are discounted as long as the study is not so small as to create spurious findings. That is the case with their primary BMI instrumental variable model - they find an association so we can presume it was adequately powered. But the primary models they share are not the pleiotropy-robust methods MR-Egger, weighted median, and weighted mode. The tests for these models are null, and that could mean a couple of things: (1) the original primary significant association between the BMI genetic instrument was due to pleiotropy, and they therefore don't have a robust model to explore the effects of the tobacco genetic instrument. (2) The power for the sensitivity analysis models (the pleiotropy-robust methods) is inadequate, and the authors share no discussion about the relative power of the different MR approaches. If they do have adequate power, then again, there is no need to explore the tobacco instrument.

      We would like to highlight that post-hoc power calculations are often considered redundant since the statistical power estimated for an observed association is directly related to its p-value[1]. In other words, the uncertainty of the association is already reflected in its 95% confidence interval. However, we understand power calculations may still be of interest to the reader, so we will incorporate them in the revised manuscript.

      The reason we use inverse variance weighted (IVW) Mendelian randomization (MR) to obtain our main results rather than the pleiotropy-robust methods mentioned by the reviewer/editors (i.e., MR-Egger, weighted median and weighted mode) is that the former has greater statistical power than the latter[2]. Hence, instead of focussing on the statistical significance of the pleiotropy-robust analyses, we consider it is of more value to compare the consistency of the effect sizes and direction of the effect estimates across methods. Any evidence of such consistency increases our confidence in our main findings, since each method relies on different assumptions. As we cannot be sure about the presence and nature of horizontal pleiotropy, it is useful to compare results across methods even though they are not equally powered. It is true that our results for the genetically predicted effects of body mass index (BMI) on the risk of head and neck cancer (HNC) differ across methods. This is precisely what led us to question the validity of our main finding (suggesting a positive effect of BMI on HNC risk). We will clarify this in the discussion section of the revised manuscript as advised.

      We understand that the reviewer/editors are concerned that we do not have a robust model to explore the role of tobacco consumption in the link between BMI and HNC. However, we have a different perspective on the matter. If indeed, the main IVW finding for BMI and HNC is due to pleiotropy (since some of the pleiotropy-robust methods suggest conflicting results), then the IVW multivariable MR method is a way to explore the potential source of this bias[3]. We were particularly interested in exploring the role of smoking in the observed association because smoking and adiposity are known to influence each other [4-9] and share a genetic basis[10, 11].

      References:

      (1) Heinsberg LW, Weeks DE: Post hoc power is not informative. Genet Epidemiol 2022, 46(7):390-394.

      (2) Burgess S, Butterworth A, Thompson SG: Mendelian randomization analysis with multiple genetic variants using summarized data. Genet Epidemiol 2013, 37(7):658-665.

      (3) Burgess S, Davey Smith G, Davies NM, Dudbridge F, Gill D, Glymour MM, Hartwig FP, Kutalik Z, Holmes MV, Minelli C et al: Guidelines for performing Mendelian randomization investigations: update for summer 2023. Wellcome Open Res 2019, 4:186.

      (4) Morris RW, Taylor AE, Fluharty ME, Bjorngaard JH, Asvold BO, Elvestad Gabrielsen M, Campbell A, Marioni R, Kumari M, Korhonen T et al: Heavier smoking may lead to a relative increase in waist circumference: evidence for a causal relationship from a Mendelian randomisation meta-analysis. The CARTA consortium. BMJ Open 2015, 5(8):e008808.

      (5) Taylor AE, Morris RW, Fluharty ME, Bjorngaard JH, Asvold BO, Gabrielsen ME, Campbell A, Marioni R, Kumari M, Hallfors J et al: Stratification by smoking status reveals an association of CHRNA5-A3-B4 genotype with body mass index in never smokers. PLoS Genet 2014, 10(12):e1004799.

      (6) Taylor AE, Richmond RC, Palviainen T, Loukola A, Wootton RE, Kaprio J, Relton CL, Davey Smith G, Munafo MR: The effect of body mass index on smoking behaviour and nicotine metabolism: a Mendelian randomization study. Hum Mol Genet 2019, 28(8):1322-1330.

      (7) Asvold BO, Bjorngaard JH, Carslake D, Gabrielsen ME, Skorpen F, Smith GD, Romundstad PR: Causal associations of tobacco smoking with cardiovascular risk factors: a Mendelian randomization analysis of the HUNT Study in Norway. Int J Epidemiol 2014, 43(5):1458-1470.

      (8) Carreras-Torres R, Johansson M, Haycock PC, Relton CL, Davey Smith G, Brennan P, Martin RM: Role of obesity in smoking behaviour: Mendelian randomisation study in UK Biobank. BMJ 2018, 361:k1767.

      (9) Freathy RM, Kazeem GR, Morris RW, Johnson PC, Paternoster L, Ebrahim S, Hattersley AT, Hill A, Hingorani AD, Holst C et al: Genetic variation at CHRNA5-CHRNA3-CHRNB4 interacts with smoking status to influence body mass index. Int J Epidemiol 2011, 40(6):1617-1628.

      (10) Thorgeirsson TE, Gudbjartsson DF, Sulem P, Besenbacher S, Styrkarsdottir U, Thorleifsson G, Walters GB, Consortium TAG, Oxford GSKC, consortium E et al: A common biological basis of obesity and nicotine addiction. Transl Psychiatry 2013, 3(10):e308.

      (11) Wills AG, Hopfer C: Phenotypic and genetic relationship between BMI and cigarette smoking in a sample of UK adults. Addict Behav 2019, 89:98-103.

    1. Author response:

      Reviewer #1 (Public review):

      Summary:

      Mast cells have previously been reported to play an important role in bacterial immune defense and act protectively in sepsis. However, many of these findings were based on studies using Kit mutant mice. In this study, the authors conducted a detailed investigation using mast cell-deficient Cpa3 Cre-Master mice. As a result, the authors found that the Cpa3 Cre-Master mice exhibited responses similar to wild-type mice in terms of bacterial immune defense. This suggests that the observed phenotype is not due to mast cell-dependent bacterial immune defense, but rather is associated with dysbiosis of the gut microbiota.

      Strengths:

      Mast cells have long been reported to play an important role in the protective response against sepsis, and their function in infection defense has been demonstrated. However, Kit mutant mice have been reported to exhibit impaired peristalsis, and several mast cell-specific genetically modified mouse lines have since been developed and examined in detail. This study presents an important finding by logically demonstrating that the exacerbation of sepsis in Kit mice is due to alterations in the gut microbiota, and that the phenotype previously thought to be mast cell-dependent was, in fact, not.

      In addition, the experiments were carefully designed using mice with matched genetic backgrounds. These findings underscore the importance of microbiota composition in interpreting immune phenotypes and highlight the need for co-housing controls in mutant mouse studies.

      A major strength of this work is the robustness of the CLP data, generated over eight years by three independent researchers across two institutions with large sample sizes, lending strong support to the conclusions.

      Weaknesses:

      The study assesses only a limited subset of gut bacterial species, leaving the extent to which E. coli expansion contributes to the observed phenotype unclear.

      We will add new data based on 16S rRNA sequencing to the revised version.

      Moreover, in the cohousing experiments, there is no evidence provided to confirm successful microbiota normalization between groups.

      We note that co-housing is a generally accepted method for microbiota equalization or conversion (Caruso et al., Cell Rep. 2019, Ridaura et al., Science 2013, and reviewed in Moore et al., Clin. Transl. Immunol. 2016). In any case, Kit<sup>W/Wv</sup> mutants were made resistant to CLP by co-housing. Similar microbiota sequencing results between groups,while useful, would again only be correlative.

      A more detailed analysis of the microbial composition would be necessary to strengthen the reliability of the findings.

      See above

      It is also important to note that Cpa3-deficient mice exhibit not only mast cell depletion but also defects in basophils and T cells. These additional immunological alterations may counterbalance one another, potentially masking phenotypic changes and complicating interpretation.

      Regarding basophils in Cpa3<sup>Cre</sup> mice, compared to wild-type mice, basophils are reduced to about 39% of normal (Feyerabend et al., Immunity 2011). In Kit<sup>W/Wv</sup> mice, compared to wild-type mice, basophils are reduced to about 11% of normal. To our knowlegde, there has been no phenotype reported in which a reduction in basophils compensates for the loss for mast cells. Given that Kit<sup>W/Wv</sup> mice have about threefold lower numbers of basophils, and are highly susceptible to sepsis, there is no evidence that a reduction in basophils is protective in mast cell-deficient mice. On the contrary, mice that were normal for mast cells but had their basophils depleted were more susceptible to sepsis (Piliponsky et al., Nat. Immunol. 2019). Hence, basophils appear to be protective, and their reduction increases susceptibility. In light of these data and considerations, there is no evidence for a reduction in basophils to counterbalance the loss of mast cells in Cpa3<sup>Cre</sup> mice.

      Regarding T cells, there is no evidence, and there are no reports, that Cpa3<sup>Cre</sup> mice have defects in T cells (Feyerabend et al., Immunity 2011, Feyerabend et al., Cell Metabolism 2016). Cpa3 is weakly and transiently expressed early in the T cell lineage (Feyerabend et al., Immunity 2009; for expression levels in T cells versus mast cells, see below figure from the Immgen Database). In summary, in contrast to the reviewer's claim, there are no known defects in T cell development or functions in Cpa3<sup>Cre</sup> mice.

      Author response image 1.

      Generated from the Immgen database. Shown are RNAseq gene expression levels of diverse T-cell and mast cell populations.

      Furthermore, it remains to be determined whether the altered gut microbiota observed in Kit<sup>W/Wv</sup> mice is a consequence of impaired intestinal motility, whether a similar phenotype is observed in KitW-sh/W-sh mice, and whether comparable results occur in SCF-deficient models. Addressing these questions would provide greater clarity on the contribution of mast cells versus secondary factors in the observed phenotypes.

      Mice without mast cells (Cpa3<sup>Cre</sup> mice) are as resistant to sepsis as wild-type mice. Hence, mast cells are not involved in the immunity against sepsis, and 'secondary factors' are not involved in this simple experiment (both groups of mice, wild type and Cpa3<sup>Cre</sup> mice, were on the idential genetic background). Second, Kit<sup>W/Wv</sup> mice are also as resistant to sepsis as wild-type mice when confronted with the identical intestinal slurry. Therefore, Kit<sup>W/Wv</sup> mice have no immune deficit in response to sepsis. Hence, in our view, the underlying immunological question regarding the role of mast cells in sepsis has been conclusively addressed by our data. Future studies may address the mechanism that causes dysbiosis in Kit<sup>W/Wv</sup> mice, and other Kit mutants and steel mutants could be examined as well. These questions are, however, unrelated to the role of mast cells in sepsis, or the response of Kit<sup>W/Wv</sup> mice to sepsis, and would therefore not affect the central conclusion of our manuscript ("Susceptibility of Kit-mutant mice to sepsis caused by enteral dysbiosis, not mast cell deficiency").

      Given that Kit<sup>W/Wv</sup> mice exhibit impaired peristalsis, is the observed increase in E. coli a consequence of this dysfunction?

      See above

      Previous studies with BMMC reconstitution experiments have indicated that mast cells are a source of TNF - how does this align with the current findings?

      It is possible that cultured and transplanted mast cells (BMMC) produce TNF. Given that we did not find a reduction in TNF levels in the peritoneal lavage or serum in mice without mast cells undergoing sepsis, under physiological conditions mast cell-derived TNF does not seem to have a measuable impact on total TNF levels.

      Reviewer #2 (Public review):

      Summary:

      This study presents a useful finding that the high susceptibility to CLP sepsis of Kit-mutant mice is not due to mast cell deficiency, but to dysbiosis.

      However, the present data are insufficient and incomplete to support the conclusion, and would benefit from more rigorous approaches. With the mechanism part strengthened, this paper would be of interest to researchers on mast cell biology and mucosal immunology.

      We disagree with this view that our data are insufficient and incomplete. Our results demonstrate that mice lacking mast cells (Cpa3<sup>Cre</sup> mice) are as resistant to sepsis as wild-type mice, indicating that mast cells do not play a detectable role in immunity against sepsis. Additionally, we show that Kit<sup>W/Wv</sup> mice exhibit the same resistance to sepsis as wild-type mice when confronted with the identical intestinal slurry. This finding demonstrates that Kit<sup>W/Wv</sup> mice have no immune deficit in response to sepsis. These central data are both sufficient and complete, given that our data fully address the immunological questions regarding the role of mast cells in sepsis. Our study aimed to investigate the role of mast cells in sepsis, not to examine the mechanisms of dysbiosis or associated pathological phenotypes in Kit mutant controls.

      Recommendations:

      (1) The authors showed that E. coli increases in the cecum of Kit-mutant mice, which causes high CLP susceptibility. However, they did not provide any evidence E. coli is responsible for the high susceptibility.

      We showed that E. coli CFUs were increased in the cecum of Kit-mutant mice, but we did not state that this causes CLP susceptibility. We wrote: 'Hence, Kit<sup>W/Wv</sup> microbiota contains high levels of E. coli, which may underlie the observed pathogenicity'. We demonstrated that intestinal slurry from Kit<sup>W/Wv</sup> mice is more pathogenic compared to intestinal slurry from wild-type mice. However, we did not search for, or identify the bacterial species that causes this increased pathogenicity because we were adressing the role of mast cell in sepsis. 

      In the Figure 3 experiments, the authors administered the same number of cecal bacteria and did not show the number of E. coli after the administration.

      The samples were split and one aliquot was analysed by microbiology and the other aliquot was injected intraperitoneally. Fig. 3d shows the colony forming units (for Lactobacilli and E coli) from aliquots of cecal slurry used in the intraperitoneal injection experiments shown in Fig. 3a-c. Hence, our data show the colony forming units that were injected into the mice. It is unclear to us why this is not the key information rather than 'the number of E. coli after the administration'.

      The authors should provide evidence showing that depletion of E. coli decreases susceptibility.

      See response to point 1 above.

      (2) The author should provide direct evidence of dysbiosis by, for example, shotgun sequencing of cecal and fecal contents.

      The large increase in E coli counts in Kit<sup>W/Wv</sup> is evidence of dysbiosis. To obtain data beyond classical microbiology, we also performed 16S rRNA sequencing which will be included in the revision.

      (3) In case the authors find dysbiosis, they should analyze the mechanisms by which Kit mutation causes dysbiosis.

      The mechanism that causes dysbiosis in Kit<sup>W/Wv</sup> mice (which emerged from our work) belongs to other research areas that address the role of Kit in intestinal pathophysiology. These questions are unrelated to the role of mast cells in sepsis, or the response of Kit<sup>W/Wv</sup> mice to sepsis. Regardless of the results of such experiments, the conclusion ("Susceptibility of Kit-mutant mice to sepsis caused by enteral dysbiosis, not mast cell deficiency") remains unaffected. In brief, further explorations of pathological phenotypes of a control mutant will not add to the core message. Along these lines, the review process and the revision shall center on making the core of a paper as conclusive as possible, and not widen a paper by requests 'tangential to the main conclusion' (Kaelin Jr. Nature 2017).

      References

      Caruso, R., Ono, M., Bunker, M. E., Núñez, G. & Inohara, N. Dynamic and Asymmetric Changes of the Microbial Communities after Cohousing in Laboratory Mice. Cell Rep. 27, 3401-3412.e3 (2019).

      Feyerabend, T. B. et al. Deletion of Notch1 Converts Pro-T Cells to Dendritic Cells and Promotes Thymic B Cells by Cell-Extrinsic and Cell-Intrinsic Mechanisms. Immunity 30, 67–79 (2009).

      Feyerabend, T. B. et al. Cre-Mediated Cell Ablation Contests Mast Cell Contribution in Models of Antibody- and T Cell-Mediated Autoimmunity. Immunity 35, 832–844 (2011).

      Feyerabend, T. B., Gutierrez, D. A. & Rodewald, H.-R. Of Mouse Models of Mast Cell Deficiency and Metabolic Syndrome. Cell Metab 24, 1–2 (2016).

      Kaelin Jr, W. G. Publish houses of brick, not mansions of straw. Nature 545, 387–387 (2017).

      Moore, R. J. & Stanley, D. Experimental design considerations in microbiota/inflammation studies. Clin. Transl. Immunol. 5, e92 (2016).

      Piliponsky, A. M. et al. Basophil-derived tumor necrosis factor can enhance survival in a sepsis model in mice. Nat. Immunol. 20, 129–140 (2019).

      Ridaura, V. K. et al. Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice. Science 341, 1241214 (2013).

    1. Author response:

      The following is the authors’ response to the previous reviews

      In response to Reviewer #1, we have replaced the original images in Figure 1A with new immunofluorescence data showing matched DAPI staining density between control and AD patient samples. We also have updated the PINK1 staining images of mouse brain sections in Figure 1C to eliminate potential non-specific signals. These revisions provide clearer evidence supporting our conclusions about PINK1/pUb’s role in neurodegeneration.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary

      In this beautiful paper the authors examined the role and function of NR2F2 in testis development and more specifically on fetal Leydig cells development. It is well known by now that FLC are developed from an interstitial steroidogenic progenitors at around E12.5 and are crucial for testosterone and INSL3 production during embryonic development, which in turn shapes the internal and external genitalia of the male. Indeed, lack of testosterone or INSL3 are known to cause DSD as well as undescended testis, also termed as cryptorchidism. The authors first characterized the expression pattern of the NR2R2 protein during testis development and then used two cKO systems of NR2F2, namely the Wt1-creERT2 and the Nr5a1-cre to explore the phenotype of loss of NR2F2. They found in both cases that mice are presenting with undescended testis and major reduction in FLC numbers. They show that NR2F2 has no effect on the amount and expression of the progenitor cells but in its absence, there are less FLC and they are immature.

      The effect of NR2F2 is cell autonomous and does not seem to affect other signalling pathways implemented in Leydig cell development as the DHH, PDGFRA and the NOTCH pathway.

      Overall, this paper is excellent, very well written, fluent and clear. The data is well presented, and all the controls and statistics are in place. I think this paper will be of great interest to the field and paves the way for several interesting follow up studies as stated in the discussion

      Reviewer #2 (Public review):

      The major conclusion of the manuscript is expressed in the title: "NR2F2 is required in the embryonic testis for Fetal Leydig Cell development" and also at the end of the introduction and all along the result part. All the authors' assertions are supported by very clear and statistically validated results from ISH, IHC, precise cell counting and gene expression levels by qPCR. The authors used two different conditional Nr2f2 gene ablation systems that demonstrate the same effects at the FLC level. They also showed that the haplo-insufficiency of Wt1 in the first system (knock-in Wt1-cre-ERT2) aggravated the situation in FLC differentiation by disturbing the differentiation of Sertoli cells and their secretion of pro-FLC factors, which had a confounding effect and encouraged them to use the second system. This demonstrates the great rigor with which the authors interpreted the results. In conclusion, all authors' claims and conclusions are justified by their high-quality results.

      Recommendations for the authors:

      We thank the reviewers for their comments which have improved and strengthened our manuscript. Please see our responses to specific comments below in blue.

      Reviewer #1 (Recommendations for the authors):

      I have several small comments:

      (1) There has been recently a preprint from the Yao lab about the role of NR2F2 is steroidogenic cells (https://www.biorxiv.org/content/10.1101/2024.09.16.613312v1). They performed cKO of NR2F2 using the Wt1creERT2 and found similar results. You should present and discuss this paper in light of your results.

      Estermann et al., report a very similar phenotype of FLC hypoplasia in an independent mouse model of Nr2f2 conditional mutation. We have now referred to this article in the discussion of our manuscript as suggested.

      (2) In the introduction I think it is important to mention that the steroidogenic progenitors are derived from Wnt5a positive cells (https://pubmed.ncbi.nlm.nih.gov/35705036/).

      We have mentioned this point in the introduction as suggested.

      (3) In both models you show a decrease in the number of FLC (60% or 40%) and yet they both present with undescended testis. It is important to discuss the fact that there is no need for a complete ablation of testosterone and INSL3 in order to get cryptorchidism.

      We have mentioned this point in the discussion as suggested.

      The fact that you get only partial reduction in FLC is likely due to redundancy with additional factors, possibly the ARX like you stated in the discussion and it will be interesting to explore that in the future but is beyond the scope of the current paper.

      We agree with the reviewer, this question could be addressed by analyzing Arx,Nr2f2 double mutants.

      (4) In page 8 line 11 you mention data not shown- not sure if this is allowed in the journal .

      The data is now shown in Figure S5A as suggested.

      (5) In Figure 2- it will be good if you add a schematic model of the mouse strains used as well as the experimental and control mice next to the Tam scheme. Similar scheme should be in figure 3 for Nr5a1-cre.

      We have modified Figures 2 and 3 as suggested.

      (6) There is a clear and pronounced effect of the testis cords number and size. It will be good if you could qualify testis cord numbers/ diameter in the mutants even if you do not follow in detail the effect on Sertoli cells

      We have quantified testis cords numbers and area in E14.5 Control and Wt1<sup>CreERT2/+</sup>; Nr2f2<sup>flox/flox</sup> testes. This data is now shown in Figure S2M.

      (7) It will be good to present the undescended testis in the Wt1-cre model in figure 2 and not in the supp figure

      The data is now shown in Figure 2H-I as suggested.

      (8) Please add labelling of the testis, kidney, bladder, vas deferens in figure 3 N+O and in the Wt1-cre model

      We have added the labels in Figures 2 and 3 as suggested.

      (9) In figure 5 which present both models- it will be good to use the scheme I suggested before to highlight which results refer to which ko model.

      We have modified Figure 5 as suggested.

      Reviewer #2 (Recommendations for the authors):  

      The work presented in this manuscript gave me food for thought. I have always been intrigued by the fact that of the large number of interstitial cells in the testis, a minority differentiate into mature androgen-producing Leydig cells. In other words, how is the number of functional steroidogenic cells defined from a large pool of progenitor cells (ARX and NR2F2 positive ones)? This may have a link with the levels of androgens produced (a kind of feedback control) or the effectiveness of these androgens on the target tissues (i.e.: as spermatogenesis efficiency in adults). In addition, there must be specific signals (probably linked to gonadotropins) that induce the recruitment of Leydig cells from the progenitor pool. Perhaps the genetic models generated in this study could help to address these questions. I leave it to the authors to judge.

      We agree with the reviewer. How NR2F2 (and other factors) integrate extrinsic cues to regulate the recruitment of a subset of interstitial steroidogenic progenitors along the Leydig cell differentiation pathway is a fascinating question beyond the scope of this work.

      In addition to this reflection, I propose a few minor modifications likely to improve the quality of the manuscript:

      (1) Page 3, lane 3: I suggest to replace "growth" by "differentiation"

      We have modified the text as suggested.

      (2) Page 3, lane 4: the "scrotum" is missing in the parenthesis. Please add it before "and penis"

      We have modified the text as suggested.

      (3) Page 5, lanes 21-24: kidney hypoplasia is also evident on Fig S2H (stated in the figure legend). It could be also mentioned in this sentence and it implies "...that NR2F2 function is required for testicular and kidney development."

      We have modified the text as suggested.

      (4) Page 5, lanes 28-30. In addition to the reduction in the number of HSD3B-positive cells, HSD3B staining seems clearly more faint in mutant FLC (Fig 2M) compared to adrenal cells on the same section or FLC in control gonads. This fits well with other results on the level of steroidogenic enzymes (Fig 2O) and those presented thereafter (Fig S4 I-J and Fig 5). Perhaps the author could mention this fact.

      We have modified the text as suggested in the results section “NR2F2 is required for FLC maturation” (Page 8).

      (5) Page 5, lanes 31-34: testicular descent is hugely sensible to INSL3 in the mouse (by contrast with other species where androgens seem to be more critical). I was wondering if you can check a better phenotypic marker for the absence (or reduction) of androgens like the differentiation of epididymides by HE staining or the anogenital distance at birth.

      We have measured the anogenital distance at P0 and P1 as suggested and have included the corresponding graph in Fig. S3P

      (6) Page 8, lanes 21-22: "HSD3B positive FLC were smaller and more elongated". It is clear on Fig 5F but not evident on Fig 5D. Could the authors propose another image?

      We have modified Figure 5 as suggested and provide now another example of HSD3B positive FLCs in a Nr5a1Cre; Nr2f2<sup>flox/flox</sup> mutant gonad (Fig. 5D) and the corresponding control littermate (Fig. 5C).

      (7) Page 14, lane 12: "(arrow in I)" should be "(arrow in H)"

      We have modified the text as suggested. Please note that ACTA 2 expression is now shown in Figure S2 G-H.

      (8) Page 15, lane 6: "Arrows indicate NR5A1 positive FLC". There is no arrow on Fig4 C,D; but a kind of scale bar on the enlargement shown in C.

      We have modified Figure 4 as suggested.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review):

      Summary:

      This paper provides a computational model of a synthetic task in which an agent needs to find a trajectory to a rewarding goal in a 2D-grid world, in which certain grid blocks incur a punishment. In a completely unrelated setup without explicit rewards, they then provide a model that explains data from an approach-avoidance experiment in which an agent needs to decide whether to approach or withdraw from, a jellyfish, in order to avoid a pain stimulus, with no explicit rewards. Both models include components that are labelled as Pavlovian; hence the authors argue that their data show that the brain uses a Pavlovian fear system in complex navigational and approach-avoid decisions.

      Thanks to the reviewer’s comments, we have now added the following text to our Discussion section (Lines 290-302):

      “When it comes to our experiments, both the simulation and VR experiment models are related and derived from the same theoretical framework maintaining an algebraic mapping. They differ only in task-specific adaptations i.e. differ in action sets and differ in temporal difference learning rules - multi-step decisions in the grid world vs. Rescorla-Wagner rule for single-step decisions in the VR task. This is also true for Dayan et al. [2006] who bridge Pavlovian bias in a Go-No Go task (negative auto-maintenance pecking task) and a grid world task. A further minor difference between the simulation and VR experiment models is the use of a baseline bias in the human experiment's RL and the RLDDM model, where we also model reaction times with drift rates which is not a behaviour often simulated in the grid world simulations. As mentioned previously, we use the grid world tasks for didactic purposes, similar to Dayan et al. [2006] and common to test-beds for algorithms in reinforcement learning [Sutton et al., 1998]. The main focus of our work is on Pavlovian fear bias in safe exploration and learning, rather than on its role in complex navigational decisions. Future work can focus on capturing more sophisticated safe behaviours, such as escapes [Evans et al., 2019, Sporrer et. al., 2023] and model-based planning, which span different aspects of the threat-imminence continuum [Mobbs et al., 2020].”

      In the first setup, they simulate a model in which a component they label as Pavlovian learns about punishment in each grid block, whereas a Q-learner learns about the optimal path to the goal, using a scalar loss function for rewards and punishments. Pavlovian and Q-learning components are then weighed at each step to produce an action. Unsurprisingly, the authors find that including the Pavlovian component in the model reduces the cumulative punishment incurred, and this increases as the weight of the Pavlovian system increases. The paper does not explore to what extent increasing the punishment loss (while keeping reward loss constant) would lead to the same outcomes with a simpler model architecture, so any claim that the Pavlovian component is required for such a result is not justified by the modelling. 

      Thanks to the reviewer’s comments, we have now added the following text to our Discussion section (Line 303-313):

      “In our simulation experiments, we assume the coexistence of the Pavlovian fear system and the instrumental system to demonstrate the emergent safety-efficiency trade-off from their interaction. It is possible that similar behaviours could be modelled using an instrumental system alone, with higher punishment sensitivity, therefore we do not argue for the necessity for the Pavlovian fear system here. Instead, the Pavlovian fear system itself could be a potential biologically plausible implementation of punishment sensitivity. Unlike punishment sensitivity (scaling of the punishments), which has not been robustly mapped to neural substrates in fMRI studies; the neural substrates for the Pavlovian fear system are well known (e.g., the limbic loop and amygdala, further see Supplementary Fig. 16). Additionally, Pavlovian fear system provides a separate punishment memory that cannot be erased by greater rewards like [Elfwing and Seymour, 2017, Wang et al., 2018]. This fundamental point can be observed in our simple T-maze simulations, where the Pavlovian fear system encourages avoidance behaviour and the agent chooses the smaller reward instead of the greater reward.”

      In the second setup, an agent learns about punishments alone. "Pavlovian biases" have previously been demonstrated in this task (i.e. an overavoidance when the correct decision is to approach). The authors explore several models (all of which are dissimilar to the ones used in the first setup) to account for the Pavlovian biases. 

      Thanks to the reviewer’s comments, we have now added a paragraph in our Discussion section (Line 290-302) explaining the similarity of our models and their integrated interpretation. We hope this addresses the reviewer’s concerns.

      Strengths: 

      Overall, the modelling exercises are interesting and relevant and incrementally expand the space of existing models. 

      Weaknesses: 

      I find the conclusions misleading, as they are not supported by the data. 

      First, the similarity between the models used in the two setups appears to be more semantic than computational or biological. So it is unclear to me how the results can be integrated. 

      Thanks to the reviewer’s comments, we have now added a paragraph in our Discussion section (Line 290-302 onwards) explaining the similarity of our models and their integrated interpretation. We hope this addresses the reviewer’s concerns.

      Secondly, the authors do not show "a computational advantage to maintaining a specific fear memory during exploratory decision-making" (as they claim in the abstract). Making such a claim would require showing an advantage in the first place. For the first setup, the simulation results will likely be replicated by a simple Q-learning model when scaling up the loss incurred for punishments, in which case the more complex model architecture would not confer an advantage. The second setup, in contrast, is so excessively artificial that even if a particular model conferred an advantage here, this is highly unlikely to translate into any real-world advantage for a biological agent. The experimental setup was developed to demonstrate the existence of Pavlovian biases, but it is not designed to conclusively investigate how they come about. In a nutshell, who in their right mind would touch a stinging jellyfish 88 times in a short period of time, as the subjects do on average in this task? Furthermore, in which real-life environment does withdrawal from a jellyfish lead to a sting, as in this task? 

      Crucially, simplistic models such as the present ones can easily solve specifically designed lab tasks with low dimensionality but they will fail in higher-dimensional settings. Biological behaviour in the face of threat is utterly complex and goes far beyond simplistic fight-flight-freeze distinctions (Evans et al., 2019). It would take a leap of faith to assume that human decision-making can be broken down into oversimplified sub-tasks of this sort (and if that were the case, this would require a meta-controller arbitrating the systems for all the sub-tasks, and this meta-controller would then struggle with the dimensionality j). 

      Thanks to the reviewer’s comments, we have now mentioned this point in Lines 299-302.

      On the face of it, the VR task provides higher "ecological validity" than previous screen-based tasks. However, in fact, it is only the visual stimulation that differs from a standard screen-based task, whereas the action space is exactly the same. As such, the benefit of VR does not become apparent, and its full potential is foregone. 

      If the authors are convinced that their model can - then data from naturalistic approach-avoidance VR tasks is publicly available, e.g. (Sporrer et al., 2023), so this should be rather easy to prove or disprove. In summary, I am doubtful that the models have any relevance for real-life human decision-making. 

      Finally, the authors seem to make much broader claims that their models can solve safety-efficiency dilemmas. However, a combination of a Pavlovian bias and an instrumental learner (study 1) via a fixed linear weighting does not seem to be "safe" in any strict sense. This will lead to the agent making decisions leading to death when the promised reward is large enough (outside perhaps a very specific region of the parameter space). Would it not be more helpful to prune the decision tree according to a fixed threshold (Huys et al., 2012)? So, in a way, the model is useful for avoiding cumulatively excessive pain but not instantaneous destruction. As such, it is not clear what real-life situation is modelled here. 

      We hope our additions to the Discussion section, from Line 290 to Line 313 address the reviewer’s concerns.  

      A final caveat regarding Study 1 is the use of a PH associability term as a surrogate for uncertainty. The authors argue that this term provides a good fit to fear-conditioned SCR but that is only true in comparison to simpler RW-type models. Literature using a broader model space suggests that a formal account of uncertainty could fit this conditioned response even better (Tzovara et al., 2018). 

      We have now added a line discussing this. (Line 356-358)

      “Future work could also use a formal account of uncertainty which could fit the fear-conditioned skin-conductance response better than Pearce-Hall associability [Tzovara et al., 2018].”

      Reviewer #2 (Public review): 

      Summary: 

      The authors tested the efficiency of a model combining Pavlovian fear valuation and instrumental valuation. This model is amenable to many behavioral decision and learning setups - some of which have been or will be designed to test differences in patients with mental disorders (e.g., anxiety disorder, OCD, etc.). 

      Strengths: 

      (1) Simplicity of the model which can at the same time model rather complex environments. 

      (2) Introduction of a flexible omega parameter. 

      (3) Direct application to a rather advanced VR task. 

      (4) The paper is extremely well written. It was a joy to read. 

      Weaknesses: 

      Almost none! In very few cases, the explanations could be a bit better. 

      Thank you, we have added further explanations in the discussion section. We have further improved the writing in abstract, introduction and Methods section taking into account recommendations from reviewer #2 and #3.

      Reviewer #2 (Recommendations for the authors): 

      (1) Why is there no flexible omega in Figures 3B and 3C? Did I miss this? 

      Thank you. We have now added additional text to explain our motivation in Experiment 2, which only varies the fixed omega and omits the flexible omega (Lines 136-140).

      “In this set of results, we wish to qualitatively tease apart the role of a Pavlovian bias in shaping and sculpting the instrumental value and also provide more insight into the resulting safety-efficiency trade-off. Having shown the benefits of a flexible ω in the previous section, here we only vary the fixed ω to illustrate the effect of a constant bias and are not concerned with the flexible bias in this experiment.”

      We encourage the reader to consider this akin to an additional study that will explain how Pavlovian bias to withdraw can play a role in avoiding punishments similar to that of punishment sensitivity. This is particularly important as we do have neural correlates for Pavlovian biases but lack a clear neural correlation for punishment sensitivity so far, as mentioned in our new additions to the Discussion section (Lines 303-313).

      (2) The introduction of the flexible omega and the PAL agent in the results is a bit sudden. Some more details are needed to understand this during the first read of this passage. 

      We thank reviewer #2 for bringing this to our notice. We have attempted to refine our passage by including sentences like - 

      “The standard (rational) reinforcement learning system is modelled as the instrumental learning system. The additional Pavlovian fear system biases the withdrawal actions to aid in safe exploration, in line with our hypothesis.”

      “Both systems learn using a basic temporal difference updating rule (or in instances, its special case, the Rescorla-Wagner rule)”

      “We implement the flexible ω using Pearce-Hall associability (see equation 15 in Methods). The Pearce-Hall associability maintains a running average of absolute temporal difference errors (δ) as per equation 14. This acts as a crude but easy-to-compute metric for outcome uncertainty which gates the influence of the Pavlovian fear system, in line with our hypothesis. This implies that higher the outcome uncertainty, as is the case in early exploration, the more cautious our agent will be, resulting in safer exploration”

      (3) In my view, the possibility of modeling moving predators is extremely interesting. I would include Figure 8D and the corresponding explanation in the main text. 

      Response with revision: We thank the reviewer for finding our simulation on moving predators extremely interesting. Unfortunately, since our instrumental system is not model-based, and especially is not explicitly modelling the predator dynamics, our simulation might not be a very accurate representation of real moving predator environments. As pointed out by Reviewer #1, perhaps several other systems other than Pavlovian fear responses are necessary for safe behaviour in such environments and we hope to address these in future studies. Thanks again for taking an interest in our simulations.

      (4) The VR experiment should be mentioned more clearly in the abstract and the introduction. It should be mentioned a bit more clearly why VR was helpful and why the authors did not use a simple bird's eye grid world task. 

      I cannot assess the RLDDM and I did not check the code. 

      Thank you, we have now mentioned the VR experiment more clearly in the abstract and the introduction. We also now further mention that the VR experiment “builds upon previous Go-No Go studies studying Pavlovian-Instrumental transfer (Guitart-Masip et al, 2012; Cavanagh et al, 2013). The virtual-reality approach confers a greater ecological validity and the immersive nature may contribute better fear conditioning, making it easier to distinguish the aversive components.”

      A bird’s eye grid world may not invoke a strong withdrawal response, as seen in these immersive approach-withdrawal tasks where we can clearly distinguish a Pavlovian fear-based withdrawal response. We did include immersive VR maze results in the supplementary materials, but future work is needed to isolate the different systems at play in such a complex behaviour.

      Reviewer #3 (Public review): 

      Summary: 

      This paper aims to address the problem of exploring potentially rewarding environments that contain the danger, based on the assumption that an independent Pavlovian fear learning system can help guide an agent during exploratory behaviour such that it avoids severe danger. This is important given that otherwise later gains seem to outweigh early threats, and agents may end up putting themselves in danger when it is advisable not to do so. 

      The authors develop a computational model of exploratory behaviour that accounts for both instrumental and Pavlovian influences, combining the two according to uncertainty in the rewards. The result is that Pavlovian avoidance has a greater influence when the agent is uncertain about rewards. 

      Strengths: 

      The study does a thorough job of testing this model using both simulations and data from human participants performing an avoidance task. Simulations demonstrate that the model can produce "safe" behaviour, where the agent may not necessarily achieve the highest possible reward but ensures that losses are limited. Interestingly, the model appears to describe human avoidance behaviour in a task that tests for Pavlovian avoidance influences better than a model that doesn't adapt the balance between Pavlovian and instrumental based on uncertainty. The methods are robust, and generally, there is little to criticise about the study. 

      Weaknesses: 

      The extent of the testing in human participants is fairly limited but goes far enough to demonstrate that the model can account for human behaviour in an exemplar task. There are, however, some elements of the model that are unrealistic (for example, the fact that pre-training is required to select actions with a Pavlovian bias would require the agent to explore the environment initially and encounter a vast amount of danger in order to learn how to avoid the danger later). The description of the models is also a little difficult to parse. 

      Thank you, we have now attempted to clarify these points in the Discussion section by adding the following text (Lines 313-321):

      “ We next discuss the plausibility of pre-training to select the hardwired actions In the human experiment, the withdrawal action is straightforwardly biased, as noted, while in the grid world, we assume a hardwired encoding of withdrawal actions for each state/grid. This innate encoding of withdrawal actions could be represented in the dPAG [Kim et al., 2013]. We implement this bias using pre-training, which we assume would be a product of evolution. Alternatively, this could be interpreted as deriving from an appropriate value initialization where the gradient over initialized values determines the action bias. Such aversive value initialization, driving avoidance of novel and threatening stimuli, has been observed in the tail of the striatum in mice, which is hypothesised to function as a Pavlovian fear/threat learning system [Menegas et al., 2018].”

      Reviewer #3 (Recommendations for the authors): 

      I have relatively little to suggest, as in my view the paper is robust, thorough, and creative, and does enough to support the primary argument being made at the most fundamental level. My suggestions for improvement are as follows: 

      (1) Some aspects of the model are potentially unrealistic (as described in the public review), and the paper may benefit from some discussion of these issues or attempts to make the model more realistic - i.e., to what extent is this plausible in explaining more complex avoidance behaviour? Primarily, the fact that pre-training is required to identify actions subject to Pavlovian bias seems unlikely to be effective in real-world situations - is there a better way to achieve this in cases where there isn't necessarily an instinctual Pavlovian response? 

      Thank you, we agree that the advantage of Pavlovian bias is restricted to the bias/instinctual Pavlovian response conferred by evolution. Future work is needed to model more complex avoidance behaviour such as escapes. We hope to have made this more clear with our edits to the Discussion (Lines 299-302) in our response to Reviewer #1’s comments, specifically:

      “The main focus of our work is on Pavlovian fear bias in safe exploration and learning, rather than on its role in complex navigational decisions. Future work can focus on capturing more sophisticated safe behaviours, such as escapes [Evans et al., 2019, Sporrer et. al., 2023] and model-based planning which span different aspects of the threat-imminence continuum [Mobbs et al., 2020]”  

      (2) The description of the model in the method can be a little hard to follow and would benefit from further explanation of certain parameters. In general, it would be good to ensure that all terms mentioned in equations are described clearly in the text (for example, in Equation1 it isn't clear what k refers to). 

      Thank you, we have now added further information on all of the parameters in Equation 1 and overall improved the Methods section writing, for instance using time subscript for less confusion while introducing the parameters. We use the standard notation used in Sutton and Barto textbook. k refers to the timesteps into the future, and is now explained better in the Methods section.

      (3) Another point of clarification in Equation 1 - does the policy account for the Pavlovian influence or is this purely instrumental? 

      Thank you, Equation 1 is purely instrumental. We have now specifically mentioned this. The Pavlovian influence follows later. They are combined into propensities for action as per equations 11-13.

      (4) I was curious whether similar outcomes could be achieved by more complex instrumental models without the need for Pavlovian influences. For example, could different risk-sensitive decision rules (e.g., conditional value at risk) that rely only on the instrumental system afford safe behaviour without the need for an additional Pavlovian system? 

      Thank you for your comment. Yes, CVaR can achieve safe exploration/cautious behaviour in choices similar to Pavlovian avoidance learning. But we think both differ in the following ways:

      (1) CVaR provides the correct solution to the wrong problem (objective that only maximises the lower tail of the distribution of outcomes)

      (2) Pavlovian bias provides the wrong solution to the right problem (normative objective, but a Pavlovian bias which may be vestige of evolution)

      Here we use the “wrong problem, wrong solution, wrong environment” categorisation terminology from Huys et al. 2015.

      Huys, Q. J., Guitart-Masip, M., Dolan, R. J., & Dayan, P. (2015). Decision-theoretic psychiatry. Clinical Psychological Science, 3(3), 400-421.

      Secondly, we find an effect of Pavlovian bias on reaction times - slowing down of approach responses and faster withdrawal responses. We do not think this can be best explained in a CVaR type model and is a direction for future work. We think such model-based methods are slower to compute, but Pavlovian withdrawal bias is quicker response.

      We have now included this in brief in Lines 280-288.

      (5) Figure 5 would benefit from a clearer caption as it is not necessarily clear from the current one that the left panels refer to choices and the right panels to reaction times. 

      Thank you, we have improved the caption for Fig. 5.

      (6) It would be good to include some indication of the quality of the model fits for the human behavioural study (i.e., diagnostics such as R-hat) to ensure that differences in model fit between models are not due to convergence issues with different models. This would be especially helpful for the RLDDM models as these can be difficult to fit successfully.

      Thank you, we observed that all Rhat values were strictly less than 1.05 (most parameters were less than 1.01 and generally close to 1), indicating that the models converged. We have now added this line to the results (Line 246-248). Thanks to the reviewer’s comments, we have now added the following text to our Discussion section (Lines 290-302): “When it comes to our experiments, both the simulation and VR experiment models are related and derived from the same theoretical framework maintaining an algebraic mapping. They differ only in task-specific adaptations i.e. differ in action sets and differ in temporal difference learning rules - multi-step decisions in the grid world vs. Rescorla-Wagner rule for single-step decisions in the VR task. This is also true for Dayan et al. [2006] who bridge Pavlovian bias in a Go-No Go task (negative auto-maintenance pecking task) and a grid world task. A further minor difference between the simulation and VR experiment models is the use of a baseline bias in the human experiment's RL and the RLDDM model, where we also model reaction times with drift rates which is not a behaviour often simulated in the grid world simulations. As mentioned previously, we use the grid world tasks for didactic purposes, similar to Dayan et al. [2006] and common to test-beds for algorithms in reinforcement learning [Sutton et al., 1998]. The main focus of our work is on Pavlovian fear bias in safe exploration and learning, rather than on its role in complex navigational decisions. Future work can focus on capturing more sophisticated safe behaviours, such as escapes [Evans et al., 2019, Sporrer et. al., 2023] and model-based planning, which span different aspects of the threat-imminence continuum [Mobbs et al., 2020].” In the first setup, they simulate a model in which a component they label as Pavlovian learns about punishment in each grid block, whereas a Q-learner learns about the optimal path to the goal, using a scalar loss function for rewards and punishments. Pavlovian and Q-learning components are then weighed at each step to produce an action. Unsurprisingly, the authors find that including the Pavlovian component in the model reduces the cumulative punishment incurred, and this increases as the weight of the Pavlovian system increases. The paper does not explore to what extent increasing the punishment loss (while keeping reward loss constant) would lead to the same outcomes with a simpler model architecture, so any claim that the Pavlovian component is required for such a result is not justified by the modelling.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Azlan et al. identified a novel maternal factor called Sakura that is required for proper oogenesis in Drosophila. They showed that Sakura is specifically expressed in the female germline cells. Consistent with its expression pattern, Sakura functioned autonomously in germline cells to ensure proper oogenesis. In Sakura KO flies, germline cells were lost during early oogenesis and often became tumorous before degenerating by apoptosis. In these tumorous germ cells, piRNA production was defective and many transposons were derepressed. Interestingly, Smad signaling, a critical signaling pathway for GSC maintenance, was abolished in sakura KO germline stem cells, resulting in ectopic expression of Bam in whole germline cells in the tumorous germline. A recent study reported that Bam acts together with the deubiquitinase Otu to stabilize Cyc A. In the absence of sakura, Cyc A was upregulated in tumorous germline cells in the germarium. Furthermore, the authors showed that Sakura co-immunoprecipitated Otu in ovarian extracts. A series of in vitro assays suggested that the Otu (1-339 aa) and Sakura (1-49 aa) are sufficient for their direct interaction. Finally, the authors demonstrated that the loss of otu phenocopies the loss of sakura, supporting their idea that Sakura plays a role in germ cell maintenance and differentiation through interaction with Otu during oogenesis.

      Strengths:

      To my knowledge, this is the first characterization of the role of CG14545 genes. Each experiment seems to be well-designed and adequately controlled.

      Weaknesses:

      However, the conclusions from each experiment are somewhat separate, and the functional relationships between Sakura's functions are not well established. In other words, although the loss of Sakura in the germline causes pleiotropic effects, the cause-and-effect relationships between the individual defects remain unclear.

      Reviewer #2 (Public review):

      In this study, the authors identified CG14545 (and named it Sakura), as a key gene essential for Drosophila oogenesis. Genetic analyses revealed that Sakura is vital for both oogenesis progression and ultimate female fertility, playing a central role in the renewal and differentiation of germ stem cells (GSC).

      The absence of Sakura disrupts the Dpp/BMP signaling pathway, resulting in abnormal bam gene expression, which impairs GSC differentiation and leads to GSC loss. Additionally, Sakura is critical for maintaining normal levels of piRNAs. Also, the authors convincingly demonstrate that Sakura physically interacts with Otu, identifying the specific domains necessary for this interaction, suggesting a cooperative role in germline regulation. Importantly, the loss of otu produces similar defects to those observed in Sakura mutants, highlighting their functional collaboration.

      The authors provide compelling evidence that Sakura is a critical regulator of germ cell fate, maintenance, and differentiation in Drosophila. This regulatory role is mediated through the modulation of pMad and Bam expression. However, the phenotypes observed in the germarium appear to stem from reduced pMad levels, which subsequently trigger premature and ectopic expression of Bam. This aberrant Bam expression could lead to increased CycA levels and altered transcriptional regulation, impacting piRNA expression. Given Sakura's role in pMad expression, it would be insightful to investigate whether overexpression of Mad or pMad could mitigate these phenotypic defects (UAS-Mad line is available at Bloomington Drosophila Stock Center).

      As suggested reviewer 1, we tested whether overexpression of Mad could rescue or mitigate the loss of sakura phenotypic defects, by using nos-Gal4-VP16 > UASp-Mad-GFP in the background of sakura<sup>null</sup>. As shown in Fig S11, we did not observe any mitigation of defects.

      Then, we also tested whether expressing a constitutive active form of Tkv, by using UAS-Dcr2, NGT-Gal4 > UASp-tkv.Q235D in the background of sakura<sup>RNAi</sup>. As shown in Fig S12, we did not observe any mitigation of defects by this approach either.

      A major concern is the overstated role of Sakura in regulating Orb. The data does not reveal mislocalized Orb; rather, a mislocalized oocyte and cytoskeletal breakdown, which may be secondary consequences of defects in oocyte polarity and structure rather than direct misregulation of Orb. The conclusion that Sakura is necessary for Orb localization is not supported by the data. Orb still localizes to the oocyte until about stage 6. In the later stage, it looks like the cytoskeleton is broken down and the oocyte is not positioned properly, however, there is still Orb localization in the ~8-stage egg chamber in the oocyte. This phenotype points towards a defect in the transport of Orb and possibly all other factors that need to localize to the oocyte due to cytoskeletal breakdown, not Orb regulation directly. While this result is very interesting it needs further evaluation on the underlying mechanism. For example, the decrease in E-cadherin levels leads to a similar phenotype and Bam is known to regulate E-cadherin expression. Is Bam expressed in these later knockdowns?

      We examined Bam and DE-Cadherin expression in later RNAi knockdowns driven by ToskGal4. As shown in Fig S9, Bam was not expressed in these later knockdowns compared with controls. DE-Cadherin staining suggested a disorganized structure in late-stage egg chambers.

      We agree that we overstated a role of Sakura in regulating Orb in the initial manuscript. We changed the text to avoid overstating.

      The manuscript would benefit from a more balanced interpretation of the data concerning Sakura's role in Orb regulation. Furthermore, a more expanded discussion on Sakura's potential role in pMad regulation is needed. For example, since Otu and Bam are involved in translational regulation, do the authors think that Mad is not translated and therefore it is the reason for less pMad? Currently the discussion presents just a summary of the results and not an extension of possible interpretation discussed in context of present literature.

      We changed the text to avoid overstating a role of Sakura in regulating Orb localization.

      Based on our newly added results showing that transgenic overexpression of Mad could not rescue or mitigate the phenotypic defects of sakura<sup>null</sup> mutant (Fig S11), we do not think the reason for less pMad is less translation of Mad.

      Reviewer #3 (Public review):

      In this very thorough study, the authors characterize the function of a novel Drosophila gene, which they name Sakura. They start with the observation that sakura expression is predicted to be highly enriched in the ovary and they generate an anti-sakura antibody, a line with a GFP-tagged sakura transgene, and a sakura null allele to investigate sakura localization and function directly. They confirm the prediction that it is primarily expressed in the ovary and, specifically, that it is expressed in germ cells, and find that about 2/3 of the mutants lack germ cells completely and the remaining have tumorous ovaries. Further investigation reveals that Sakura is required for piRNA-mediated repression of transposons in germ cells. They also find evidence that sakura is important for germ cell specification during development and germline stem cell maintenance during adulthood. However, despite the role of sakura in maintaining germline stem cells, they find that sakura mutant germ cells also fail to differentiate properly such that mutant germline stem cell clones have an increased number of "GSC-like" cells. They attribute this phenotype to a failure in the repression of Bam by dpp signaling. Lastly, they demonstrate that sakura physically interacts with otu and that sakura and otu mutants have similar germ cell phenotypes. Overall, this study helps to advance the field by providing a characterization of a novel gene that is required for oogenesis. The data are generally high-quality and the new lines and reagents they generated will be useful for the field. However, there are some weaknesses and I would recommend that they address the comments in the Recommendations for the authors section below.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      General Comments:

      (1) The gene nomenclature: As mentioned in the text, Sakura means cherry blossom and is one of the national flowers of Japan. I am not sure whether the phenotype of the CG14545 mutant is related to Sakura or not. I would like to suggest the authors reconsider the naming.

      The striking phenotype of sakura mutant­ is tumorous and germless ovarioles. The tumorous phenotype, exhibiting lots of round fusome in germarium visualized by anti-Hts staining, looks like cherry blossom blooming to us. Also, the germless phenotype reminds us falling of the cherry blossom, especially considering that the ratio of tumorous phenotype decreases and that of germless decreases over fly age. Furthermore, “Sakura” symbolizes birth and renewal in Japanese culture (the last author of this manuscript is Japanese). Our findings indicated that the gene sakura is involved in regulation of renewal and differentiation of GSCs (which leads to birth). These are the reasons for the naming, which we would like to keep.

      (2) In many of the microscopic photographs in the figures, especially for the merged confocal images, the resolution looks low, and the images appear blurred, making it difficult to judge the authors' claims. Also, the Alpha Fold structure in Figure 10A requires higher contrast images. The magnification of the images is often inadequate (e.g. Figures 3A, 3B, 5E, 7A, etc). The authors should take high-magnification images separately for the germarium and several different stages of the egg chambers and lay out the figures.

      We are very sorry for the low-resolution images. This was caused when the original PDF file with high-resolution images was compressed in order to meet the small file size limit in the eLife submission portal. In the revised submission, we used high-resolution images.

      Specific Comments

      (1) How Sakura can cooperate with Otu remains unanswered. Sakura does not regulate deubiquitinase activity in vitro. Both sakura and otu appear to be involved in the Dpp-Smad signaling pathway and in the spatial control of Bam expression in the germarium, whereas Otu has been reported to act in concert with Bam to deubiquitinate and stabilize Cyc A for proper cystoblast differentiation. Therefore, it is plausible that the stabilization of Cyc A in the Sakura mutant is an indirect consequence of Bam misexpression and independent of the Sakura-Otu interaction. The authors may need to provide much deeper insight into the mechanism by which Sakura plays roles in these seemingly separable steps to orchestrate germ cell maintenance and differentiation during early oogenesis.

      Yes, it is possible that the stabilization of CycA in the sakura mutant is an indirect consequence of Bam misexpression and independent of the Sakura-Otu interaction. To test the significance and role of the Sakura-Otu interaction, we have attempted to identify Sakura point mutants that lose interaction with Otu. If such point mutants were successfully obtained, we were planning to test if their transgene expression could rescue the phenotypes of sakura mutant as the wild-type transgene did. However, after designing and testing the interaction of over 30 point mutants with Otu, we could not obtain such mutant version of Sakura yet. We will continue making efforts, but it is beyond the scope of the current study. We hope to address this important point in future studies.

      (2) Figure 3A and Figure 4: The authors show that piRNA production is abolished in Sakura KO ovaries. It is known that piRNA amplification (the ping-pong cycle) occurs in the Vasa-positive perinuclear nuage in nurse cells. Is the nuage normally formed in the absence of Sakura? The authors provide high-magnification images in the germarium expressing Vas-GFP. How does Sakura, and possibly Out, contribute to piRNA production? Are the defects a direct or indirect consequence of the loss of Sakura?

      We provided higher magnification images of germarium expressing Vasa-EGFP in sakura mutant background (Fig 3A and 3B). The nuage formation does not seem to be dysregulated in sakura mutant. Currently, we do not know if the piRNA defects are direct or indirect consequence of the loss of Sakura. This question cannot be answered easily. We hope to address this in future studies.

      (3) Figure 7 and Figure 12: The authors showed that Dpp-Smad signaling was abolished in Sakura KO germline cells. The same defects were also observed in otu mutant ovaries (Figure 12B). How does the Sakura-Otu axis contribute to the Dpp-Smad pathway in the germline?

      As we mentioned in the response to comment (1), we attempted to test the significance and role of the Sakura-Otu interaction, including in the Dpp-Smad pathway in the germline, but we have not yet been able to obtain loss-of-interaction mutant(s) of Sakura. We hope to address this in future studies.

      (4) Figure 9 and Fig 10: The authors raised antibodies against both Sakura and Otu, but their specificities were not provided. For Western blot data, the authors should provide whole gel images as source data files. Also, the authors argue that the Otu band they observed corresponds to the 98-kDa isoform (lines 302-304). The molecular weight on the Western blot alone would be insufficient to support this argument.

      When we submitted the initial manuscript, we also submitted original, uncropped, and unmodified whole Western blot images for all gel images to the eLife journal, as requested. We did the same for this revised submission. I believe eLife makes all those files available for downloading to readers.

      In the newly added Fig S13B, we used very young 2-5 hours ovaries and 3-7 days ovaries. 2-5 days ovaries contain only mostly pre-differentiated germ cells. Older ovaries (3-7 days in our case here) contain all 14 stages of oogenesis and later stages predominate in whole ovary lysates.

      As reported in previous literature (Sass et al. 1995), we detected a higher abundance of the 104 kDa Otu isoform than the 98 kDa isoform in from 2-5 hours ovaries and predominantly the 98 kDa isoform in 3-7 days ovaries (Fig S13B). These results confirmed that the major Otu isoform we detected in Western blot, all of which uses old ovaries except for the 2-5 hours ovaries in Fig S13B, is the 98 kDa isoform.

      (5) Otu has been reported to regulate ovo and Sxl in the female germline. Is Sakura involved in their regulation?

      We examined sxl alternative splicing pattern in sakura mutant ovaries. As shown in Fig S6, we detected the male-specific isoform of sxl RNA and a reduced level of the female-specific sxl isoform in sakura mutant ovaries. Thus Sakura seems to be involved in sxl splicing in the female germline, while further studies will be needed to understand whether Sakura has a direct or indirect role here.

      (6) Lines 443-447: The GSC loss phenotype in piwi mutant ovaries is thought to occur in a somatic cell-autonomous manner: both piwi-mutant germline clones and germline-specific piwi knockdown do not show the GSC-loss phenotype. In contrast, the authors provide compelling evidence that Sakura functions in the germline. Therefore, the Piwi-mediated GSC maintenance pathway is likely to be independent of the Sakura-Otu axis.

      We changed the text accordingly.

      Reviewer #2 (Recommendations for the authors):

      Overall, this is a cleanly written manuscript, with some sentences/sections that are confusing the way they are constructed (i.e. Line 37-38, 334, section on Flp/FRT experiments).

      We rewrote those sections to avoid confusion.

      Comment for all merged image data: the quality of the merged images is very poor - the individual channels are better but should also be reprocessed for more resolved image data sets. Also, it would be helpful to have boundaries drawn in an individual panel to identify the regions of the germarium, as cartooned in Figure S1A (which should be brought into Figure 1) F-actin or Vsg staining would have helped throughout the manuscript to enhance the visualization of described phenotypes.

      We are very sorry for the low-resolution images. This was caused when the original PDF file with high-resolution images was compressed in order to meet the small file size limit in the eLife submission portal. In the revised submission, we used high-resolution images.

      We outlined the germarium in Fig 1E.

      We brought the former FigS1 into Fig 1A.

      We provided Phalloidin (F-Actin) staining images in Fig S7.

      All p-values seem off. I recommend running the data through the student t-test again.

      We used the student t-test to calculate p-values and confirmed that they are correct. We don’t understand why the reviewer thinks all p-values seem off.

      In the original manuscript, as we mentioned in each figure legends, we used asterisk (*) to indicate p-value <0.05, without distinguishing whether it’s <0.001, <0.01< or <0.05.

      Probably reviewer 2 is suggesting us to use ***, **, and *, to indicate p-value of <0.001, <0.01, and <0.05, respectively? If so, we now followed reviewer2’s suggestions.

      Figure 1

      (1) Within the text, C is mentioned before A.

      We updated the text and now we mentioned Fig 1A before Fig 1C.

      (2) B should be the supplemental figure.

      We moved the former Fig 1B to Supplemental Figure 1.

      (3) C - How were the different egg chamber stages selected in the WB? Naming them 'oocytes' is deceiving. Recommend labeling them as 'egg chambers', since an oocyte is claimed to be just the one-cell of that cyst.

      We changed the labeling to egg chambers.

      (4) Is the antibody not detecting Sakura in IF? There is no mention of this anywhere in the manuscript.

      While our Sakura antibody detects Sakura in IF, it seems to detect some other proteins as well. Since we have Sakura-EGFP fly strain (which fully rescues sakura<sup>null</sup> phenotypes) to examine Sakura expression and localization without such non-specific signal issues, we relied on Sakura-EGFP rather than anti-Sakura antibodies for IF.

      (5) Expand on the reliance of the sakura-EGFP fly line. Does this overexpression cause any phenotypes?

      sakura-EGFP does not cause any phenotypes in the background of sakura[+/+] and sakura[+/-].

      (6) Line 95 "as shown below" is not clear that it's referencing panel D.

      We now referenced Fig 1D.

      (7) Re: Figures 1 E and F. There is no mention of Hts or Vasa proteins in the text.<br /> "Sakura-EGFP was not expressed in somatic cells such as terminal filament, cap cells, escort cells, or follicle cells (Figure 1E). In the egg chamber, Sakura-EGFP was detected in the cytoplasm of nurse cells and was enriched in developing oocytes (Figure 1F)". Outline these areas or label these structures/sites in the images. The color of Merge labels is confusing as the blue is not easily seen.

      We mentioned Hts and Vasa in the text. We labeled the structures/sites in the images and updated the color labeling.

      Figure 2

      (1) Entire figure is not essential to be a main figure, but rather supplemental.

      We don’t agree with the reviewer. We think that the female fertility assay data, where sakura null mutant exhibits strikingly strong phenotype, which was completely rescued by our Sakura-EGFP transgene, is very important data and we would like to present them in a main figure.

      (2) 2A- one star (*) significance does not seem correct for the presented values between 0 and 100+.

      In the original manuscript, as we mentioned in each figure legends, we used asterisk (*) to indicate p-value <0.05, without distinguishing whether it’s <0.001, <0.01< or <0.05.

      Probably reviewer 2 is suggesting us to use ***, **, and *, to indicate p-value of <0.001, <0.01, and <0.05, respectively? If so, we now followed reviewer2’s suggestions.

      (3) 2C images are extremely low quality. Should be presented as bigger panels.

      We are very sorry for the low-resolution images. This was caused when the original PDF file with high-resolution images was compressed in order to meet the small file size limit in the eLife submission portal. In the revised submission, we used high-resolution images. We also presented as bigger panels.

      Figure 3

      (1) "We observed that some sakura<sup>null</sup> /null ovarioles were devoid of germ cells ("germless"), while others retained germ cells (Fig 3A)" What is described is, that it is hard to see. Must have a zoomed-in panel.

      We provided zoomed-in panels in Fig 3B

      (2) C - The control doesn't seem to match. Must zoom in.

      We provided matched control and also zoomed in.

      (3) For clarity, separate the tumorous and germless images.

      In the new image, only one tumorous and one germless ovarioles are shown with clear labeling and outline, for clarity.

      (4) Use arrows to help clearly indicate the changes that occur. As they are presented, they are difficult to see.

      We updated all the panels to enhance clarity.

      (5) Line 158 seems like a strong statement since it could be indirect.

      We softened the statement.

      Figure 4

      (1) Line 188-189 - Conclusion is an overstatement.

      We softened the statement.

      (2) Is the piRNA reduction due to a change in transcription? Or a direct effect by Sakura?

      We do not know the answers to these questions. We hope to address these in future studies.

      Figure 5

      (1) D - It might make more sense if this graph showed % instead of the numbers.

      We did not understand the reviewer’s point. We think using numbers, not %, makes more sense.

      (2) Line 213 - explain why RNAi 2 was chosen when RNAi 1 looks stronger.

      Fly stock of RNAi line 2 is much healthier than RNAi line 1 (without being driven Gal4) for some reasons. We had a concern that the RNAi line 1 might contain an unwanted genetic background. We chose to use the RNAi 2 line to avoid such an issue.

      (3) In Line 218 there's an extra parenthesis after the PGC acronym.

      We corrected the error.

      (4) TOsk-Gal4 fly is not in the Methods section.

      We mentioned TOsk-Gal4 in the Methods.

      Figure 6:

      (1) The FLP-FRT section must be rewritten.

      We rewrote the FLP-FRT section.

      (2) A - include statistics.

      We included statistics using the chi-square test.

      (3) B - is not recalled in the Results text.

      We referred Fig 6B in the text.

      (4) Line 232 references Figure 3, but not a specific panel.

      We referred Fig 3A, 3C, 3D, and 3E, in the text.

      Figure 7/8 - can go to Supplemental.

      We moved Fig 8 to supplemental. However, we think Fig 7 data is important and therefore we would like to present them as a main figure.

      (1) There should be CycA expression in the control during the first 4 divisions.

      Yes, there is CycA expression observed in the control during the first 4 divisions, while it’s much weaker than in sakura<sup>null</sup> clone.

      (2) Helpful to add the dotted lines to delineate (A) as well.

      We added a dotted outline for germarium in Fig 7A.

      (3) Line 263 CycA is miswritten as CyA.

      We corrected the typo.

      Figure 9

      (1) Otu antibody control?

      We validated Otu antibody in newly added Fig 10C and Fig S13A.

      (2) Which Sakura-EGFP line was used? sakura het. or null background? This isn't mentioned in the text, nor legend.

      We used Sakura-EGFP in the background of sakura[+/+]. We added this information in the methods and figure legend.

      (3) C - Why the switch to S2 cells? Not able to use the Otu antibody in the IP of ovaries?

      We can use the Otu antibody in the IP of ovaries. However, in anti-Sakura Western after anti-Otu IP, antibody light chain bands of the Otu antibodies overlap with the Sakura band. Therefore, we switched to S2 cells to avoid this issue by using an epitope tag.

      Figure 10

      (1) A- The resolution of images of the ribbon protein structure is poor.

      We are very sorry for the low-resolution images. This was caused when the original PDF file with high-resolution images was compressed in order to meet the small file size limit in the eLife submission portal. In the revised submission, we used high-resolution images.

      (2) A table summarizing the interactions between domains would help bring clarity to the data presented.

      We added a table summarizing the fragment interaction results.

      (3) Some images would be nice here to show that the truncations no longer colocalize.

      We did not understand the reviewer’s points. In our study, even for the full-length proteins.

      We have not shown any colocalization of Sakura and Otu in S2 cells or in ovaries, except that they both are enriched in developing oocytes in egg chambers.

      Figure 12

      (1) A - control and RNAi lines do not match.

      We provided matched images.

      (2) In general, since for Sakura, only its binding to Otu was identified and since they phenocopy each other, doesn't most of the characterization of Sakura just look at Otu phenotypes? Does Sakura knockdown affect Otu localization or expression level (and vice versa)?

      We tested this by Western (Fig S15) and IF (Fig 12). Sakura knockdown did not decrease Otu protein level, and Otu knockdown did not decrease Sakura protein level (Fig S15). In sakura<sup>null</sup> clone, Otu level was not notably affected (Fig 12). In sakura<sup>null</sup> clone, Otu lost its localization to the posterior position within egg chambers.

      Figure S6

      (1) It is Luciferase, not Lucifarase.

      We corrected the typo.

      Reviewer #3 (Recommendations for the authors):

      (1) It is interesting that germless and tumorous phenotypes coexist in the same population of flies. Additional consideration of these essentially opposite phenotypes would significantly strengthen the study. For example, do they co-exist within the same fly and are the tumorous ovarioles present in newly eclosed flies or do they develop with age? The data in Figure 8 show that bam knockdown partially suppresses the germless phenotype. What effect does it have on the tumorous phenotype? Is transposon expression involved in either phenotype? Do Sakura mutant germline stem cell clones overgrow relative to wild-type cells in the same ovariole? Does sakura RNAi driven by NGT-Gal4 only cause germless ovaries or does it also cause tumorous phenotypes? What happens if the knockdown of Sakura is restricted to adulthood with a Gal80ts? It may not be necessary to answer all of these questions, but more insight into how these two phenotypes can be caused by loss of sakura would be helpful.

      We performed new experiments to answer these questions.

      do they co-exist within the same fly and are the tumorous ovarioles present in newly eclosed flies or do they develop with age?

      Tumorous and germless ovarioles coexist in the same fly (in the same ovary). Tumorous ovarioles are present in very young (0-1 day old) flies, including newly eclosed (Fig S5). The ratio of germless ovarioles increases and that of tumorous ovarioles decreases with age (Fig S5).

      The data in Figure 8 show that bam knockdown partially suppresses the germless phenotype. What effect does it have on the tumorous phenotype?

      bam knockdown effect on tumorous phenotype is shown in Fig S10. bam knockdown increased the ratio of tumorous ovarioles and the number of GSC-like cells.

      Is transposon expression involved in either phenotype?

      Since our transposon-piRNA reporter uses germline-specific nos promoter, it is expressed only in germ line cells, so we cannot examine in germless ovarioles.

      Do Sakura mutant germline stem cell clones overgrow relative to wild-type cells in the same ovariole?

      Yes, Sakura mutant GSC clones overgrow. Please compare Fig 6C and Fig S8.

      Does sakura RNAi driven by NGT-Gal4 only cause germless ovaries or does it also cause tumorous phenotypes?

      Fig S10 and Fig S12 show the ovariole phenotypes of sakura RNAi driven by NGT-Gal4. It causes both germless and tumorous phenotypes.

      What happens if the knockdown of Sakura is restricted to adulthood with a Gal80ts?

      Our mosaic clone was induced at the adult stage, so we already have data of adulthood-specific loss of function. Gal80ts does not work well with nos-Gal4.

      (2) The idea that the excessive bam expression in tumorous ovaries is due to a failure of bam repression by dpp signaling is not well-supported by the data. Dpp signaling is activated in a very narrow region immediately adjacent to the niche but the images in Figure 7A show bam expression in cells that are very far away from the niche. Thus, it seems more likely to be due to a failure to turn bam expression off at the 16-cell stage than to a failure to keep it off in the niche region. To determine whether bam repression in the niche region is impaired, it would be important to examine cells adjacent to the niche directly at a higher magnification than is shown in Figure 7A.

      We provided higher magnification images of cells adjacent to the niche in new Fig 7A.

      We found that cells adjacent to the niche also express Bam-GFP.

      That said, we agree with the reviewer. A failure to turn bam expression off at the 16-cell stage may be an additional or even a main cause of bam misexpression in sakura mutant. We added this in the Discussion.

      (3) In addition, several minor comments should be addressed:

      a. Does anti-Sakura work for immunofluorescence?

      While our Sakura antibody detects Sakura in IF, it seems to detect some other proteins as well. Since we have Sakura-EGFP fly strain to examine Sakura expression and localization without such non-specific signal issues, we relied on Sakura-EGFP rather than anti-Sakura antibodies.

      b. Please provide insets to show the phenotypes indicated by the different color stars in Figure 3C more clearly.

      We provided new, higher-magnification images to show the phenotypes more clearly.

      c. Please indicate the frequency of the expression patterns shown in Figure 4D (do all ovarioles in each genotype show those patterns or is there variable penetrance?).

      We indicated the frequency.

      d. An image showing TOskGal4 driving a fluorophore should be provided so that readers can see which cells express Gal4 with this driver combination.

      It has been already done in the paper ElMaghraby et al, GENETICS, 2022, 220(1), iyab179, so we did not repeat the same experiment.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Mallimadugula et al. combined Molecular Dynamics (MD) simulations, thiol-labeling experiments, and RNA-binding assays to study and compare the RNA-binding behavior of the Interferon Inhibitory Domain (IID) from Viral Protein 35 (VP35) of Zaire ebolavirus, Reston ebolavirus, and Marburg marburgvirus. Although the structures and sequences of these viruses are similar, the authors suggest that differences in RNA binding stem from variations in their intrinsic dynamics, particularly the opening of a cryptic pocket. More precisely, the dynamics of this pocket may influence whether the IID binds to RNA blunt ends or the RNA backbone.

      Overall, the authors present important findings to reveal how the intrinsic dynamics of proteins can influence their binding to molecules and, hence, their functions. They have used extensive biased simulations to characterize the opening of a pocket which was not clearly seen in experimental results - at least when the proteins were in their unbound forms. Biochemical assays further validated theoretical results and linked them to RNA binding modes. Thus, with the combination of biochemical assays and state-of-the-art Molecular Dynamics simulations, these results are clearly compelling.

      Strengths:

      The use of extensive Adaptive Sampling combined with biochemical assays clearly points to the opening of the Interferon Inhibitory Domain (IID) as a factor for RNA binding. This type of approach is especially useful to assess how protein dynamics can affect its function.

      Weaknesses:

      Although a connection between the cryptic pocket dynamics and RNA binding mode is proposed, the precise molecular mechanism linking pocket opening to RNA binding still remains unclear.

      Reviewer #2 (Public review):

      Summary:

      The authors aimed to determine whether a cryptic pocket in the VP35 protein of Zaire ebolavirus has a functional role in RNA binding and, by extension, in immune evasion. They sought to address whether this pocket could be an effective therapeutic target resistant to evolutionary evasion by studying its role in dsRNA binding among different filovirus VP35 homologs. Through simulations and experiments, they demonstrated that cryptic pocket dynamics modulate the RNA binding modes, directly influencing how VP35 variants block RIG-I and MDA5-mediated immune responses.

      The authors successfully achieved their aim, showing that the cryptic pocket is not a random structural feature but rather an allosteric regulator of dsRNA binding. Their results not only explain functional differences in VP35 homologs despite their structural similarity but also suggest that targeting this cryptic pocket may offer a viable strategy for drug development with reduced risk of resistance.

      This work represents a significant advance in the field of viral immunoevasion and therapeutic targeting of traditionally "undruggable" protein features. By demonstrating the functional relevance of cryptic pockets, the study challenges long-standing assumptions and provides a compelling basis for exploring new drug discovery strategies targeting these previously overlooked regions.

      Strengths:

      The combination of molecular simulations and experimental approaches is a major strength, enabling the authors to connect structural dynamics with functional outcomes. The use of homologous VP35 proteins from different filoviruses strengthens the study's generality, and the incorporation of point mutations adds mechanistic depth. Furthermore, the ability to reconcile functional differences that could not be explained by crystal structures alone highlights the utility of dynamic studies in uncovering hidden allosteric features.

      Weaknesses:

      While the methodology is robust, certain limitations should be acknowledged. For example, the study would benefit from a more detailed quantitative analysis of how specific mutations impact RNA binding and cryptic pocket dynamics, as this could provide greater mechanistic insight. This study would also benefit from providing a clear rationale for the selection of the amber03 force field and considering the inclusion of volume-based approaches for pocket analysis. Such revisions will strengthen the robustness and impact of the study.

      Reviewer #3 (Public review):

      Summary:

      The authors suggest a mechanism that explains the preference of viral protein 35 (VP35) homologs to bind the backbone of double-stranded RNA versus blunt ends. These preferences have a biological impact in terms of the ability of different viruses to escape the immune response of the host.

      The proposed mechanism involves the existence of a cryptic pocket, where VP35 binds the blunt ends of dsRNA when the cryptic pocket is closed and preferentially binds the RNA double-stranded backbone when the pocket is open.

      The authors performed MD simulation results, thiol labelling experiments, fluorescence polarization assays, as well as point mutations to support their hypothesis.

      Strengths:

      This is a genuinely interesting scientific question, which is approached through multiple complementary experiments as well as extensive MD simulations. Moreover, structural biology studies focused on RNA-protein interactions are particularly rare, highlighting the importance of further research in this area.

      Weaknesses:

      - Sequence similarity between Ebola-Zaire (94% similarity) explains their similar behaviour in simulations and experimental assays. Marburg instead is a more distant homolog (~80% similarity relative to Ebola/Zaire). This difference is sequence and structure can explain the propensities, without the need to involve the existence of a cryptic pocket.  

      - No real evidence for the presence of a cryptic pocket is presented, but rather a distance probability distribution between two residues obtained from extensive MD simulations. It would be interesting to characterise the modelled RNA-protein interface in more detail

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Before assessing the overall quality and significance of this work, this reviewer needs to specify the context of this review. This reviewer's expertise lies in biased and unbiased molecular dynamics simulations and structural biology. Hence, while this reviewer can overall understand the results for thiol-labeling and RNA-binding assays, this review will not assess the quality of these biochemical assays and will mainly focus on the modelling results.

      Overall, the authors present important findings to reveal how the intrinsic dynamics of proteins can influence their binding to molecules and, hence, their functions. They have used extensive biased simulations to characterize the opening of a pocket which was not clearly seen in experimental results - at least when the proteins were in their unbound forms. Biochemical assays further validated theoretical results and linked them to RNA binding modes. Thus, with the combination of biochemical assays and state-of-the-art Molecular Dynamics simulations, these results are clearly compelling.

      Beyond the clear qualities of this work, I would like to mention a few points that may help to better contextualize and rationalize the results presented here.

      - First, both the introduction and discussion sections seem relatively condensed. Extending them to, for example, better describe the methodological context and discuss the methodological limitations and potential future developments related to biased simulations may help the reader get a better idea of the significance of this work.

      - The authors presented 3 homologs in this study: IIDs of Reston, Zaire, and Marburg viruses. While Zaire and Reston are relatively similar in terms of sequence (Figure S1). The sequences clearly differ between Marburg and the two other viruses. Can the author indicate a similarity/identity score for each sequence alignment and extend Figure S1 to really compare Marburg sequence with Reston and Zaire? Can they also discuss how these differences may impact the comparison of the three IIDs? This may also help the reader to understand why sometimes the authors compare the three viruses and why sometimes they are focusing only on comparing Zaire and Reston.

      We would like to thank the reviewer for raising this point and we agree that additional details about the sequence comparison provide more context for the choices of substitutions we made. Therefore, we have updated Fig S1 to include a detailed pairwise comparison of all the IID sequences including the percentage sequence similarity and identity. We have also added the following sentences to the results section where we first introduced the substitutions between Zaire and Reston IIDs

      “While the sequence of Marburg IID differs significantly from Reston and Zaire IIDs with a sequence identity of 42% and 45% respectively (Fig S1), the sequences of Reston and Zaire IID are 88% identical and 94% similar. Particularly, substitutions between these homologs are all distal to the RNA-binding interfaces and all the residues known to make contacts with dsRNA from structural studies are identical. Therefore, we reasoned that comparing these two homologs would help us identify minimal substitutions that control pocket opening probability and allow us to study its effect on dsRNA binding with minimal perturbation of other factors.”

      - In this work, the authors mentioned the cryptic pocket but only illustrated the opening of this pocket by using a simple distance between residues (Figure 2) and a SASA of one cysteine (Figure 3). In previous work done by the authors (Cruz et al. , Nature Communications, 2022), they better characterized residues involved in RNA binding and forming the cryptic pocket. Thus, would it be possible to better described this cryptic pocket (residues involved, volume, etc ..) and better explain how, structurally speaking, it can affect RNA binding mode (blunt ends vs backbone) ?

      We thank the reviewer for pointing out the need for clarification on the residues involved in RNA binding and pocket opening and the mechanism linking them. We have performed the CARDS analysis on Reston and Marburg IID simulations as we had done on Zaire IID simulations in Cruz et al, 2022. The results are shown in Fig S3 and discussed in the main text in the first results section.

      - As a counter-example, the authors used C315 for SASA calculation and thiol labeling (Figure 3). This cysteine is mainly buried as seen by SASA for Reston and Marburg and thiol labelling (Figure 3 E,G,H). Would it be possible to also get thiol labeling rates for Cystein 264 in Reston and its equivalent to see a case where the residue is solvent exposed?

      We have shown the SASA for C264 from the simulations in Fig S4 and the thiol labeling rates for all 4 cysteines in Reston IID in Fig S6. Comparing these rates to the rates of all 4 cysteines obtained for Zaire IID (Fig 4 in Cruz et Al, 2022), we observe that the rates for C264, which is expected to be exposed are significantly faster than those of C315 which is largely buried in all variants.  

      - I strongly support here the will of the authors to share their data by depositing them in an OSF repository. These data help this reviewer to assess some of the results produced by the authors and help to better understand the dynamics of their respective systems. I have just a few comments that need to be addressed regarding these data: o While there are data for WT Reston and Marburg, there is no data for Zaire. Is this because these data correspond to the previous work (Cruz et al. 2022) (in this case, it would be good to make this clear in the main text) or is it an omission? o There is no center.xtc file in the Marburg-MSM directory o There is no protmasses.pdb in the Reston-MSM directory

      - In general, if possible, it would be good to use the same name for each type of file presented in each directory to help a potential user understand a bit more how to use these data.

      - If possible, adding a bit more of metadata and explanations on the OSF webpage would be very beneficial to help find these data. To help in this direction, the authors may have a look to the guidelines presented at the end of this article: https://elifesciences.org/articles/90061

      We thank the reviewer for pointing out the omissions from the OSF repository. We have added the missing files and followed a uniform naming convention. We have also added documentation in the metadata section of the OSF repository to help others use the data.  

      Indeed, the simulation data used for Zaire IID is available on the OSF repository corresponding to Cruz et al. 2022 at https://osf.io/5pg2a. We have also clarified this in the data availability section of the main text.  

      Minor point:

      In Figure 2, there is a slight bump for the 225-295 distance around 1 nm for Reston. Can the author comment it ? As these results are based on long AS, even if very small, do the authors think this population is significant?

      Comparing the probability distributions obtained from bootstrapping the frames used to calculate the MSM equilibrium probabilities (Revised Fig1), we observe that the bump for the Reston IID distribution is persistent in all bootstraps indicating that it might indeed be significant. This is also consistent with our observation that the cysteine 296 does get fully labeled in our thiol labeling experiments, albeit significantly slowly compared to the other homologs.  

      Reviewer #2 (Recommendations for the authors):

      I recommend that the authors implement moderate revisions prior to the publication of this research article, addressing the identified weaknesses (see below).

      The authors should provide a rationale for their selection of the amber03 force field (Duan et al., JCTC 24, 1999-2012, 2003) for molecular dynamics simulations, particularly given the availability of more recent and optimized versions of the AMBER force fields. These newer force fields may offer improved parameterization for biomolecular systems, potentially enhancing the accuracy and reliability of the simulation results.

      We chose the Amber03 force field because it has performed well in much of our past work, including the original prediction of the cryptic pocket that we study in this manuscript. The results presented in this manuscript also demonstrate the predictive power of Amber03.

      Additionally, while the authors utilized solvent-accessible surface area (SASA) for cryptic pocket analysis, volume-based approaches may be more suitable for this purpose. Several studies (e.g., Sztain et al. J. Chem. Inf. Model. 2021, 61, 7, 3495-3501) have demonstrated the utility of volume analysis in identifying and characterizing cryptic pockets. The authors could consider incorporating such methodologies to provide a more comprehensive assessment of pocket dynamics.

      The authors propose that the cryptic pocket is not merely a random structural feature but functions as an allosteric regulator of dsRNA binding. To further substantiate this claim, an in-depth analysis of this allosteric effect using for instance network analysis could significantly enhance the study. Such an approach could identify key residues and interaction networks within the protein that mediate the allosteric regulation. This type of mechanistic insight would not only provide a stronger theoretical framework but also offer valuable information for the rational design of therapeutic interventions targeting the cryptic pocket.  

      We thank the reviewer for pointing out the need for clarification on the molecular mechanism linking the opening of the cryptic pocket to RNA binding. We have performed the CARDS analysis on Reston and Marburg IID simulations as was done on Zaire IID simulations in Cruz et al, 2022. The results are shown in Fig S3 and discussed in the main text in the first results section. Briefly, we do find a community (blue) comprising the pocket residues in Reston and Marburg IIDs as we did in Zaire. Similarly, we find that many of the RNA binding residues fall into the orange and green communities as in Zaire. However, there are differences in exactly which residues are clustered into which of these two communities. There are also differences in how strongly connected these communities are in the three homologs. Therefore, while we can conclude that pocket residues likely have varying influence on the RNA binding residues in the homologs, it is hard to say exactly what that variation is from this analysis alone.  

      Reviewer #3 (Recommendations for the authors):

      - MD simulations: All simulations were initialised from the 3 crystal structures, is it correct? In all cases, RNA ds was not included in simulations, right? Were crystallographic MG ions in the vicinity of the binding site included? these are known to influence structural dynamics to a large extent.

      All simulations were indeed initialized using only protein atoms from the crystal structures 3FKE, 4GHL, and 3L2A. Therefore, crystallographic Mg ions were not included in the simulations. However, we do agree with the reviewer and think that the effect of parameters such as salt concentration, specifically Mg ions which are known to be important for the stability of dsRNA, on the pocket opening equilibrium merits detailed study in future work.

      - Figure 2: Would it be possible to perform e.g. a block error analysis and show the statistical errors of the distributions?

      We agree that showing the statistical variation in the MSM equilibrium probabilities is important for comparing the different distributions. Therefore, we have updated Figs 2 and 5 to show the distributions obtained from MSMs constructed using 100 and 10 random samples of the data respectively to indicate the extent of the statistical variability in the MSM construction.  

      - More detailed structural biology experiments (such as NMR or HDX-MS) could potentially shed more light on the differential behaviour of the three different homologs, providing more evidence for the presence of the cryptic pocket.

      We agree that NMR and HDX-MS are powerful means to study dynamics and are actively exploring these approaches for our future work.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      In the manuscript by Tie et.al., the authors couple the methodology which they have developed to measure LQ (localization quotient) of proteins within the Golgi apparatus along with RUSH based cargo release to quantify the speed of different cargos traveling through Golgi stacks in nocodazole induced Golgi ministacks to differentiate between cisternal progression vs stable compartment model of the Golgi apparatus. The debate between cisternal progression model and stable compartment model has been intense and going on for decades and important to understand the basic way of function/organization of the Golgi apparatus. As per the stable compartment model, cisterna are stable structures and cargo moves along the Golgi apparatus in vesicular carriers. While as per cisternal progression model, Golgi cisterna themselves mature acquiring new identity from the cis face to the trans face and act as transport carriers themselves. In this work, authors provide a missing part regarding intra-Golgi speed for transport of different cargoes as well as the speed of TGN exit and based on the differences in the transport velocities for different cargoes tested favor a stable compartment model. The argument which authors make is that if there is cisternal progression, all the cargoes should have a similar intra-Golgi transport speed which is essentially the rate at which the Golgi cisterna mature. Furthermore, using a combination of BFA and Nocodazole treatments authors show that the compartments remain stable in cells for at least 30-60 minutes after BFA treatment.

      Strengths:

      The method to accurately measure localization of a protein within the Golgi stack is rigorously tested in the previous publications from the same authors and in combination with pulse chase approaches has been used to quantify transport velocities of cargoes through the Golgi. This is a novel aspect in this paper and differences in intra-Golgi velocities for different cargoes tested makes a case for a stable compartment model.

      Weaknesses:

      Experiments are only tested in one cell line (HeLa cells) and predominantly derived from experimental paradigm using RUSH assays where a secretory cargo is released in a wave (not the most physiological condition) and therefore additional approaches would make a more compelling case for the model.

      We have added datasets from 293T cells in the revamped manuscript.

      Reviewer #2 (Public Review):

      Summary:

      This manuscript describes the use of quantitative imaging approaches, which have been a key element of the labs work over the past years, to address one of the major unresolved discussions in trafficking: intra-Golgi transport. The approach used has been clearly described in the labs previous papers, and is thus clearly described. The authors clearly address the weaknesses in this manuscript and do not overstate the conclusions drawn from the data. The only weakness not addressed is the concept of blocking COPI transport with BFA, which is a strong inhibitor and causes general disruption of the system. This is an interesting element of the paper, which I think could be improved upon by using more specific COPI inhibitors instead, although I understand that this is not necessarily straightforward.

      I commend the authors on their clear and precise presentation of this body of work, incorporating mathematical modelling with a fundamental question in cell biology. In all, I think that this is a very robust body of work, that provides a sound conclusion in support of the stable compartment model for the Golgi.

      General points:

      The manuscript contains a lot of background in its results sections, and the authors may wish to consider rebalancing the text: The section beginning at Line 175 is about 90% background and 10% data. Could some data currently in supplementary be included here to redress this balance, or this part combined with another?

      In the revamped manuscript, we have moved the background information on rapid partitioning and rim progression models to the Introduction.

      Reviewer #3 (Public Review):

      The manuscript by Tie et al. provides a quantitative assessment of intra-Golgi transport of diverse cargos. Quantitative approaches using fluorescence microscopy of RUSH synchronized cargos, namely GLIM and measurement of Golgi residence time, previously developed by the author's team (publications from 20216 to 2022), are being used here.

      Most of the results have been already published by the same team in 2016, 2017, 2020 and 2021. In this manuscript, very few new data have been added. The authors have put together measurements of intra-Golgi transport kinetics and Golgi residence time of many cargos. The quantitative results are supported by a large number of Golgi mini-stacks/cells analyzed. They are discussed with regard to the intra-Golgi transport models being debated in the field, namely the cisternal maturation/progression model and the stable compartments model. However, over the past decades, the cisternal progression model has been mostly accepted thanks to many experimental data.

      The authors show that different cargos have distinct intra-Golgi transport kinetics and that the Golgi residence time of glycosyltransferases is high. From this and the experiment using brefeldinA, the authors suggest that the rim progression model, adapted from the stable compartments model, fits with their experimental data.

      Strengths:

      The major strength of this manuscript is to put together many quantitative results that the authors previously obtained and to discuss them to give food for thought about the intraGolgi transport mechanism.

      The analysis by fluorescence microscopy of intra-Golgi transport is tough and is a tour de force of the authors even if their approach show limitations, which are clearly stated. Their work is remarkable in regards to the numbers of Golgi markers and secretory cargos which have been analyzed.

      Weaknesses:

      As previously mentioned, most of the data provided here were already published and thus accessible for the community. Is there is a need to publish them again?

      The authors' discussion about the intra-Golgi transport model is rather simplistic. In the introduction, there is no mention of the most recent models, namely the rapid partitioning and the rim progression models. To my opinion, the tubular connections between cisternae and the diffusion/biochemical properties of cargos are not enough taken into account to interpret the results. Indeed, tubular connections and biochemical properties of the cargos may affect their transit through the Golgi and the kinetics with which they reach the TGN for Golgi exit.

      Nocodazole is being used to form Golgi mini-stacks, which are necessary to allow intra-Golgi measurement. The use of nocodazole might affect cellular homeostasis but this is clearly stated by the authors and is acceptable as we need to perturb the system to conduct this analysis. However, the manual selection of the Golgi mini-stack being analyzed raises a major concern. As far as I understood, the authors select the mini-stacks where the cargo and the Golgi reference markers are clearly detectable and separated, which might introduce a bias in the analysis.

      The terms 'Golgi residence time ' is being used but it corresponds to the residence time in the trans-cisterna only as the cargo has been accumulated in the trans-Golgi thanks to a 20{degree sign}C block. The kinetics of disappearance of the protein of interest is then monitored after 20{degree sign}C to 37{degree sign}C switch.

      Another concern also lies in the differences that would be introduced by different expression levels of the cargo on the kinetics of their intra-Golgi transport and of their packaging into post-Golgi carriers.

      Please see below for our replies to intra-Golgi transport models, the Golgi residence time, and different expression levels of cargos.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      The data shown by the authors to measure differential intra Golgi velocities based on previously established methodology make a case for a stable compartment model, however more data is needed to make a complete story and the clarity of presentation can be improved.

      We sincerely appreciate the reviewer's insightful, detailed, and constructive feedback. Your thoughtful comments have helped us refine our analyses, clarify key points, and strengthen the overall quality of our manuscript. We are grateful for the time and effort you have dedicated to reviewing our work and providing valuable suggestions. Your input has been instrumental in improving both the scientific rigor and presentation of our findings. Thank you for your thorough and thoughtful review.

      Main points:

      (1) Along with the studies in yeast, which authors describe in this paper, the main evidence for cisternal maturation model in mammalian cells comes from Bonfanti et.al., (https://doi.org/10.1016/S0092-8674(00)81723-7), which used EM to visualize a wave of Collagen through Golgi stacks. It is therefore important this work needs to include collagen as one of the cargos tested. Can the authors use the RUSH-Col1AGFP (see: https://doi.org/10.1083/jcb.202005166) as a cargo to monitor intra-Golgi velocities?

      I understand that Hela cells are not professional collagen-secreting, but the authors can use U2OS cells to measure collagen export and two other extreme (slow and fast) cargos to validate the same trend in intra-Golgi transport velocities is seen in other cell lines. This will address three concerns: a. This is not a Hela-specific phenomenon; b. Transport of large cargoes like collagen agree with their proposal; c. To see if the same cargo has the same (similar) intra-Golgi speed and the trend between different cargoes is conserved across cell lines.

      Due to the difficulty of manipulating and imaging the procollagen-I RUSH reporter, we selected the collagenX-RUSH reporter (SBP-GFP-collagenX) instead. Our previous study (Tie et al., eLife, 2028) demonstrated that SBP-GFP-collagenX assembles as a large molecular weight particle, each having ~ 190 copies of SBP-GFP-collagenX. With an estimated mean size of ~ 40 nm, these aggregates are not as large as FM4 aggregates and procollagen-I (> 300 nm) and, therefore, are not excluded from conventional transport vesicles, which typically have a size of 50 – 100 nm. However, collagenX has distinct intra-Golgi transport behaviour from conventional secretory cargos -- while conventional secretory cargos localize to the cisternal interior, collagenX partitions to the cisternal rim (Tie et al., eLife, 2028).

      We studied the intra-Golgi transport of SBP-GFP-collagenX in HeLa cells via GLIM and side averaging. The new results are included in Figure 3 of the revamped manuscript. CollagenX has similar intra-Golgi transport kinetics as conventional secretory cargos, displaying the first-order exponential function in LQ vs. time and velocity vs. time plots.

      The side-averaging images are consistent with previous and current results. collagenX displays a double-punctum during the intra-Golgi transport, indicating a cisternal rim localization, as expected for large secretory cargos. Therefore, our new data demonstrated that cisternal rim partitioned large-size secretory cargos might follow intra-Golgi transport kinetics similar to those of cisternal interior partitioned conventional secretory cargos.

      We tried SBP-GFP-CD59 and SBP-GFP-Tac-TC, cargos with fast and slow intra-Golgi transport velocities, respectively, in 293T cells. Results are included in Figure 2, Supplementary Figure 2, and Table 1 of the revamped manuscript. We found that SBP-GFPTac-TC showed similar t<sub>intra</sub>s, 17 and 14 min, respectively, in HeLa and 293T cells. Considering our previous finding that glycosylation has an essential role in the Golgi exit (Sun et al., JBC, 2020), the distinct intra-Golgi transport kinetics of SBP-GFP-CD59 (t<sub>intra</sub>s, 13 and 5 min, respectively, in HeLa and 293T cells) might be due to its distinct luminal glycosylation between HeLa and 293T cells. Supporting this hypothesis, SBP-GFP-Tac-TC does not have any glycosylation sites due to the truncation of the Tac luminal domain.

      (2) RUSH assay has its own caveats which authors also refer to in the manuscript. Authors should test their model by using pulse chase approaches by SNAP tagged constructs which will allow them to do pulse chase assays without the requirement to release cargo as a wave (see: doi: 10.1242/jcs.231373). It is not necessary to test all the cargoes but the two on the ends of the spectrum (slow and fast). To avoid massive overexpression, authors could express the proteins using weaker promoters. Authors could also use this approach to simultaneously measure the two cargoes by tagging them with CLIP and SNAP tags and doing the pulse chase simultaneously (see: DOI: 10.1083/jcb.202206132). In this case it may be difficult to stain both GM130 and TGN, but authors could monitor the rate of segregation from the GM130 signal.

      During the RUSH assay, the sudden release of a large amount of secretory reporters does not occur under native secretory conditions and, consequently, might introduce artifacts. The reviewer suggests using pulse-chase labeling of SNAP (or CLIP)-tagged secretory cargos, which occurs in a steady state and hence more closely resembles native secretory transport. This is an excellent suggestion. However, we have not yet tested this method due to the following concerns.

      The standard protocol involves blocking existing reporters, pulse-labeling newly synthesized reporters, and chasing their movement along the secretory pathway. However, the typical 20minute pulse labeling period used in the two references would be too long, as a substantial portion of the reporters would already reach the trans-Golgi or exit the Golgi before the chase begins. Conversely, reducing the pulse labeling time would significantly weaken the GLIM signal.

      (3) While the intra-Golgi velocities are different for different cargoes tested, authors should show a control that the arrival of the cargoes from ER to the cis-Golgi follows similar kinetics or if there are differences there is no correlation with the intra-Golgi velocities. In other words, do cargoes which show slow intra-Golgi velocities also take more time to reach the cis-Golgi and vice versa.

      In nocodazole-induced Golgi ministacks, the ER exit site, ERGIC, and cis-Golgi are spatially closely associated. At the earliest measurable time point—5 minutes after biotin treatment— we observed that the secretory cargo had already reached the cis-Golgi (Figure 2 and Supplementary Figure 2). The rapid ER-to-cis-Golgi transport exceeds the temporal resolution of our current protocol, making it difficult to address the reviewer’s question (see our reply to Minor Points (2) of Reviewer #2 for more detailed discussion on this).

      (4) Were the different cargos traveling (at different speeds) through Golgi at the rims, or in the middle of ministack, or by vesicles?

      Please also refer to our reply to Question 1 of Reviewer #1. For the nocodazole-induced Golgi ministack, we previously investigated the lateral cisternal localization of RUSH secretory reporters using our en face average imaging (Tie et al., eLife, 2018). We found that small or conventional cargos (such as CD59 and E-cadherin) partition to the cisternal interior while large cargos (collagenX and FM4-CD8a) partition to the cisternal rim during their intra-Golgi transport. Using GLIM, we showed that the intra-Golgi transport kinetics of collagenX is similar to that of small cargos as both follow the first-order exponential function (Figure 3A-C). Therefore, cisternal rim partitioned large size secretory cargos might have intra-Golgi transport kinetics similar to those of cisternal interior partitioned conventional secretory cargos.

      (5) Figure 4, under both nocodazole and BFA treatment for 30mins, would the stacks have the same number (274 nm per LQ) as thickness? Or does it shrink a little? Considering extended BFA treatment reduced intact Golgi ministacks. This is important to understand the LQ numbers of those Golgi proteins. Besides, can they include one ERGIC marker in this assay, would it be approaching cis-Golgi? Images used for quantification in Figure 4 should be shown in the main figure.

      We define the axial size of the Golgi ministack as the axial distance from the GM130 to the GalT-mCherry, d<sub>(GM130-GalT-mCherry)</sub>, measured using the Gaussian centers of their line intensity profiles. As the reviewer suggested, we measured the axial size of the ministack during the nocodazole and BFA treatment. Indeed, we found a decrease in the ministack axial size from 300 ± 10 nm at 0 min to 190 ± 30 nm at 30 min of BFA treatment. This observation is further confirmed by our side average imaging. The new data is presented in Fig. 6G.

      Our study focuses on changes in the organization of the Golgi ministack. So, we didn’t include ERGIC53 in the current analysis. Instead, we quantified the axial distance between GalTmCherry and CD8a-furin, d<sub>(GalT-mCherry-CD8a-furin)</sub>, and found that it decreased from 200 ± 20 nm at 0 min to 100 ± 30 nm at 30 min of BFA treatment, suggesting the collapse of the TGN. The collapse of the TGN is further visualized by our side average imaging. The new data is presented in Fig. 6H.

      Therefore, our new data demonstrates that the Golgi ministack shrinks, and the TGN collapses under BFA treatment.

      Minor points:

      (1) The LQ data come from confocal/airy scan images, but no such images were shown in this paper. The authors can't assume every reader to have prior knowledge of their previous work. It will be beneficial to have one example image and how the LQ was measured.

      As advised by the reviewer, we have prepared Supplementary Figure 1 to provide a brief illustration of the principle behind GLIM and image processing steps involved.

      (2) The cargos used in this paper need to be introduced: what are they, how were they used in previous literature. Especially the furin constructs come out of the blue (also see point 7).

      As suggested by the reviewer, we have included a schematic diagram in Fig. 1 of the revised manuscript to illustrate all RUSH reporters and their corresponding ER hooks. In this diagram, we also highlight the key sequence differences in the cytosolic tails of different furin mutants.

      Additionally, we have added references for each RUSH reporter at the beginning of the Results and Discussion section.

      (3) There are two categories of exocytosis, constitutive and regulated. It important to state that the phenomenon observed is in cells predominantly showing only constitutive secretion.

      As the reviewer advised, we have added the following sentences in the section titled “Limitations of the study”.

      “Third, all RUSH reporters used in this study are constitutive secretory cargos. As a result, the intra-Golgi transport dynamics observed here might not reflect those of regulated secretion, which involves the synchronized release of a large quantity of cargo in response to a specific signal.”

      (4) All the cargoes show a progressive reduction in instantaneous velocities from cis to medial to trans. Authors should discuss how do they mechanistically explain this. Is the rate of vesicle production progressively decreasing from cis to trans and if so, why?

      As our imaging methods cannot differentiate vesicles from the cisternal rim, we could not tell if the vesicle production rate had changed during the intra-Golgi transport. We have provided an explanation of the progressive reduction of the intra-Golgi transport velocity in the Results and Discussion section. Please see the text below.

      “The progressive reduction in intra-Golgi transport of secretory cargo might result from the enzyme matrix's retention at the trans-Golgi. As the secretory cargos progress along the Golgi stack from the cis to the trans-side, more and more cargos become temporarily retained in the trans-Golgi region, gradually reducing their overall intra-Golgi transport velocity. If the release or Golgi exit of these cargos from the enzyme matrix follows a constant probability per unit time, i.e., a first-order kinetics process, the rate of cargo exiting from the Golgi should follow the first-order exponential function. Since the mechanism underlying intra-Golgi transport kinetics reflects fundamental molecular and cellular processes of the Golgi, further experimental data are essential to rigorously test this hypothesis.”

      (5) The supp file 1 nicely listed the raw data for plotting, and n for numbers of ministacks. Could the authors also show number of cells or experiment repeats?

      In the revamped version of the Supplementary File 1, we have added the cell number for each LQ measurement.

      (6) This recent work used novel multiplexing methods to show that nocodazole-treated cells had similar protein organization as in control may be cited. It also showed the effect of BFA. https://www.cell.com/cell/abstract/S0092-8674(24)00236-8.

      We have added this reference to the Introduction section to support that nocodazole-induced Golgi ministacks have a similar organization as the native Golgi. However, our BFA treatment was combined with the nocodazole treatment, while this paper’s BFA treatment does not contain nocodazole.

      (7) Figure 1G-J, authors should show a schematic to show the difference between different furin constructs. Also, LQ values in Fig 1I start from 1. Authors may need to include even earlier timepoints.

      As suggested by the reviewer, we have shown the domain organization of wild type and mutant furin RUSH reporters in Figure 1, highlighting key amino acids in the cytosolic tail. Please also see our reply to Minor Points (2) of Reviewer #1.

      In the revised manuscript, Fig. 1l (SBP-GFP-CD8a-furin-AC #1) has been updated to become Fig. 2J. In this dataset, the first time point was selected at a relatively late stage (20 min), resulting in an initial LQ value of 0.92. However, this should not pose an issue, as SBP-GFPCD8a-furin-AC reaches a plateau of ~ 1.6. The number of data points is sufficient to capture the rising phase and fit the first-order exponential function curve with an adjusted R<sup>2</sup> = 0.99. Furthermore, we have four independent datasets in total on the intra-Golgi transport of SBPGFP-CD8a-furin-AC (#1-4), demonstrating the consistency of our measurements.

      (8) Figure 2A need to show the data points, not just the lines.

      In the revamped manuscript, Fig. 2A has been updated to become Fig. 4A. The plot of Fig. 4A is calculated based on Equation 3.

      So, it does not have data points. However, t<sub>intra</sub> is calculated based on the experimental LQ vs. t kinetic data. 

      (9) Imaging and camera settings like exposure time, pixel size, etc should be reported in Methods.

      As suggested by the reviewer, we have supplied this information in the Materials and Methods section of the revised manuscript.

      (1) The exposure time and pixel size for the wide-field microscopy:

      “The image pixel size is 65 nm. The range of exposure time is 400 – 5000 ms for each channel.”

      (2) The exposure time and pixel size for the spinning disk confocal microscopy: “The image pixel size is 89 nm. The range of exposure time is 200 – 500 ms for each channel.”

      (3) The pixel dwelling time and pixel size for the Airyscan microscopy:

      “For side averaging, images were acquired under 63× objective (NA 1.40), zoomed in 3.5× to achieve 45 nm pixel size using the SR mode. The pixel dwelling time is 1.16 µs.”

      Reviewer #2 (Recommendations For The Authors):

      We sincerely appreciate the reviewer's insightful, detailed, and constructive feedback. Your thoughtful comments have helped us refine our analyses, clarify key points, and strengthen the overall quality of our manuscript. We are grateful for the time and effort you have dedicated to reviewing our work and providing valuable suggestions. Your input has been instrumental in improving both the scientific rigor and presentation of our findings. Thank you for your thorough and thoughtful review.

      Minor points:

      (1) Equation 2: A should be in front of the ln2. It's already resolved in equation 3, so likely only needs changing in the text

      As suggested by the reviewer, we have changed it accordingly.

      (2) Line 152: Why is there a lack of experimental data? High ER background and low golgi signal make it difficult to select ministacks: would be good to see examples of these images. Is 0 a relevant timepoint as cargo is still at the ER? Instead would a timepoint <5' be better demonstrate initial arrival in fast cargo, and 0' discarded?

      We observed that RUSH reporters typically do not exit the ER in < 5 min of biotin treatment, resulting in a high ER background and low Golgi signal. Example images of SBP-GFP-CD59 are shown below (scale bar: 10 µm). Possible reasons include: 1) the time required for biotin diffusion into the ER, 2) the time needed to displace the RUSH hook from the RUSH reporter, and 3) the time for recruitment of RUSH reporters to ER exit sites. As a result, we could not obtain LQs for time points earlier than 5 min during the biotin chase.

      Author response image 1.

      Despite the challenge in measuring LQs at early time points, 0 is still a relevant time point. At t = 0 min, RUSH reporters should be at the ER membrane near the ER exit site, a definitive pre-Golgi location along the Golgi axis, although we still don’t have a good method to determine its LQ.

      (3) Table 1 Line 474: 1-3 independent replicates: is there a better way of incorporating this into the table to make it more streamlined? It would be useful to see each cargo as a mean with error. Is there a more demonstrative way to present the table, for example (but does not have to be) fastest cargo first (Tintra) as in Table 2?

      As suggested by the reviewer, we revised Table 1. We calculated the mean and SD of t<sub>intra</sub> and arranged our RUSH reporters in ascending order based on their t<sub>intra</sub> values.

      (4) Line 264 / Fig 3B: It's unclear to me why the VHH-anti-GFP-mCherry internalisation approach was used, when the cells were expressing GFP, that could be used for imaging. Also, this introduces a question over trafficking of the VHH itself, to access the same compartments as the GFP-proteins are localised. It would be useful to describe the choice of this approach briefly in the text.

      Here, the surface-labeling approach is used to investigate if GFP-Tac-TC possesses a Golgi retrieval pathway after its exocytosis to the plasma membrane. When VHH-anti-GFP-mCherry is added to the tissue culture medium, it binds to the cell surface-exposed GFP-fused MGAT1, MGAT2, Tac, Tac-TC, CD8a, and CD8a-TC. Next, VHH-anti-GFP-mCherry traces the internalized GFP-fused transmembrane proteins. The surface-labeling approach has two advantages in this case. 1) It is much more sensitive in revealing the minor number of GFPtransmembrane proteins at the plasma membrane and endosomes, which are usually drowned in the strong Golgi and ER background fluorescence in the GFP channel. 2) While the GFP fluorescence distribution has reached a dynamic equilibrium, the surface labeling approach can reveal the endocytic trafficking route and dynamics.

      As the reviewer suggested, we added the following sentence to describe the choice of the cellsurface labeling – “By binding to the cell surface-exposed GFP, VHH-anti-GFP-mCherry serves as a sensitive probe to track the endocytic trafficking itinerary of the above GFP-fused transmembrane proteins”. 

      Regarding the trafficking of VHH-anti-GFP-mCherry itself, in HeLa cells that do not express GFP-fused transmembrane proteins, VHH-anti-GFP-mCherry can be internalized by fluidphase endocytosis. However, the fluid-phase endocytosis is negligible under our experimental condition, as we previously demonstrated (Sun et al., JCS, 2021; PMID: 34533190).

      (5) 446 Typo "internalization"

      It has been corrected.

      Reviewer #3 (Recommendations For The Authors):

      Below are my recommendations for the authors to improve their manuscript:

      We sincerely appreciate the reviewer's insightful, detailed, and constructive feedback. Your thoughtful comments have helped us refine our analyses, clarify key points, and strengthen the overall quality of our manuscript. We are grateful for the time and effort you have dedicated to reviewing our work and providing valuable suggestions. Your input has been instrumental in improving both the scientific rigor and presentation of our findings. Thank you for your thorough and thoughtful review.

      (1) Line 48: Tie at al. 2016 is cited. Please add references to original work showing that cargos transit from cis to trans Golgi cisternae.

      After reviewing the literature, we identified two references that provide some of the earliest morphological evidence of secretory cargo transit from the cis- to the trans-Golgi:

      (1) Castle et al, JCB, 1972; PMID: 5025103

      (2) Bergmann and Singer, JCB, 1983; PMID: 6315743

      The first study utilized pulse-chase autoradiographic EM imaging to track secretory protein movement, while the second employed immuno-EM imaging to observe the synchronized release of VSVGtsO45. Accordingly, we have removed Tie et al., 2016 and replaced it with these newly identified references.

      (2) I would suggest to cite earlier (in the Introduction) the rapid partitioning and rim progression models.

      As suggested, we have moved the rapid partitioning and rim progression models to the Introduction section.

      (3) Figure 1: LQ vs. time plot for SBP-GFP-CD8a-furinAC (panel I, 0.9 to 1.75 in 150 min) is different from Fig 7G of Tie et al. 2016 (LQ O-1.5 in 100 min). Please comment on why those 2 sets of data are different.

      We appreciate the reviewer for pointing out this error. In our previous publication (Tie et al., MBoC, 2016), we presented a total of four datasets on SBP-GFP-CD8a-furin-AC. However, in the earlier version of our manuscript, we mistakenly listed only three datasets, inadvertently omitting Fig. 7G from Tie et al., MBoC, 2016.

      In the revised version, we have now included Fig. S2T (SBP-GFP-CD8a-furin-AC #4), which corresponds to Fig. 7G from Tie et al., MBoC, 2016.

      (4) As mentioned in the public review, I think measurement of the expression level of the cargos is necessary to compare their transport kinetics.

      The reviewer raises a valid concern that is challenging to address. All our data were obtained by imaging overexpressed reporters, and we assume that their overexpression does not significantly impact the Golgi or the secretory pathway. Our previous studies have demonstrated that overexpression does not substantially affect LQs (Figure S2 of Tie et al., MBoC, 2016, and Figure S1 of Tie et al., JCB, 2022).

      We acknowledge this concern as one of the limitations in our study at the end of our manuscript:

      “First, our approach relied on the overexpression of fluorescence protein-tagged cargos. The synchronized release of a large amount of cargo could significantly saturate and skew the intra-Golgi transport.” 

      (5) To my opinion, cisternal continuities would also affect retrograde transport (accelerate) (by diffusion for instance) and not only retrograde transport. Please comment on how this would affect intra-Golgi transport kinetics.

      We believe the reviewer is suggesting “cisternal continuities would also affect retrograde transport (accelerate) (by diffusion for instance) and not only anterograde transport.”

      Transient cisternal continuities have been reported to facilitate the anterograde transport of large quantities of secretory cargos (Beznoussenko et al., 2014; PMID: 24867214) (Marsh et al., 2004; PMID: 15064406) (Trucco et al., 2004; PMID: 15502824). However, we are not aware of any reports demonstrating that such continuities facilitate the retrograde transport of secretory cargo, although Trucco et al. (2004) speculated that Golgi enzymes might use these connections to diffuse bidirectionally (anterograde and retrograde direction). For this reason, we did not discuss this scenario in our manuscript.

      (6) Lines 188-190: I don't understand why the rapid partitioning model is excluded. Please detail more the arguments used for this statement.

      Below is the section from the Introduction that addresses the reviewer's question.

      “This model (rapid partitioning model) suggests that cargos rapidly diffuse throughout the Golgi stack, segregating into multiple post-translational processing and export domains, where cargos are packed into carriers bound for the plasma membrane. Nonetheless, synchronized traffic waves have been observed through various techniques, including EM (Trucco et al., 2004) and advanced light microscopy methods we developed, such as GLIM and side-averaging(Tie et al., 2016; Tie et al., 2022). These findings suggest that the rapid partitioning model might not accurately represent the true nature of the intra-Golgi transport.”

      (7) I would suggest replacing the 'Golgi residence time' by another name as it reflects mainly the time of Golgi exit if I am not mistaken.

      We believe the term “Golgi residence time” more accurately reflects the underlying mechanism – retention. The same approach to measure the Golgi residence time can also be applied to Golgi enzymes such as ST6GAL1. Its slow Golgi exit kinetics (t<sub>1/2</sub> = 5.3 hours) (Sun et al., JCS, 2021) should be primarily due to a strong Golgi retention at its steady state Golgi localization.

      In contrast, the conventional secretory cargos’ Golgi exit times are usually much shorter (t<sub>1/2</sub> < 20 min) (Table 2) due to weaker Golgi retention. In a broader sense, the Golgi exit kinetics of a secretory cargo should be influenced by its Golgi retention. Furthermore, we have consistently used the term “Golgi residence time” in our previous publications. So, we propose maintaining this terminology in the current manuscript.

      (8) Lines 300-306: I would suggest that the authors remove this part as it is highly speculative and not supported by data.

      We have relocated this discussion to the section titled "Our data supports the rim progression model, a modified version of the stable compartment model."

      Our enzyme matrix hypothesis offers a potential explanation for key observations, including the differential cisternal localization of small and large cargos and the interior localization of Golgi enzymes. Cryo-FIB-ET has shown that the interior of Golgi cisternae is enriched with densely packed Golgi enzymes (Engel et al., PNAS, 2015; PMID: 26311849), supporting this hypothesis.

      Additionally, this hypothesis helps explain the gradual reduction in intra-Golgi transport velocities of secretory cargos, as requested by Reviewer #1 (Minor Points 4). For these reasons, we propose retaining this discussion in the manuscript.

      (9) In Figure 3B, percentage of MGAT2-GFP cells with anti-GFP signal at the Golgi is of 41% while Sun et al. 2021 reported 25%, please comment this difference. Reply:

      We included more cells for the quantification. The percentage of cells showing Golgi localization of VHH-anti-GFP-mCherry is now 32% (n = 266 cells). The observed difference, 32% vs. 25% (Sun et al., JCS, 2021), is likely due to uncontrollable variations in experimental conditions, which might have influenced the endocytic Golgi targeting efficiency.

      (10) The effects of brefeldinA are pleiotropic as it disassembles COPI and clathrin coats but also induces tubulation of endosomes. I would recommend using Golgicide A, which is more specific.

      We agree with the reviewer that Golgicide A might be more specific as an inhibitor of Arf1. We will certainly consider using this inhibitor next time.

    1. Author response:

      Reviewer #1:

      We appreciate the Reviewer's positive feedback on the strengths of our study.

      The timescales of the peptide recognition and unbinding process are much longer than what can be sampled from unbiased simulations. Therefore, the proposed mechanism of recognition should only be considered a hypothesis based on the results presented here. For example, peptides that do not dissociate within one one-microsecond MD simulation are considered to be stable binders. However, they may not have a viable way to bind to the narrow protein cleft in the first place.

      We thank the Reviewer for this valuable feedback. We agree with the Reviewer. Our work on the IRE1 cLD activation mechanism is focused on generating hypotheses of the binding mechanism driven by MD simulations. We recognize the limitations in defining a stable binder due to the time scales sampled. However, our primary focus was to sample and characterize a possible binding pose in the center of the cLD dimer. We will contextualize our statements about stable binders and limit our claims to stating that the protein-peptide complex is stable within 1 μs-long simulations. However, we believe that our finding that the cLD dimer groove is not able to accommodate peptides is solid, as the steric impediment described is present in all our replicas, both with and without peptides, in a cumulative sampling time of 72 μs. Additionally, we will include a plot showing the distribution of groove width across all replicas.

      Oftentimes, representative structures sampled from MD simulation are used to draw conclusions (e.g., Figure 4 about the role of R161 mutation in binding affinity). This is not appropriate as one unbinding event being observed or not observed in a microsecond-long trajectory does not provide sufficient information about the binding strength of the free energy difference.

      We thank the Reviewer for the insightful comment. As explained in the previous point, we believe that our simulations provide useful hypotheses, and we agree that we do not currently have data to comment on binding affinity. We will, therefore, remove all references to this term. We are aware of the limitations due to the timescale and agree that these limitations cannot be overcome with standard equilibrium simulations. To address these limitations, we plan to use orthogonal methods, namely MM/PB(GB)SA calculations for calculating binding free energies from existing trajectories (as performed by https://doi.org/10.1021/acs.jcim.4c00975). We will add predictions of all the peptides using AlphaFold 3, to confirm the binding region.

      Reviewer #2:

      We thank the Reviewer for their positive feedback.

      Improving presentation to include more computational details.

      We thank the Reviewer for raising this critical point. We agree that the manuscript is tailored for a biology audience, as the data are particularly relevant for that community. Nevertheless, we also understand the importance of providing sufficient methodological detail for computational readers. We will add appropriate computational information in the main text.

      More quantitative analysis in addition to visual structures.

      We will add an uncertainty estimate for the HDX calculations using bootstrapping and include additional information on bond distances for Y161. We will also incorporate time-series data showing the distance of the peptide from the groove across all replicas.

      Reviewer #3:

      We appreciate the Reviewer's positive feedback on our work.

      A potential weakness of the study is the usage of equilibrium (unbiased) molecular dynamics simulations so that processes and conformational changes on the microsecond time scale can be probed. Furthermore, there can be inaccuracies and biases in the description of unfolded peptides and protein segments due to the protein force fields. Here, it should be noted that the authors do acknowledge these possible limitations of their study in the conclusions.

      We appreciate the Reviewer's thoughtful comment. As noted in our response to Reviewer 1, we plan to address the concern about sampling by applying orthogonal methods. We agree with the Reviewer that some form of enhanced sampling is necessary if we want to assess binding in a more quantitative way, e.g., via free energy calculations. However, we also realize that applying any enhanced sampling scheme to our system is very challenging, given its large size and the complex peptide-protein interactions, which are not easily captured in a few collective variables. After a careful assessment and some preliminary tests, we decided that estimating free energies using enhanced sampling would necessitate a separate paper due to both the conceptual complexity of the project and the size of the necessary sampling campaign.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Contractile Injection Systems (CIS) are versatile machines that can form pores in membranes or deliver effectors. They can act extra or intracellularly. When intracellular they are positioned to face the exterior of the cell and hence should be anchored to the cell envelope. The authors previously reported the characterization of a CIS in Streptomyces coelicolor, including significant information on the architecture of the apparatus. However, how the tubular structure is attached to the envelope was not investigated. Here they provide a wealth of evidence to demonstrate that a specific gene within the CIS gene cluster, cisA, encodes a membrane protein that anchors the CIS to the envelope. More specifically, they show that:

      - CisA is not required for assembly of the structure but is important for proper contraction and CIS-mediated cell death

      - CisA is associated to the membrane (fluorescence microscopy, cell fractionation) through a transmembrane segment (lacZ-phoA topology fusions in E. coli)

      - Structural prediction of interaction between CisA and a CIS baseplate component<br /> - In addition they provide a high-resolution model structure of the >750-polypeptide Streptomyces CIS in its extended conformation, revealing new details of this fascinating machine, notably in the baseplate and cap complexes.

      All the experiments are well controlled including trans-complemented of all tested phenotypes.

      One important information we miss is the oligomeric state of CisA.

      Thank you for this suggestion. We now provide information on the potential oligomeric state of CisA. We performed further AlphaFold3 modelling of CisA using an increasing number of CisA protomers (1 to 8). We ran predictions for the configuration using the sequence of the well-folded C-terminal CisA domain (amino acids 285-468), which includes the transmembrane domain and the conserved domain that shares similarities to carbohydrate-degrading domains. The obtained confidence scores (mean values for pTM=0.73, ipTM=0.7, n=5) indicate that CisA can assemble into a pentamer and that this oligomerization is mediated through the interaction of the C-terminal solute-binding like superfamily domain.

      We have added this information to the revised manuscript (Fig. 3b/c) and further discuss the possible implications of CisA oligomerization for its proposed mode of action.

      While it would have been great to test the interaction between CisA and Cis11, to perform cryo-electron microscopy assays of detergent-extracted CIS structures to maintain the interaction with CisA, I believe that the toxicity of CisA upon overexpression or upon expression in E. coli render these studies difficult and will require a significant amount of time and optimization to be performed. It is worth mentioning that this study is of significant novelty in the CIS field because, except for Type VI secretion systems, very few membrane proteins or complexes responsible for CIS attachment have been identified and studied.

      We thank this reviewer for their highly supportive and positive comments on our manuscript and we are grateful for their recognition of the novelty of our study, particularly in the context of membrane proteins and complexes involved in CIS attachment.

      We agree that further experimental evidence on direct interaction between CisA and Cis11 would have strengthened our model on CisA function. However, as noted by this reviewer, this additional work is technically challenging and currently beyond the scope of this study.

      Reviewer #2 (Public review):

      Summary:

      The overall question that is addressed in this study is how the S. coelicolor contractile injection system (CISSc) works and affects both cell viability and differentiation, which it has been implicated to do in previous work from this group and others. The CISSc system has been enigmatic in the sense that it is free-floating in the cytoplasm in an extended form and is seen in contracted conformation (i.e. after having been triggered) mainly in dead and partially lysed cells, suggesting involvement in some kind of regulated cell death. So, how do the structure and function of the CISSc system compare to those of related CIS from other bacteria, does it interact with the cytoplasmic membrane, how does it do that, and is the membrane interaction involved in the suggested role in stress-induced, regulated cell death? The authors address these questions by investigating the role of a membrane protein, CisA, that is encoded by a gene in the CIS gene cluster in S. coelicolor. Further, they analyse the structure of the assembled CISSc, purified from the cytoplasm of S. coelicolor, using single-particle cryo-electron microscopy.

      Strengths:

      The beautiful visualisation of the CIS system both by cryo-electron tomography of intact bacterial cells and by single-particle electron microscopy of purified CIS assemblies are clearly the strengths of the paper, both in terms of methods and results. Further, the paper provides genetic evidence that the membrane protein CisA is required for the contraction of the CISSc assemblies that are seen in partially lysed or ghost cells of the wild type. The conclusion that CisA is a transmembrane protein and the inferred membrane topology are well supported by experimental data. The cryo-EM data suggest that CisA is not a stable part of the extended form of the CISSc assemblies. These findings raise the question of what CisA does.

      We thank Reviewer #2 for the overall positive evaluation of our manuscript and the constructive criticism.

      Weaknesses:

      The investigations of the role of CisA in function, membrane interaction, and triggering of contraction of CIS assemblies, are important parts of the paper and are highlighted in the title. However, the experimental data provided to answer these questions appear partially incomplete and not as conclusive as one would expect.

      We acknowledge that some aspects of our work remain unanswered. We are currently unable to conduct additional experiments because the two leading postdoctoral researchers on this project have moved on to new positions. We currently don’t have the extra manpower with a similar skill set to pick up the project.

      The stress-induced loss of viability is only monitored with one method: an in vivo assay where cytoplasmic sfGFP signal is compared to FM5-95 membrane stain. Addition of a sublethal level of nisin lead to loss of sfGFP signal in individual hyphae in the WT, but not in the cisA mutant (similarly to what was previously reported for a CIS-negative mutant). Technically, this experiment and the example images that are shown give rise to some concern. Only individual hyphal fragments are shown that do not look like healthy and growing S. coelicolor hyphae. Under the stated growth conditions, S. coelicolor strains would normally have grown as dense hyphal pellets. It is therefore surprising that only these unbranched hyphal fragments are shown in Fig. 4ab.

      We thank this Reviewer for their thoughtful criticism regarding the viability assays and the data presented in Figure 4. We acknowledge the importance of ensuring that the presented images reflect the physiological state of S. coelicolor under the stated growth conditions and recognize that hyphal fragments shown in Figure 4 do not fully capture the typical morphology of S. coelicolor. As pointed out by this reviewer, S. coelicolor grows in large hyphal clumps when cultured in liquid media, making the quantification of fluorescence intensities in hyphae expressing cytoplasmic GFP or stained with the membrane dye FM5-95 particularly challenging. To improve the image analysis and quantification of GFP and FM5-95-fluorescent intensities across the three S. coelicolor strains (wildtype, cisA deletion mutant and the complemented cisA mutant), we vortexed the cell samples before imaging to break up hyphal clumps, increasing hyphal fragments. The hyphae shown in our images were selected as representative examples across three biological replicates.

      Further, S. coelicolor would likely be in a stationary phase when grown 48 h in the rich medium that is stated, giving rise to concern about the physiological state of the hyphae that were used for the viability assay. It would be valuable to know whether actively growing mycelium is affected in the same way by the nisin treatment, and also whether the cell death effect could be detected by other methods.

      The reasoning behind growing S. coelicolor for 48 h before performing the fluorescence-based viability assay was that we (DOI: 10.1038/s41564-023-01341-x ) and others (e.g.: DOI: 10.1038/s41467-023-37087-7 ) previously showed that the levels of CIS particles peak at the transition from vegetative to reproductive/stationary growth, thus indicating that CIS activity is highest during this growth stage. The obtained results in this manuscript are consistent with previous results, in which we showed a similar effect on the viability of wildtype versus cis-deficient S. coelicolor strains (DOI: 10.1038/s41564-023-01341-x ) using nisin, the protonophore CCCP and UV radiation. The results presented in this study and our previous study are based on biological triplicate experiments and appropriate controls. Furthermore, our results are in agreement with the findings reported in a complementary study by Vladimirov et al. (DOI: 10.1038/s41467-023-37087-7 ) that used a different approach (SYTO9/PI staining of hyphal pellets) to demonstrate that CIS-deficient mutants exhibit decreased hyphal death.

      Taken together, we believe that the results obtained from our fluorescence-based viability assay provide strong experimental evidence that functional CIS mediate hyphal cell death in response to exogenous stress.

      The model presented in Fig. 5 suggests that stress leads to a CisA-dependent attachment of CIS assemblies to the cytoplasmic membrane, and then triggering of contraction, leading to cell death. This model makes testable predictions that have not been challenged experimentally. Given that sublethal doses of nisin seem to trigger cell death, there appear to be possibilities to monitor whether activation of the system (via CisA?) indeed leads to at least temporally increased interaction of CIS with the membrane.

      We thank this reviewer for their suggestions on how to test our model further. This is a challenging experiment because we do not know the exact dynamics of how nisin stress is perceived and transmitted to CisA and CIS particles.

      In an attempt to address this point, we have performed co-immunoprecipitation experiments using S. coelicolor cells that produced CisA-FLAG as bait, and which were treated with a sub-lethal nisin concentration for 0/15/45 min.  Mass spectrometry analysis of co-eluted peptides did not show the presence of CIS-associated peptides at the analyzed timepoints. While we cannot exclude the possibility that our experimental assay requires further optimization to successfully demonstrate a CisA-CIS interaction (e.g. optimization of the use of detergents to improve the solubilization of CisA from Streptomyces membrane, which is currently not an established method), an alternative and equally valid hypothesis is that the interaction between CIS particles and CisA is transient and therefore difficult to capture. We would like to mention, however, that we did detect CisA peptides in crude purifications of CIS particles from nisin-stressed cells (Supplementary Table 2, manuscript: line 301/302), supporting our proposed model that CisA can associate with CIS particles in vivo.

      Further, would not the model predict that stress leads to an increased number of contracted CIS assemblies in the cytoplasm? No clear difference in length of the isolated assemblies if Fig. S7 is seen between untreated and nisin-exposed cells, and also no difference between assemblies from WT and cisA mutant hyphae.

      The reviewer is correct that there is no clear difference in length in the isolated CIS particles shown in Figure S7. This is in line with our results, which show that CisA is not required for the correct assembly of CIS particles and their ability to contract in the presence and absence of nisin treatment. The purpose of Figure S7 was to support this statement. We would like to note that the particles shown in Figure S7 were purified from cell lysates using a crude sheath preparation protocol, during which CIS particles generally contract irrespective of the presence or absence of CisA. Thus, we cannot comment on whether there is an increased number of contracted CIS assemblies in the cytoplasm of nisin-exposed cells. To answer this point, we would need to acquire additional cryo-electron tomograms (cyroET) of the different strains treated with nisin. CryoET is an extremely time and labor-intensive task and given that we currently don’t know the exact dynamics of the CIS-CisA interaction following exogenous stress, we believe this experiment is beyond the scope of this work.

      The interaction of CisA with the CIS assembly is critical for the model but is only supported by Alphafold modelling, predicting interaction between cytoplasmic parts of CisA and Cis11 protein in the baseplate wedge. An experimental demonstration of this interaction would have strengthened the conclusions.

      We agree that direct experimental evidence of this interaction would have further strengthened the conclusions of our study, and we have extensively tried to provide additional experimental evidence. Unfortunately, because of the toxicity of cisA expression in E. coli and the possibly transient nature of the interaction under the experimental conditions used, we were unable to confirm this interaction by biochemical or biophysical techniques, such as co-purification or bacterial two-hybrid assays. Despite these technical challenges, we believe that the AlphaFold predictions provided a valuable hypothesis about the role of CisA in firing and the function of CIS particles in S. coelicolor.

      The cisA mutant showed a similarly accelerated sporulation as was previously reported for CIS-negative strains, which supports the conclusion that CisA is required for function of CISSc. But the results do not add any new insights into how CIS/CisA affects the progression of the developmental life cycle and whether this effect has anything to do with the regulated cell death that is caused by CIS. The same applies to the effect on secondary metabolite production, with no further mechanistic insights added, except reporting similar effects of CIS and CisA inactivations.

      Thank you for your feedback on this aspect of the manuscript. We would like to note that the main focus of this study was to provide further insight into how CIS contraction and firing are mediated in Streptomyces. We used the analysis of accelerated sporulation and secondary metabolite production as a readout to directly assess the functionality of CIS in the presence or absence of CisA and to complement the in situ cryoET data. In summary, our data significantly expand our knowledge of CIS function and firing in Streptomyces and suggest a model in which CisA plays an essential role in mediating the interaction of CIS particles with the membrane, which is required for CIS-mediated cell death. We discuss this model in more detail in the revised manuscript (Line 274-283).

      We agree that we still don’t fully understand the full nature of the signals that trigger CIS contraction, but we do know that the production of CIS is an integral part of the Streptomyces multicellular life cycle as demonstrated by two independent previous studies by us and others (DOI: 10.1038/s41564-023-01341-x and DOI: 10.1038/s41467-023-37087-7 ).

      We further speculate that the assembly and CisA-dependent firing of Streptomyces CIS particles could present a molecular mechanism to dismantle part of the vegetative mycelium. This form of “regulated cell death” could provide two key benefits: (1) to prevent the spread of local cellular damage to the rest of mycelium and (2) to provide additional nutrients for the rest of the mycelium to delay the terminal differentiation into spores, which in turn also affects the production of secondary metabolites.

      Concluding remarks:

      The work will be of interest to anyone interested in contractile injection systems, T6SS, or similar machineries, as well for people working on the biology of streptomycetes. There is also a potential impact of the work in the understanding of how such molecular machineries could have been co-opted during evolution to become a mechanism for regulated cell death. However, this latter aspect remains still poorly understood. Even though this paper adds excellent new structural insights and identifies a putative membrane anchor, it remains elusive how the Streptomyces CIS may lead to cell death. It is also unclear what the advantage would be to trigger death of hyphal compartments in response to stress, as well as how such cell death may impact (or accelerate) the developmental progression. Finally, it is inescapable to wonder whether the Streptomyces CIS could have any role in protection against phage infection.

      We thank Reviewer #2 for the overall supportive assessment of our work. We will briefly discuss functional CIS's impact on Streptomyces development in the revised manuscript. We previously tested if Streptomyces could defend against phages but have not found any experimental evidence to support this idea (unpublished data). The analysis of phage defense mechanisms is an underdeveloped area in Streptomyces research, partly due to the currently limited availability of a diverse phage panel.

      Reviewer #3 (Public review):

      Summary:

      In this work, Casu et al. have reported the characterization of a previously uncharacterized membrane protein CisA encoded in a non-canonical contractile injection system of Streptomyces coelicolor, CISSc, which is a cytosolic CISs significantly distinct from both intracellular membrane-anchored T6SSs and extracellular CISs. The authors have presented the first high-resolution structure of extended CISSc structure. It revealed important structural insights in this conformational state. To further explore how CISSc interacted with cytoplasmic membrane, they further set out to investigate CisA that was previously hypothesized to be the membrane adaptor. However, the structure revealed that it was not associated with CISSc. Using fluorescence microscope and cell fractionation assay, the authors verified that CisA is indeed a membrane-associated protein. They further determined experimentally that CisA had a cytosolic N-terminal domain and a periplasmic C-terminus. The functional analysis of cisA mutant revealed that it is not required for CISSc assembly but is essential for the contraction, as a result, the deletion significantly affects CISSc-mediated cell death upon stress, timely differentiation, as well as secondary metabolite production. Although the work did not resolve the mechanistic detail how CisA interacts with CISSc structure, it provides solid data and a strong foundation for future investigation toward understanding the mechanism of CISSc contraction, and potentially, the relation between the membrane association of CISSc, the sheath contraction and the cell death.

      Strengths:

      The paper is well-structured, and the conclusion of the study is supported by solid data and careful data interpretation was presented. The authors provided strong evidence on (1) the high-resolution structure of extended CISSc determined by cryo-EM, and the subsequent comparison with known eCIS structures, which sheds light on both its similarity and different features from other subtypes of eCISs in detail; (2) the topological features of CisA using fluorescence microscopic analysis, cell fractionation and PhoA-LacZα reporter assays, (3) functions of CisA in CISSc-mediated cell death and secondary metabolite production, likely via the regulation of sheath contraction.

      Weaknesses:

      (1) The data presented are not sufficient to provide mechanistic details of CisA-mediated CISSc contraction, as authors are not able to experimentally demonstrate the direct interaction between CisA with baseplate complex of CISSc (hypothesized to be via Cis11 by structural modeling), since they could not express cisA in E. coli due to its potential toxicity. Therefore, there is a lack of biochemical analysis of direct interaction between CisA and baseplate wedge. In addition, there is no direct evidence showing that CisA is responsible for tethering CISSc to the membrane upon stress, and the spatial and temporal relation between membrane association and contraction remains unclear. Further investigation will be needed to address these questions in future.

      We thank Reviewer #3 for the supportive evaluation and constructive feedback of our study in the non-public review. We appreciate the recognition of the technical limitations of experimentally demonstrating a direct interaction between CisA and CIS baseplate complex, and we agree that further investigations in the future will hopefully provide a full mechanistic understanding of the spatiotemporal interaction of CisA and CIS particular and the subsequent CIS firing.

      To further improve the manuscript, we will revise the text and clarify figures and figure legends as suggested in the non-public review.

      Discussion:

      Overall, the work provides a valuable contribution to our understanding on the structure of a much less understood subtype of CISs, which is unique compared to both membrane-anchored T6SSs and host-membrane targeting eCISs. Importantly, the work serves as a good foundation to further investigate how the sheath contraction works here. The work contributes to expanding our understanding of the diverse CIS superfamilies.

      Thank you.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      - Magnification of the potential CisA-Cis11 model, with side chains at the interface, should be shown in Supplementary Figures 9/10 to help the reader appreciates the intercation between the two subunits.

      Done. A zoomed-in view of the relevant side chains at the CisA-Cis11 interface has been added to Supplementary Figure 9e. For clarity, we decided not to highlight these residues in Supplementary Figure 10 because they are identical to those in Figure 9e.

      - A model where CisA is positionned onto the baseplate (by merging the CisA-Cis11 model and the baseplate structure) will also be informative for the reader.

      We agree that such a presentation would be helpful to visualize the proposed CisA-Cis11 interaction. However, the Cis11 residues predicted to bind CisA are buried in our cryoEM single-particle structure of the elongated Streptomyces CIS. This is not surprising, as the structure is based on a previously established non-contractile CIS mutant variant (PMCID: PMC10066040), which means we were only able to capture one specific configuration of the baseplate complex in the current work. This baseplate configuration is most likely structurally distinct from the baseplate configuration in contracted CIS particles. A similar observation was also reported for the baseplate complex of eCIS particles from Algoriphagus machipongonesis (PMCID: PMC8894135 ).  

      We speculate that in Streptomyces, initial non-specific contacts between CisA and cytoplasmic CIS particles induce a rearrangement of baseplate components, resulting in the exposure of the relevant Cis11 residues, which in turn facilitates a transient interaction between CisA and Cis11. This interaction then leads to additional conformational changes within the baseplate complex, triggering sheath contraction and CIS firing.

      We believe that a transient binding step is a crucial part of the activation process, contributing to the dynamic nature of the system.

      - Providing information on the oligomeric state of CisA will strenghten the manuscript. Authors may consider having blue-native gel analysis of CisA-3xFLAG extracted from Streptomyces or E. coli membranes, or in vivo chemical cross-linking coupled to SDS-PAGE analyses. In case these quite straightforward experiments are not possible, the authors may consider providing AF3 models of various CisA multimers.

      Thank you for these suggestions. Unfortunately, we currently don’t have the capability to conduct additional experiments. However, we have performed additional AF3 modelling to explore potential different configurations of CisA. The results of these analyses suggest that CisA can assemble into a pentamer (see also Response to reviewer 1). We speculate that CisA may exist in different oligomeric states and that membrane-localized CisA monomers oligomerize into a larger protein complex in response to a cellular or extracellular (e.g. nisin) signal, which could then directly or indirectly interact with CIS particles in the cytoplasm to facilitate their recruitment to the membrane and CIS firing. Such a stress-dependent conformational change of CisA could also be a safety mechanism to prevent accidental interaction of CisA with CIS particles and CIS firing.

      We now show the AF model for the predicted CisA pentamer in Figure 3b/c and discuss the potential implications of the different CisA configurations in the revised manuscript.

      Reviewer #2 (Recommendations for the authors):

      - The quantification of contracted versus extended CIS assemblies in the cytoplasm is only presented for the tomograms from the cisA mutant (graph in Fig. S2d). However, there are no data for the WT and complemented mutant to compare with. It would help to add such data, or at least refer to the previous quantification done for the WT in the previous paper. Further, would it be possible to illustrate the difference by measuring lengths of CIS assemblies and plot length distributions (assuming the extended ones are long and contracted are short)?

      Thank you for your suggestions. We have included the results from our previous quantification of CIS assembly states observed in the WT in the revised manuscript (lines 106–110).

      In the acquired tomograms of CIS particles observed in intact and dead hyphae, we consistently observed only two CIS conformations: the fully extended state (average length of 233 nm, diameter of 18 nm) and the fully contracted state (average length of 124 nm, diameter of 23 nm). We have added this information to the revised manuscript (lines 112-114).

      - The Western blot in Fig. 3d, top panel, contains additional bands that are not mentioned. Are they non-specific bands? Absent in disA mutant? It would help if it was clarified in the legend what they are.

      Correct, these additional bands are unspecific bands, which are also visible in the lysate and soluble fraction of wild-type sample (negative control, no FLAG-tagged protein). We have now labelled these bands in the figure and clarified the figure legend.

      - Fig. S8a needs improvement. It was not possible to clearly see the stated effect of disA deletion on secondary metabolite production in these photos.

      We agree and have removed figure panel S8a from the manuscript. The quantification of total actinorhodin production shown in Figure S8b convincingly shows a significantly reduction of actinorhodin production in the cisA deletion mutant compared to the wildtype and the complement mutant.

      - It is not an important point, but the paragraph in lines 109-116 appears more like a re-iteration of the Introduction than Results.

      We agree. We have removed the highlighted text from the Results section and added some of the information to the introduction.

      - Line 206 appears to have a typo. Should it not be WT instead of WT cisA?

      Correct. This is a typo which has been fixed. Thank you.

      - At the end of the Discussion, it is suggested that a stepwise mechanism of recruiting CIS to the membrane and then triggering firing would prevent unwanted activation and self-inflicted death. Since both steps appear to be dependent in DisA, it would be good to more clearly spell out how such a stepwise mechanism would work and how it could prevent spontaneous and erroneous firing of the system.

      Thank you for this suggestion. We have revised the text to clarify the proposed stepwise mechanism. Based on additional structural modeling, we propose that the conserved extra-cytoplasmic domain of CisA may play a role in sensing stress signals. Binding of a ‘stress-associated molecule’ could induce a conformational change in CisA, a hypothesis supported by: (1) Foldseek protein structure searches, which suggest that the conserved C-terminal CisA domain resembles substrate/solute-binding proteins, and (2) AlphaFold3 models predicting that CisA can form a pentamer via its putative substrate-binding domain. This suggests that a transition from CisA monomers to pentamers in response to stress may serve as a key checkpoint, activating CisA and facilitating the recruitment of CIS assemblies to the membrane, either directly or indirectly. Conversely, in the absence of a stress signal, CisA is likely to remain in its monomeric (resting) form, incapable of triggering CIS firing. We have revised the discussion to explain the proposed model in more detail.

      We recognize that this model poses many testable hypotheses that we currently cannot test but aim to address in the future.

      Reviewer #3 (Recommendations for the authors):

      There are a few concerns potentially worth addressing to strengthen the study or for future investigation.

      (1) It would be worth considering moving the first part of the result ('CisA is required for CISSc contraction in situ') after presenting the structure of extended CISSc, and combining it with the last part of the result section ('CisA is essential for the cellular function of CISSc'), as both parts describe the functional characterization of CisA.

      We appreciate the reviewer’s suggestion but have chosen to retain the current order of the results. As this manuscript focuses on the role of CisA, we believe that first establishing a functional link between CisA and CIS contraction provides essential context and motivation for the study.

      (2) Line 169: it is not clear to me if the fusion of CisA with mCherry is functional (if it complements the native CisA). Moreover, it was not shown if its localization changes under nisin stress or in the strain with non-contractile CISSc.

      We have not tested if the CisA-mCherry fusion is fully functional. While we cannot exclude the possibility that the activity of this protein fusion is compromised in vivo, we believe that the described accumulation of CisA-mCherry at the membrane is accurate. This conclusion is further supported by the results obtained from protein fractionation experiments and the membrane topology assay (Figure 3).

      We did not examine if the localization of CisA-mCherry changes in CIS mutant strains under nisin-stress, but this is something we will follow up on in the future.

      (3) In ref 18, the previous work from the same team presented a functional fluorescent fusion of Cis2 (sheath), thus, it will be interesting to see if (i) Cis2 localization and dynamics is affected by the absence of CisA under normal and stressed conditions; (ii) if Cis2 shows any co-localization with CisA under normal and especially stressed conditions, and potentially, its timing correlation to ghost cell formation by time-lapse imaging of both fusions.

      We thank this reviewer for the suggestions, and we plan to address these questions in the future.

      (4) Line 261: it was hypothesized by authors that the cytosolic portion of CisA was required for interacting with Cis11. While it was not possible to verify the direct interaction at current state, a S. coelicolor mutant lacking this cytosolic domain may be of help to indirectly test the hypothesis. Moreover, it would be interesting to see if the cytosolic region alone is enough to induce the contraction upon stress (by removing the TM-C region). If so, whether it leads to cell death, or if it is insufficient to cause cell death without membrane association despite the sheath contraction. If not, it would suggest that membrane association occurs before contraction.

      These are really great suggestions and if we had the manpower and resources, we would have performed these experiments. We plan to follow up on these questions in the future.

      However, additional structural modelling of CisA indicates that CisA may exist in different configurations (see response to Reviewer #1 and #2), a monomeric and/or a pentameric configuration. In these structural models (revised Figure 3), CisA oligomerization is mediated by the annotated periplasmic solute-binding domain. It is conceivable that CisA oligomerization (e.g. in response to a stress signal) presents a critical checkpoint that results in a conformational change within CisA monomers that subsequently drives CisA oligomerization into a configuration primed to interact with CIS particles. We would therefore speculate that the expression of just the cytoplasmic CisA domain may not be sufficient for CIS contraction and cell death.

      (5) Line 263: as it was not possible to express full-length cisA in E. coli, making it difficult to assess the interaction between CisA and Cis11, it may be worth considering expressing the cytosolic portion of CisA (ΔTM-C) instead of full-length CisA, or alternatively performing a co-immunoprecipitation assay of CisA (i.e., with an affinity tag) from S. coelicolor cultures under stressed conditions. However, I am aware that these may be beyond the scope of this work but can be considered for future investigation in general.

      Thank you for your suggestions and your understanding that some of this work is beyond the scope of this work. We have performed CisA-FLAG co-immunoprecipitation experiments from S. coelicolor cultures that were treated with nisin for 0/15/45 min. However, mass spectrometry analysis of co-eluted peptides did not show the presence of CIS-associated peptides at the analysed timepoints. While we cannot exclude technical issues with our assays that resulted in an inefficient solubilization of CisA from Streptomyces membranes, an alternative hypothesis is that the interaction between CIS particles and CisA is very transient and therefore difficult to capture. We would like to mention, however, that we did detect CisA peptides in crude purifications of CIS particles from nisin-stressed cells (Supplementary Table 2, manuscript: line 301/302), supporting our proposed model that CisA can associate with CIS particles in vivo.

      Minor points:

      (1) I will suggest moving Supplementary Fig 2d with control quantification of WT strain and complementation strain (similar to Fig 3g from ref 18) to the main Fig 1, as the quantitative representation with better comparison without going back and forth to ref 18.

      Thank you for your suggestion. Instead of moving Supplementary Fig. 2d to the main figure, we have added additional information in lines 106–110 to discuss the previous quantification of CIS assembly states in the WT, as described in our earlier work. We believe this approach allows readers to easily reference our established quantification without compromising the flow of the main figures.

      (2) Line 52/785: as work of Ref 12 has recently been published DOI: 10.1126/sciadv.adp7088, the reference should be updated accordingly.

      This reference has been updated. Thank you.

      (3) A brief description of key differences between contracted (ref 18) and extended sheath structure will be a good addition for a broader audience.

      Thank you for this suggestion. We have added more information on lines 178–180.

      (4) Fig 3d: it is not clear how well the samples from different fractions were normalized in amount (volume and cell density), but there was an inconsistency in the amount of CisA-Flag in lysate, vs. soluble and membrane fractions (total protein amount combined from soluble fraction and membrane fraction together seemed to be more than in the lysate, while in theory it should be more or less equal; and the amount of WhiA from WT seemed to be less than from the CisA-Flag strain). In the method section, it was mentioned that 'The final pellet was dissolved in 1/10 of the initial volume with wash buffer (no urea). Equi-volume amounts of fractions were mixed with 2x SDS sample buffer and analyzed by immunoblotting.' But it is still not clear whether equivalent amounts (normalized to the same OD for example) were used and if we could directly compare. A brief clarification in the legend of how samples were prepared is needed.

      The samples were normalized by first using the same volume of starting material (similar culture density and incubation period for each strain) and by loading equal volumes of each fraction for analysis. After fractionation, equi-volume amounts of the soluble and membrane protein fractions were mixed with 2× SDS sample buffer and subjected to immunoblotting, ensuring a consistent basis for comparison between samples. We have revised the figure legend and Material and Method sections to make this clear.

      We agree that the amount of CisA-3xFLAG appears slightly lower in the “Lysate” fraction compared to the “Membrane” fraction in Figure 3d (now Fig. 3f). However, this does not affect the overall conclusion of this experiment, showing that CisA-3xFLAG is clearly enriched in the membrane fraction.

      For reference, please find below the uncropped version of this Western blot image. Based on the signal of the unspecific bands, we would like to argue that equal amounts of samples obtained from the WT control strain (no FLAG epitope present) and a strain producing CisA-3xFLAG were loaded for each of the fractions. When we revisited this data, we noted that the protein size marker was wrong. This has been fixed.

      Author response image 1.

      (5) Fig. 4f: statistical analysis is missing.

      The missing statistical analysis has been added to this figure and figure legend.

    1. Author response:

      The following is the authors’ response to the current reviews.

      We wanted to clarify Reviewer #1’s latest comment in the last round of review, “Furthermore, the referee appreciates that the authors have echoed the concern regarding the limited statistical robustness of the observed scrambling events.” We appreciate the follow up information provided from Reviewer #1 that their comment is specifically about the low count alternative pathway events that we view at the dimer interface, and not the statistics of the manuscript overall as they believe that “the study presents a statistically rigorous analysis of lipid scrambling events across multiple structures and conformations (Reviewer #1)”. We agree with the Reviewer and acknowledge that overall our coarse-grained study represents the most comprehensive single manuscript of the entire TMEM16 family to date.


      The following is the authors’ response to the original reviews.

      Public Review:

      Reviewer #1 (Public review):

      Summary:

      The manuscript investigates lipid scrambling mechanisms across TMEM16 family members using coarse-grained molecular dynamics (MD) simulations. While the study presents a statistically rigorous analysis of lipid scrambling events across multiple structures and conformations, several critical issues undermine its novelty, impact, and alignment with experimental observations.

      Critical issues:

      (1) Lack of Novelty:

      The phenomenon of lipid scrambling via an open hydrophilic groove is already well-established in the literature, including through atomistic MD simulations. The authors themselves acknowledge this fact in their introduction and discussion. By employing coarse-grained simulations, the study essentially reiterates previously known findings with limited additional mechanistic insight. The repeated observation of scrambling occurring predominantly via the groove does not offer significant advancement beyond prior work.

      We agree with the reviewer’s statement regarding the lack of novelty when it comes to our observations of scrambling in the groove of open Ca2+-bound TMEM16 structures. However, we feel that the inclusion of closed structures in this study, which attempts to address the yet unanswered question of how scrambling by TMEM16s occurs in the absence of Ca2+, offers new observations for the field. In our study we specifically address to what extent the induced membrane deformation, which has been theorized to aid lipids cross the bilayer especially in the absence of Ca2+, contributes to the rate of scrambling (see references 36, 59, and 66). There are also several TMEM16F structures solved under activating conditions (bound to Ca2+ and in the presence of PIP2) which feature structural rearrangements to TM6 that may be indicative of an open state (PDB 6P48) and had not been tested in simulations. We show that these structures do not scramble and thereby present evidence against an out-of-the-groove scrambling mechanism for these states. Although we find a handful of examples of lipids being scrambled by Ca2+-free structures of TMEM16 scramblases, none of our simulations suggest that these events are related to the degree of deformation.

      (2) Redundancy Across Systems:

      The manuscript explores multiple TMEM16 family members in activating and non-activating conformations, but the conclusions remain largely confirmatory. The extensive dataset generated through coarse-grained MD simulations primarily reinforces established mechanistic models rather than uncovering fundamentally new insights. The effort, while statistically robust, feels excessive given the incremental nature of the findings.

      Again, we agree with the reviewer’s statement that our results largely confirm those published by other groups and our own. We think there is however value in comparing the scrambling competence of these TMEM16 structures in a consistent manner in a single study to reduce inconsistencies that may be introduced by different simulation methods, parameters, environmental variables such as lipid composition as used in other published works of single family members. The consistency across our simulations and high number of observed scrambling events have allowed us to confirm that the mechanism of scrambling is shared by multiple family members and relies most obviously on groove dilation.

      (3) Discrepancy with Experimental Observations:

      The use of coarse-grained simulations introduces inherent limitations in accurately representing lipid scrambling dynamics at the atomistic level. Experimental studies have highlighted nuances in lipid permeation that are not fully captured by coarse-grained models. This discrepancy raises questions about the biological relevance of the reported scrambling events, especially those occurring outside the canonical groove.

      We thank the reviewer for bringing up the possible inaccuracies introduced by coarse graining our simulations. This is also a concern for us, and we address this issue extensively in our discussion. As the reviewer pointed out above, our CG simulations have largely confirmed existing evidence in the field which we think speaks well to the transferability of observations from atomistic simulations to the coarse-grained level of detail. We have made both qualitative and quantitative comparisons between atomistic and coarse-grained simulations of nhTMEM16 and TMEM16F (Figure 1, Figure 4-figure supplement 1, Figure 4-figure supplement 5) showing the two methods give similar answers for where lipids interact with the protein, including outside of the canonical groove. We do not dispute the possible discrepancy between our simulations and experiment, but our goal is to share new nuanced ideas for the predicted TMEM16 scrambling mechanism that we hope will be tested by future experimental studies.

      (4) Alternative Scrambling Sites:

      The manuscript reports scrambling events at the dimer-dimer interface as a novel mechanism. While this observation is intriguing, it is not explored in sufficient detail to establish its functional significance. Furthermore, the low frequency of these events (relative to groove-mediated scrambling) suggests they may be artifacts of the simulation model rather than biologically meaningful pathways.

      We agree with the reviewer that our observed number of scrambling events in the dimer interface is too low to present it as strong evidence for it being the alternative mechanism for Ca2+-independent scrambling. This will require additional experiments and computational studies which we plan to do in future research. However, we are less certain that these are artifacts of the coarse-grained simulation system as we observed a similar event in an atomistic simulation of TMEM16F.

      Conclusion:

      Overall, while the study is technically sound and presents a large dataset of lipid scrambling events across multiple TMEM16 structures, it falls short in terms of novelty and mechanistic advancement. The findings are largely confirmatory and do not bridge the gap between coarse-grained simulations and experimental observations. Future efforts should focus on resolving these limitations, possibly through atomistic simulations or experimental validation of the alternative scrambling pathways.

      Reviewer #2 (Public review):

      Summary:

      Stephens et al. present a comprehensive study of TMEM16-members via coarse-grained MD simulations (CGMD). They particularly focus on the scramblase ability of these proteins and aim to characterize the "energetics of scrambling". Through their simulations, the authors interestingly relate protein conformational states to the membrane's thickness and link those to the scrambling ability of TMEM members, measured as the trespassing tendency of lipids across leaflets. They validate their simulation with a direct qualitative comparison with Cryo-EM maps.

      Strengths:

      The study demonstrates an efficient use of CGMD simulations to explore lipid scrambling across various TMEM16 family members. By leveraging this approach, the authors are able to bypass some of the sampling limitations inherent in all-atom simulations, providing a more comprehensive and high-throughput analysis of lipid scrambling. Their comparison of different protein conformations, including open and closed groove states, presents a detailed exploration of how structural features influence scrambling activity, adding significant value to the field. A key contribution of this study is the finding that groove dilation plays a central role in lipid scrambling. The authors observe that for scrambling-competent TMEM16 structures, there is substantial membrane thinning and groove widening. The open Ca2+-bound nhTMEM16 structure (PDB ID 4WIS) was identified as the fastest scrambler in their simulations, with scrambling rates as high as 24.4 {plus minus} 5.2 events per μs. This structure also shows significant membrane thinning (up to 18 Å), which supports the hypothesis that groove dilation lowers the energetic barrier for lipid translocation, facilitating scrambling.

      The study also establishes a correlation between structural features and scrambling competence, though analyses often lack statistical robustness and quantitative comparisons. The simulations differentiate between open and closed conformations of TMEM16 structures, with open-groove structures exhibiting increased scrambling activity, while closed-groove structures do not. This finding aligns with previous research suggesting that the structural dynamics of the groove are critical for scrambling. Furthermore, the authors explore how the physical dimensions of the groove qualitatively correlate with observed scrambling rates. For example, TMEM16K induces increased membrane thinning in its open form, suggesting that membrane properties, along with structural features, play a role in modulating scrambling activity.

      Another significant finding is the concept of "out-of-the-groove" scrambling, where lipid translocation occurs outside the protein's groove. This observation introduces the possibility of alternate scrambling mechanisms that do not follow the traditional "credit-card model" of groove-mediated lipid scrambling. In their simulations, the authors note that these out-of-the-groove events predominantly occur at the dimer interface between TM3 and TM10, especially in mammalian TMEM16 structures. While these events were not observed in fungal TMEM16s, they may provide insight into Ca2+-independent scrambling mechanisms, as they do not require groove opening.

      Weaknesses:

      A significant challenge of the study is the discrepancy between the scrambling rates observed in CGMD simulations and those reported experimentally. Despite the authors' claim that the rates are in line experimentally, the observed differences can mean large energetic discrepancies in describing scrambling (larger than 1kT barrier in reality). For instance, the authors report scrambling rates of 10.7 events per μs for TMEM16F and 24.4 events per μs for nhTMEM16, which are several orders of magnitude faster than experimental rates. While the authors suggest that this discrepancy could be due to the Martini 3 force field's faster diffusion dynamics, this explanation does not fully account for the large difference in rates. A more thorough discussion on how the choice of force field and simulation parameters influence the results, and how these discrepancies can be reconciled with experimental data, would strengthen the conclusions. Likewise, rate calculations in the study are based on 10 μs simulations, while experimental scrambling rates occur over seconds. This timescale discrepancy limits the study's accuracy, as the simulations may not capture rare or slow scrambling events that are observed experimentally and therefore might underestimate the kinetics of scrambling. It's however important to recognize that it's hard (borderline unachievable) to pinpoint reasonable kinetics for systems like this using the currently available computational power and force field accuracy. The faster diffusion in simulations may lead to overestimated scrambling rates, making the simulation results less comparable to real-world observations. Thus, I would therefore read the findings qualitatively rather than quantitatively. An interesting observation is the asymmetry observed in the scrambling rates of the two monomers. Since MARTINI is known to be limited in correctly sampling protein dynamics, the authors - in order to preserve the fold - have applied a strong (500 kJ mol-1 nm-2) elastic network. However, I am wondering how the ENM applies across the dimer and if any asymmetry can be noticed in the application of restraints for each monomer and at the dimer interface. How can this have potentially biased the asymmetry in the scrambling rates observed between the monomers? Is this artificially obtained from restraining the initial structure, or is the asymmetry somehow gatekeeping the scrambling mechanism to occur majorly across a single monomer? Answering this question would have far-reaching implications to better describe the mechanism of scrambling.

      The main aim of our computational survey was to directly compare all relevant published TMEM16 structures in both open and closed states using the Martini 3 CGMD force field. Our standardized simulation and analysis protocol allowed us to quantitatively compare scrambling rates across the TMEM16 family, something that has never been done before. We do acknowledge that direct comparison between simulated versus experimental scrambling rates is complicated and is best to be interpreted qualitatively. In line with other reports (e.g., Li et al, PNAS 2024), lipid scrambling in CGMD is 2-3 orders of magnitude faster than typical experimental findings. In the CG simulation field, these increased dynamics due to the smoother energy landscape are a well known phenomenon. In our view, this is a valuable trade-off for being able to capture statistically robust scrambling dynamics and gain mechanistic understanding in the first place, since these are currently challenging to obtain otherwise. For example, with all-atom MD it would have been near-impossible to conclude that groove openness and high scrambling rates are closely related, simply because one would only measure a handful of scrambling events in (at most) a handful of structures.

      Considering the elastic network: the reviewer is correct in that the elastic network restrains the overall structure to the experimental conformation. This is necessary because the Martini 3 force field does not accurately model changes in secondary (and tertiary) structure. In fact, by retaining the structural information from the experimental structures, we argue that the elastic network helped us arrive at the conclusion that groove openness is the major contributing factor in determining a protein’s scrambling rate. This is best exemplified by the asymmetric X-ray structure of TMEM16K (5OC9), in which the groove of one subunit is more dilated than the other. In our simulation, this information was stored in the elastic network, yielding a 4x higher rate in the open groove than in the closed groove, within the same trajectory.

      Notably, the manuscript does not explore the impact of membrane composition on scrambling rates. While the authors use a specific lipid composition (DOPC) in their simulations, they acknowledge that membrane composition can influence scrambling activity. However, the study does not explore how different lipids or membrane environments or varying membrane curvature and tension, could alter scrambling behaviour. I appreciate that this might have been beyond the scope of this particular paper and the authors plan to further chase these questions, as this work sets a strong protocol for this study. Contextualizing scrambling in the context of membrane composition is particularly relevant since the authors note that TMEM16K's scrambling rate increases tenfold in thinner membranes, suggesting that lipid-specific or membrane-thickness-dependent effects could play a role.

      Considering different membrane compositions: for this study, we chose to keep the membranes as simple as possible. We opted for pure DOPC membranes, because it has (1) negligible intrinsic curvature, (2) forms fluid membranes, and (3) was used previously by others (Li et al, PNAS 2024). As mentioned by the reviewer, we believe our current study defines a good, standardized protocol and solid baseline for future efforts looking into the additional effects of membrane composition, tension, and curvature that could all affect TMEM16-mediated lipid scrambling.

      Reviewer #3 (Public review):

      Strengths:

      The strength of this study emerges from a comparative analysis of multiple structural starting points and understanding global/local motions of the protein with respect to lipid movement. Although the protein is well-studied, both experimentally and computationally, the understanding of conformational events in different family members, especially membrane thickness less compared to fungal scramblases offers good insights.

      We appreciate the reviewer recognizing the value of the comparative study. In addition to valuable insights from previous experimental and computational work, we hope to put forward a unifying framework that highlights various TMEM16 structural features and membrane properties that underlie scrambling function.

      Weaknesses:

      The weakness of the work is to fully reconcile with experimental evidence of Ca²⁺-independent scrambling rates observed in prior studies, but this part is also challenging using coarse-grain molecular simulations. Previous reports have identified lipid crossing, packing defects, and other associated events, so it is difficult to place this paper in that context. However, the absence of validation leaves certain claims, like alternative scrambling pathways, speculative.

      Answer: It is generally difficult to quantitatively compare bulk measurements of scrambling phenomena with simulation results. The advantage of simulations is to directly observe the transient scrambling events at a spatial and temporal resolution that is currently unattainable for experiments. The current experimental evidence for the precise mechanism of Ca2+-independent scrambling is still under debate. We therefore hope to leverage the strength of MD and statistical rigor of coarse-grained simulations to generate testable hypotheses for further structural, biochemical, and computational studies.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The findings are largely confirmatory and do not bridge the gap between coarse-grained simulations and experimental observations. Future efforts should focus on resolving these limitations, possibly through atomistic simulations or experimental validation of the alternative scrambling pathways.

      While we agree with what the reviewer may be hinting at regarding limitations of coarse-grained MD simulations, we believe that our study holds much more merit than this comment suggests. We have provided something that has yet to be done in the field: a comprehensive study that directly compares the scrambling rates of multiple TMEM16 family members in different conformations using identical simulation conditions. Our work clearly shows that a sufficiently dilated grooves is the major structural feature that enables robust scrambling for all TMEM16 scramblases members with solved structures. While all TMEM16s cause significant distortion and thinning of the membrane, we assert that the extreme thinning observed around open grooves is significantly enhanced by the lipid scrambling itself as the two leaflets merge through lipid exchange.  We saw no evidence that membrane thinning/distortion alone, in the absence of an open groove, could support scrambling at the rates observed under activating conditions or even the low rates observed in Ca2+-independent scrambling. Moreover, our handful of observations of scrambling events outside of the groove, which has not yet been reported in any study, opens an exciting new direction for studying alternative scrambling mechanisms. That said, we are currently following up on many of the observations reported here such as: scrambling events outside the groove, the kinetics of scrambling, the possibility that lipids line the groove of non-scramblers like TMEM16A, etc. This is being done experimentally with our collaborators through site directed mutagenesis and with all-atom MD in our lab. Unfortunately, it is well beyond the scope of the current study to include all of this in the current paper.

      Reviewer #2 (Recommendations for the authors):

      Major comments and questions:

      (1) Line 214 and Figure 1- Figure Supplement 1: why have you only compared the final frame of the trajectory to the cryo-EM structure? Even if these comparisons are qualitative, they should be representative of the entire trajectory, not a single frame.

      We thank the reviewer for this suggestion and replaced the single-frame snapshots in Figure 1-figure supplement 1 for ensemble-averaged head groups densities. The overall agreement between membrane shapes in CGMD and cryo-EM was not affected by this change.

      (2) Lines 228-231: You comment 'Residues in this site on nhTMEM16 and TMEMF also seem to play a role in scrambling but the mechanism by which they do so is unclear.' This is something you could attempt to quantify in the simulations by calculating the correlation between scrambling and protein-membrane interactions/contacts in this site. Can you speculate on a mechanism that might be a contributing factor?

      We probed the correlation between these residues and scrambling lipids, as suggested by the reviewer, and interestingly not all scrambling lipids interact with these residues. Yet there is strong lipid density in this vicinity (see insets in Figure 1 and Figure 4-figure supplement 2). These observations lead us to suspect these residues impact scrambling indirectly through influencing the conformation of the protein or flexibility and shape of the membrane. This interpretation fits with mutagenesis studies highlighting a role for these residues in scrambling (see refs 59, 62, and 67). Specifically, Falzone et al. 2022 (ref 59) suggested that they may thin the membrane near the groove, but this has not been tested via structure determination and a detailed model of how they impact scrambling is missing. We could address this question with in silico mutations; however, CG simulation is not an appropriate method to study large scale protein dynamics, and AA simulations are likely best, but beyond the scope of this paper.

      (3) Lines 240-245 and Figure 1B: This section discusses the coupling between membrane distortions and the sinusoidal curve around the protein, however, Figure 1B only shows snapshots of the membrane distortions. Is it possible to understand how these two collective variables are correlated quantitatively (as opposed to the current qualitative analysis)?

      We believe that it may be possible to quantitatively capture these two key features of the membrane, as we did previously with nhTMEM16 using our continuum elasticity-based model of the membrane (Bethel and Grabe 2016). Our model agreed with all atom MD surfaces to within ~1 Å, hence showing good quantitative agreement throughout the entire membrane. However, we doubt that we could distill the essence of our model down to a simple functional relationship between the sinusoidal wave and pinching, which we think the reviewer is asking. Rather, we believe that the large-scale sinusoidal distortion (collective variable 1) and pinching/distortion (collective variable 2) near the groove arise from the interplay of the specific protein surface chemistry for each protein (patterning of polar and non-polar residues) and the membrane. This is why we chose to simply report the distinct patterns that the family members impose on the surrounding membrane, which we think is fascinating. Specifically, Fig. 1B shows that different TMEM16 family members distort the membrane in different ways. Most notably, fungal TMEM16s feature a more pronounced sinusoidal deformation, whereas the mammalian members primarily produce local pinching. Then, in Fig. 3A we show that the thinning at the groove happens in all structures and is more pronounced in open, scrambling-competent conformations. In other words, proteins can show very strong thinning (e.g. TMEM16K, 5OC9) even though the membrane generally remains flat.

      (4) Lines 257-258: Authors comment that TMEM16A lacks scramblase activity yet can achieve a fully lipid-lined groove (note the typo - should be lipid-lined, not lipid-line). Is a fully lipid-lined groove a prerequisite for scramblase activity? Are lipid-lined grooves the only requirement for scramblase activity? Could the authors clarify exactly what the prerequisite for scramblase activity is to avoid any confusion; this will be useful for later descriptions (i.e. line 295) where scrambling competence is again referred to. Additionally, the associated figure panel (Figure 1D) shows a snapshot of this finding but lacks any statistical quantifications - is a fully lipid-lined groove a single event? Perhaps the additional analyses, such as the groove-lipid contacts, may be useful here.

      The definition of lipid scrambling is that a lipid fully transitions from one membrane leaflet to the other. While a single lipid could transition through the groove on its own, it is well documented in both atomistic and CG MD simulations, that lipid scrambling typically happens through a lipid-lined groove, as shown in Fig. 1A-B. The lipids tend to form strong choline-to-phosphate interactions with nearest neighbors that make this energetically favorable. That said, lipid-lined grooves are not sufficient for robust scrambling, which is what we show in Fig. 1D where the non-scrambler TMEM16A did in fact feature a lipid-lined groove. As suggested, we performed contact analysis and found that residue K645 on TM6 in the middle of the groove contacts lipids in 9.2% of the simulation frames.

      To get a better understanding of how populated the TM4-TM6 pathway is with lipids across all simulated structures, we determined for every simulation frame how many headgroup beads resided in the groove. This indicates that the ion-conductive state of TMEM16A (5OYB*, Fig. 1D) only had 1 lipid in the pathway, on average, meaning that the configuration shown Fig. 1D is indeed exceptional. As a reference, our strongest scrambler nhTMEM16 4WIS, had an average of 2.8 lipids in the groove. We added a table containing the means and standard deviations that resulted from this analysis as Figure 1-Table supplement 1.

      (5) Lines 295-298 : The scrambling rates of the Ca²⁺-bound and Ca²⁺-free structures fall within overlapping error margins, it becomes difficult to definitively state that Ca²⁺ binding significantly enhances scrambling activity. This undermines the claim that the Ca²⁺-bound structure is the strongest scrambler. The authors should conduct statistical analyses to determine if the difference between the two conditions is statistically significant.

      In contrast to the reviewer’s comment, we do not claim that Ca2+-binding itself enhances lipid scrambling. Instead, what we show is that WT structures that are solved in an open confirmation (all of which are Ca2+-bound, except 6QM6) are robust scramblers. For nhTMEM16, we did not observe any scrambling events for the closed-groove proteins, making further statistical analysis redundant.

      (6) The authors claim that the scrambling rates derived from their MD simulations are in "excellent agreement" with experimental findings (lines 294-295), despite significant discrepancy between simulated and experimentally measured rates. For example, the simulated rate of 24.4 {plus minus} 5.2 events/µs for the open, Ca²⁺-bound fungal nhTMEM16 (PDB ID 4WIS) corresponds to approximately 24 million events per second, which is vastly higher than experimental rates. Experimental studies have reported scrambling rate constants of ~0.003 s⁻¹ for TMEM16 family members in the absence of Ca²⁺, measured under physiological conditions (https://doi.org/10.1038/s41467-019-11753-1 ). Even with Ca²⁺ activation, scrambling rates remain several orders of magnitude lower than the rates observed in simulations. Moreover, this highlights a larger problem: lipid scrambling rates occur over timescales that are not captured by these simulations. While the authors elude to these discrepancies (lines 605-606), they should be emphasised in the text, as opposed to the table caption. These should also be reconducted to differences between the membrane compositions of different studies.

      We agree with the spirit of the reviewer’s comment, and because of that, we were very careful not to claim that we reproduce experimental scrambling rates, just that the trends (scrambling-competent, or not) are correct. On lines 294-295, we actually said that the scrambling rates in our simulations excellently agree with “the presumed scrambling competence of each experimental structure”, which is true. 

      As explained extensively in the discussion section of our paper (and by many others), direct comparison between MD (e.g., Martini 3, but also atomistic force fields) dynamics and experimental measurements is challenging. The primary goal of our paper is to quantify and compare the scrambling capacity of different TMEM16 family members and different states, within a CGMD context.

      That said, we agree with the reviewer that we may have missed rare or long-timescale events (as is the case in any MD experiment) and added this point to the discussion.

      (7) To address these discrepancies, the authors should: i) emphasize that simulated rates serve as qualitative indicators of scrambling competence rather than absolute values comparable to experimental findings and ii) discuss potential reasons for the divergence, such as simulation timescale limitations or lipid bilayer compositions that may favor scrambling and force field inaccuracies.

      Please see our answer to question 6. Within the context of our CGMD survey, we confidently call our results quantitative. However, we agree with the reviewer that comparison with experimental scrambling rates is qualitative and should be interpreted with caution. To reflect this, we rewrote the first sentence of the relevant paragraph in the discussion section.

      (8) Line 310: Can the authors provide a rationale as to why one monomer has a wider groove than the other? Perhaps a contact analysis could be useful. See the comment above about ENM.

      The simulation of Ca2+-bound TMEM16K was initiated from an asymmetric X-ray structure in which chain B features a more dilated groove than chain A (PDB 5OC9). The backbones of TM4 and TM6 in the closed groove (A) are close enough together to be directly interconnected by the elastic network. In contrast, TM4 and TM6 in the more dilated subunit (B) are not restricted by the elastic network and, as a consequence, display some “breathing” behavior (Fig. 3B and Fig. 3-Suppl. 6A), giving rise to a ~4x higher scrambling rate. We explicitly added the word “cryo-EM” and the PDB ID to the sentence to emphasize that the asymmetry stems from the original experimental structure.

      When answering this question, we also corrected a mislabeled chain identifier which was in the original manuscript ‘chain A’ when it is actually ‘chain B’ in Fig.2-Suppl. 3A.

      (9) Line 312: Authors speculate that increased groove width likely accounts for increased scrambling rates. For statistical significance, authors should attempt to correlate scrambling rates and groove width over the simulation period.

      The Reviewer is referring to our description of scrambling rates we measured for TMEM16K where we noted that on average the groove with the highest scrambling rate is also on average wider than the opposite subunit which is below 6 Å. We do not suggest that the correlation between scrambling and groove width is continuous, as the Reviewer may have interpreted from our original submission, but we think it is a binary outcome – lipids cannot easily enter narrow grooves (< 6 Å) and hence scrambling can only occur once this threshold is reached at which point it occurs at a near constant rate. We showed this for 4 different family members in the original Fig. 3B, where scrambling events (black dots) were much more likely during, or right after, groove dilation to distances > 6 Å. 

      (10) Line 359: Authors have plotted the minimum distance between residues TM4 and TM6 in Fig. 3A/B, claiming that a wide groove is required for scrambling. Upon closer examination, it is clear that several of these distributions overlap, reducing the statistical significance of these claims. Statistical tests (i.e. KS-tests) should be performed to determine whether the differences in distributions are significant.

      The Reviewer appears to be asking for a statistical test between the six distance distributions represented by the data in Fig. 3A for the scrambling competent structures (6QP6*, 8B8J, 6QM6, 7RXG, 4WIS, 5OC9), and we think this is being asked because it is believed that we are making a claim that the greater the distance, the greater the scrambling rate. If we have interpreted this comment correctly, we are not making this claim. Rather, we are simply stating that we only observe robust scrambling when the groove width regularly separates beyond 6 Å. The full distance distributions can now be found in Figure 3-figure supplement 6B, and we agree there is significant overlap between some of these distributions. However, the distinguishing characteristic of the 6 distributions from scrambling competent proteins is that they all access large distances, while the others do not. Notably, TMEM16F proteins (6QP6*, 8B8J) are below the 6 Å threshold on average, but they have wide standard deviations and spend well over ¼ of their time in the permissive regime (the upper error bar in the whisker plots in Fig. 3A is the 75% boundary).

      (11) Line 363-364: The authors state that all TMEM16 structures thin the membrane. Could the authors include a description of how membrane thinning is calculated, for instance, is the entire membrane considered, or is thinning calculated on a membrane patch close to the protein? Do membrane patches closer to the transmembrane protein increase or decrease thickness due to hydrophobic packing interactions? The latter question is of particular concern since Martini3 has been shown to induce local thinning of the membrane close to transmembrane helices, yielding thicknesses 2-3 Å thinner than those reported experimentally (https://doi.org/10.1016/j.cplett.2023.140436). This could be an important consideration in the authors' comparison to the bulk membrane thickness (line 364). Finally, how is the 'bulk membrane thickness' measured (i.e., from the CG simulations, from AA simulations, or from experiments)?

      Regarding the calculation of thinning and bulk membrane thickness, as described in Method “Quantification of membrane deformations”, the minimal membrane thickness, or thinning, is defined as the shortest distance between any two points from the interpolated upper and lower leaflet surfaces constructed using the glycerol beads (GL1 and GL2). Bulk membrane thickness is calculated by taking the vertical distance between the averaged glycerol surfaces at the membrane edge.

      The concern of localized membrane deformation due to force field artifacts is well-founded. However, the sinusoidal deformations shown here are much greater than 2-3 Å Martini3 imperfections, and they extend for up to 10 Å radially away from the protein into the bulk membrane (see Figure 3-figure supplement 1-5 for more of a description). Most importantly, the sinusoidal wave patterns set up by the proteins is very similar to those described in the previous continuum calculation and all-atom MD for nhTMEM16 (https://www.pnas.org/doi/full/10.1073/pnas.1607574113).

      (12) Line 374: The authors state a 'positive correlation' between membrane thinning/groove opening and scrambling rates. To support this claim, the authors should report. the correlation coefficients.

      We have removed any discussion concerning correlations between the magnitude of the scrambling rate and the degree of membrane thinning/groove opening. Rather we simply state that opening beyond a threshold distance is required for robust scrambling, as shown in our analysis in Fig. 3A.

      Concerning the relation between thinning and scrambling: Instantaneous membrane thinning is poorly defined (because it is governed by fluctuations of single lipids), and therefore difficult to correlate with the timing of individual scrambling events in a meaningful way.  Moreover, as we state later in that same section, “we argue that the extremely thin membranes are likely correlated with groove opening, rather than being an independent contributing factor to lipid scrambling”.

      (13) Line 396: It is stated that TMEM16A is not a scramblase but the simulating scrambling activity is not zero. How can you be sure that you are monitoring the correct collective variable if you are getting a false positive with respect to experiments?

      We only observe 2 scrambling events in 10 ms, which is a very small rate compared to the scrambling competent states. In a previous large survey Martini CG simulation study that inspired our protocol (Li et al, PNAS 2024), they employed a 1 event/ms cut-off to distinguish scramblers from non-scramblers. Hence, they would have called TMEM16A a non-scrambler as well. We expect that false negatives in this context might be an artifact of the CG forcefield, or it could be that TMEM16A can scramble but too slowly to be experimentally detected. Regarding the collective variable for lipid flipping, it is correct, and we know that this lipid actually flipped.

      (14) Line 402: Distance distributions for the electrostatic interactions between E633 and K645 should be included in the manuscript. This is also the case for the interactions between E843-K850 (lines 491-492).

      Our description of interactions between lipid headgroups and E633 and K645 in TMEM16A (5OYB*) are based on qualitative observations of the MD trajectory, and we highlight an example of this interaction in Figure 3-video 4. The video clearly shows that the lipid headgroups in the center of the groove orient themselves such that the phosphate bead (red) rests just above K645 (blue) and at other times the choline bead (blue) rests just below E633 (red). We do not think an additional plot with the distance distributions between lipids and these residues will add to our understanding of how lipids interact residues in the TMEM16A pore.

      We made a similar qualitative observation for the interaction between the POPC choline to E843 and POPC phosphate to K850 while watching the AAMD simulation trajectory of TMEM16F (PDB ID 6QP6). Given that this was a single observation, and the same interactions does not appear in CG simulation of the same structure (see simulation snapshots in Figure 4-figure supplement 5) we do not think additional analysis would add significantly to our understanding of which residues may stabilize lipids in the dimer interface.

      (15) Lines 450-451: 'As the groove opens, water is exposed to the membrane core and lipid headgroups insert themselves into the water-filled groove to bridge the leaflets.' Is this a qualitative observation? Could the authors report the correlation between groove dilation and the number of water permeation events?

      Yes, this is qualitative, and it sketches the order of events during scrambling, and we revised the main text starting at line 450 to indicate this. As illustrated by the density isosurfaces in Appendix 1-Figure 2A, the amount of water found in the closed versus open grooves is striking – there is a significant flood of water that connects the upper and lower solutions upon groove opening. Moreover, Appendix 1-Figure 2B shows much greater water permeation for open structures (4WIS, 7RXG, 5OC9, 8B8J, …) compared to closed structures (6QMB, 6QMA, 8B8Q, and many of the non-labeled data in the figure that all have closed grooves and near 0 water permeation). A notable exception is TMEM16A (7ZK3*8), which has water permeation but a closed groove and little-to-no lipid scrambling.

      Minor Comments:

      (1) Inconsistent use of '10' and 'ten' throughout.

      We like to kindly point out that we do not find examples of inconsistent use.

      (2) Line 32: 'TM6 along with 3, 4 and 5...' should be 'TM6 along with TM3, TM4 and TM5...'. Same in line 142. Naming should stay consistent.

      Changes are reflected in the updated manuscript.

      (3) Line 141: do you mean traverse (i.e. to travel across)? Or transverse (i.e. to extend across the membrane)?

      This is a typo. We meant “traverse”. Thanks for pointing it out.

      (4) Line 142: 'greasy' should be 'strongly hydrophobic'.

      Changes are reflected in the updated manuscript.

      (5) Line 143-144: "credit card mechanism" requires quotation marks.

      Changes are reflected in the updated manuscript.

      (6) Line 144: state if Nectria haematococca is mammalian or fungal, this is not obvious for all readers.

      Changes are reflected in the updated manuscript.

      (7) Line 147-148: Is TMEM16A/TMEM16K fungal or mammalian? What was the residue before the mutation and which residue is mutated? Perhaps the nomenclature should read as TMEM16X10Y where X=the residue prior to the mutation, 10 is a placeholder for the residue number that is mutated and Y=the new residue following mutation.

      “TMEM16” is the protein family. “A” denotes the specific homolog rather than residue.  

      (8) Lines 157-158: same as 10, it is unclear if these are fungal or mammalian.

      Clarifications added.

      (9) Line 184: "...CGMD simulation" should be "...CGMD simulations".

      Changes made.

      (10) Line 191-192: It would help to create a table of all of the mutants (including if they are mammalian or fungal) summarizing the salt concentrations, lipid and detergent environments, the presence of modulators/activators, etc.

      We added this information to Appendix 1-Table 1 in the supplemental information. We did not specify NaCl concentrations, because they all experimental procedures used standard physiological values for this (100-150 mM).

      (11) Line 210: inconsistencies with 'CG' and 'coarse-grain'.

      Changes made.

      (12) Figure 1 caption: '...totaling ~2μs (B)...' is missing the fullstop after 2μs.

      Changes made.

      (13) Figure 1B: it may be useful to label where the Ca2+ ion binds or include a schematic.

      We updated Fig. 1A to illustrate where Ca2+ binds.

      (14) Line 311: Are these mean distances? The authors should add standard deviations.

      Yes, they are. We added the standard deviations to the text.

      (15) Line 321-322: Perhaps a schematic in Figure 2 would be useful to visualize the structural features described here.

      We would kindly refer interested readers to reference [60].

      (16) Line 377: '...are likely a correlate of groove opening...' should read as: '...are likely correlated to groove opening...'.

      Thank you for pointing it out. Changes made.

      (17) Line 398: the '...empirically determined 6Å threshold for scrambling.' Was this determined from the simulations or from experiments? What does "empirically" mean here? Please state this.

      This value was determined from the simulations. Based on our analysis of the correlation between scrambling rate and groove dilation, we found that the minimal TM4/6 distance of 6 Å can distinguish between the high and low activity scramblers. The exact numerical value is somewhat arbitrary as there is a range of values around 6 Å that serve to distinguish scramblers from non-scramblers.

      (18) Figure 4: This figure should be labelled as A, B, C and D, with the figure caption updated accordingly.

      We updated Figure 4 and its caption.

      Reviewer #3 (Recommendations for Authors):

      The authors must do additional simulations to further validate their claim with different lipids and further substantiate dimer interface independent of Ca2+ ions.

      Thank you for the suggestion. We completely agree that studying scrambling in the context of a diverse lipid environment is an exciting area to explore. We are indeed actively working on a project that shares the similar idea. We decided not to include that study because we think the additional discussion involved would be excessive for the current manuscript. We, however, look forward to publishing our findings in a separate manuscript in the near future. In terms of Ca2+-independent scrambling, we are planning with our experimental collaborator for mutagenesis studies that target the residues we identified along the dimer interface.

      Since calcium ions are critical for the stability of these structures, authors should show that they were placed throughout the simulations consistently.

      As stated in the method section “Coarse-grained system preparation and simulation detail”, all Ca2+ ions are manually placed into the coarse-grained structure from the beginning of the simulation at their identical corresponding position in the experimental structure and harmonically bonded to adjacent acidic residues throughout the duration of simulation. We have also added a label to Fig 1A to indicate where the two Ca2+ ions are located.

      The comparison with experimental structures should be consistent with complete simulation, and not the last structure of the trajectory. Depending on the conformational variability, this might be misleading.

      We agree and updated Fig. 1-supplement figure 1 accordingly. The overall agreement between membrane shapes in CGMD and cryo-EM was not affected by this change.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Review:

      Reviewer #1 (Public review):

      Summary:

      Meteorin proteins were initially described as secreted neurotrophic factors. In this manuscript, Eggeler et al. demonstrate a novel role for Meteorins in establish left-right axis formation in the zebrafish embryo. The authors generated null mutations in each of the three zebrafish meteorin genes - metrn, metrnla, and metrnlab. Triple mutant embryos displayed phenotypes strongly associated with left-right defects such as heart looping and visceral organ placement, and disrupted expression of Nodal-responsive genes, as did single mutants for metrn and metrnla. The authors then go on to demonstrate that these defects in left-right asymmetry are likely to due to defects in Kupffer's Vesicle and the progenitor dorseal forerunner cells including impaired lumen formation and reduced fluid flow, reduced clustering among DFCs, impaired DFC migration, mislocalization of apical proteins ZO-1 and aPKC, and detachment of DFCs from the EVL. Notably, the authors found that expression of marker genes sox32 and sox17 were not affected, suggesting Meteorins are required for DFC/KV morphogenesis but not necessarily fate specification. Finally, the authors show genetic interaction between Meteorins and integrin receptors, which were previously implicated in left-right patterning. In a supplemental figure, the manuscript also presents data showing expression of meteorin genes around the chick Hensen's node, suggesting that the left-right patterning functions may be conserved among vertebrates.

      Strengths:

      Strengths of this study include the generation of a triple mutant line that targets all known zebrafish meteorin family members. The experiments presented in this study were rigorous, especially with respect to quantification and statistical analysis.

      Weaknesses:

      Although the authors convincingly demonstrate a role for Meteorins in zebrafish left-right patterning, data supporting a conserved role in other vertebrates is compelling but limited to one supplemental figure.

      We thank the reviewer for their thoughtful summary of our study and for highlighting the strengths of our work, including the generation of the triple mutant line and the rigor of our experimental design and quantitative analyses. We also appreciate the constructive feedback regarding the limited functional data supporting the conservation of Meteorin function in other vertebrates. We agree that this is an important aspect that could be further explored. While functional studies in additional species are beyond the current scope, we will consider such experiments in future work.

      We would like to highlight the phylogenetic analysis of Meteorin proteins we have already performed and included in the manuscript (Fig. S7D), which illustrates the evolutionary conservation of this protein family and supports the possibility of a conserved role in left-right patterning.

      Additionally, we have expanded the methods and discussion to include: (1) details on zebrafish viability in contrast to reported embryonic lethality in metrn mutant mice, (2) the background strains used in our study, (3) observed variability in DFC number and potential batch effects and (4) clarification of our 'convergence ratio' quantification approach.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript the authors describe their study on the role of meteorins in establishing the left-right organizer. The left-right organizer is a transient organ in vertebrate embryos in which rotating cilia cause a fluid flow that breaks the left-right symmetry and coordinates lateralization of internal organs such as gut and heart. In zebrafish, the left-right organizer (also named Kupffer's vesicle) is formed by dorsal forerunner cells, but very little is known about how dorsal forerunner cells coalles and form this ciliated vesicle in the embryo. The authors mutated the three meteorin-coding genes in zebrafish and observed that mutations in each one of these causes laterality defects with the strongest defects observed in the triple mutant. Loss of meteorins affects nodal gene expression, which play essential roles in establishing organ laterality. Meteorins are widely expressed in developing embryos and expression in lateral plate mesoderm and dorsal forerunner cells was observed. The meteorin triple mutant embryos display defects in the migration and clustering of the dorsal forerunner cells impairing kupffer's vesicle formation and cilia rotation. Finally, the authors show that meteorins genetically interact with integrins.

      Strengths:

      - These authors went through the lengthy process of generating triple mutants affecting all three meteorin genes. This provides robust genetic evidence on the role of meteorins in establishing organ laterality and circumvented that interpretation of the results would be hard due to redundant functions of meteorins.

      - The use of life imaging on triple mutants is appreciated

      - High-quality imaging of dorsal forerunner to quantify cell migrations and its relation to Kupffer's vesicle formation.

      Weaknesses:

      - Lack of a model how meteorins regulate dorsal forerunner cell migration.

      - Only genetic data to suggest a link between meteorins and integrins

      - Besides its role in DFC migration, meteorins may also play a more direct role in regulating Nodal signaling, which is not addressed here.

      We appreciate the recognition of the strengths of our study, particularly the generation of the triple meteorin mutants and the use of high-resolution imaging to quantify DFC behavior and Kupffer’s vesicle formation—both of which were central to providing robust evidence for Meteorins' role in left-right patterning.

      We also value the reviewer’s comments on areas that need further exploration, including the need for a mechanistic model explaining how Meteorins regulate DFC migration, the genetic interaction with integrins, and the potential direct involvement of Meteorins in Nodal signaling.

      We agree that deeper mechanistic insights would strengthen the study. While our findings suggest that Meteorins influence DFC migration and clustering through integrin pathways, a detailed mechanistic dissection, particularly regarding the yet unidentified Meteorin receptor, lies beyond the current scope. However, we consider this a key aspect for future research and have discussed it further in the revised discussion section.

      In response to the reviewer’s suggestions, we have expanded the discussion to address the limitations of the current data linking Meteorins and integrins, including relevant citations to studies that implicate integrins in similar contexts. Additionally, we have added a more detailed discussion of the potential for Meteorins to directly influence Nodal signaling, and we cite a relevant study to support this possibility.

      Once again, we thank the reviewer for their insightful and constructive comments. These points raise important directions for future investigation that will further advance our understanding of Meteorin function in left-right axis formation.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      In the Results section (p. 9), the authors state, "...a reduced ZO-1 enrichment at the apical junctions of triplMUT GFP-positive DFCs could be detected." However, in Fig. 4F-G, the areas of ZO-1 enrichment indicated by arrowheads appear quite far from the DFCs themselves, making it unclear if these ZO-1-enriched areas are apical DFC junctions (as stated in the text) or instead are part of the EVL. Is it possible to include an additional cell membrane marker or other landmarks? In addition, the differences in ZO-1 accumulation between mutants and WT appear relatively modest. Is it possible to provide quantification of this effect?

      We appreciate the reviewer’s request for additional stainings and further clarification and we would like to highlight the requested quantifications of ZO-1 accumulation, including statistical analysis, are already provided in Fig. S5E.

      In mouse, loss of Meteorin is embryonic lethal yet the zebrafish triple mutants are viable. Could the authors discuss this discrepancy?

      We have expanded the discussion to address this point, suggesting that species-specific differences in compensatory mechanisms may explain the observed differences in viability. We would like to reiterate that while one study has reported embryonic lethality in metrn mutant mice, this specific mouse line has not been further investigated in any recent publications. Additionally, in collaboration with the lab of Alain Chédotal, we generated independent metrn and metrnl mutant mouse lines, which did not exhibit the phenotype described in the previously mentioned study.

      It has been reported that TL and AB strains exhibit variable numbers of DFCs and thus laterality defects (Moreno-Ayala et al., 2021, Cell Reports 34(2):108606). Would it be possible for the authors to report background stains used in this study and those used to generate the meteorin knock-outs?

      We appreciate the comment highlighting the importance of specifying the background strains used in our study. We have now included this information in the methods section, detailing the zebrafish strains utilized throughout our experiments.

      For statistical analysis, would be possible for the authors to report the number of clutches examined to control for batch effects (especially given the wide variability in DFC numbers as noted above)?

      For further clarification, we have now included additional explanation on number of clutches in the methods section.

      In the Methods section (p. 19), the description of how the convergence ratio was computed was somewhat unclear. Could the authors provide a citation or include a diagram/schematic?

      We have revised the Methods section to provide a clearer definition of the convergence ratio and have included a schematic (Fig. 4D) to illustrate how it was calculated.

      Reviewer #2 (Recommendations for the authors):

      - Meteorins are widely expressed in the embryo. Can the authors comment on whether meteorin expression is required in the dorsal forerunner cells (DFCs) or in other cells? This could be addressed by knockdown experiments in DFCs as described by others (PMID: 15716348)

      We thank the reviewer for this important comment. In our study, we have shown that Meteorins are not required for the identity of DFCs, as several DFC-specific markers remain expressed in the respective cells within the meteorin mutant background (see Fig. S4).

      - In fig1d and 1e the authors use heterotaxy to describe visceral organ placement. The embryo shown in 1d seems to display situs inversus instead of heterotaxy, which is defined as discordance in organ position. The authors should clarify this.

      We agree with the reviewer and have revised the figures and figure legends to clarify the distinction between situs inversus and heterotaxy.

      - In Fig2 the authors show that nodal pathway genes are reduced, suggesting reduced Nodal signaling. How do they explain this as loss of cilia rotation generally leads to randomization of Nodal signaling but not a reduction in signaling.

      Following this suggestion we have now added a further discussion on the possibility that Meteorins could directly regulate Nodal signaling in addition to their role in DFC migration and have cited a relevant study.

      - Reduced Nodal signaling in the LPM leads to organ laterality defects. Most anterior tissues like the heart are more sensitive to perturbation in Nodal signaling in the LPM compared to more posterior organs like gut (see also PMID: 25684355). Since in triple mutants the position of the heart is more affected than the position of the visceral organs this suggests that meteorins play an additional role in Nodal signaling in the LPM. As others have shown that meteorins regulate nodal activity (PMID: 24558432), the authors should address this further.

      As described above, we have now added a further discussion on the possibility that Meteorins could directly regulate Nodal signaling in addition to their role in DFC migration and have cited a relevant study. Further investigation into a possible direct role of Meteorins in Nodal signaling will be pursued in future work.

      - The term 'convergence ratio' is not clearly described and confusing as convergence is also used for the movement of LPM cells towards the midline.

      As noted in response to Reviewer #1, we have revised the Methods section and included a schematic in Fig. 4D to better explain this parameter.

      We are grateful for the thoughtful critiques from both reviewers, which have been very constructive and improved the clarity of our study. We believe that the revisions we have made address the concerns raised, and we look forward to your evaluation of our revised manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer 1 (Public review):

      (1) The authors state that they have reclassified the allelic expression status of 32 genes (shown in Table S5, Supplementary Figure 3). The concern is the source of the tissue or cell line which was originally used to make the classification of XCI status, and whether the comparisons are equivalent. For example, if cell lines (and not tissues) were used to define the XCI status for EGFL6, TSPAN6, and CXorf38, then how can the authors be sure that the escape status in whole tissues would be the same? Also, along these lines, the authors should consider whether escape status in previous studies using immortalized/cancer cell lines (such as the meta-analyses done in Balaton publication) would be different compared to healthy tissues (seems like it should be). Therefore, making comparisons between healthy whole tissues and cancer cell lines doesn't make sense.

      Indeed, many previous classifications were based on clonal cell lines, which could result in atypical patterns of escape due to the profound and varied effects of adaptation to culture. However, one of the primary goals of our study was to directly determine allele-specific expression from the X-chromosome in healthy primary tissues, in part to exclude the potential confounding effects of cell culture. 

      Whereas we do perform comparisons with cell culture-based classifications, we also provide detailed comparisons with the previous classification of Tukiainen et al, which also uses primary human tissues. In addition, whereas the comparison with Balaton et al is not optimal, we hold that it is valuable as it reveals which genes may exhibit aberrant escape patterns in culture. Finally, despite the above reservations, our comparison revealed an over-whelming agreement with previous research which suggests that in the vast majority of cases, escape appears to be correctly maintained in culture. 

      (2) The authors note that skewed XCI is prevalent in the human population, and cite some publications (references 8, 10-12). If RNAseq data is available from these female individuals with skewed XCI (such as ref 12), the authors should consider using their allelic expression pipeline to identify XCI status of more X-linked genes.

      Indeed, we completely agree and are in the process of obtaining this data which has proven complex and time-consuming in the currently regulatory environment.

      (3) It has been well established that the human inactive X has more XCI escape genes compared to the mouse inactive X. In light of the author's observations across human tissues, how does the XCI status compare with the same tissues in mice?

      This is a very interesting point, and a comparison we are currently working on. However, this is a major undertaking and one that is outside of the scope of this study. We do appreciate the differences in mice and humans on X-chromosome level and could only speculate on the overlap being relatively small as the number of escapees in mice has been shown the be far lower than in humans.

      Reviewer 2 (Public review):

      In my view there are only minor weaknesses in this work, that tend to come about due to the requirement to study individuals with highly skewed X inactivation. I wonder whether the cause of the highly skewed X inactivation may somehow influence the likelihood of observing tissue-specific escape from X inactivation. In this light, it would be interesting to further understand the genetic cause for the highly skewed X inactivation in each of these three cases in the whole exome sequencing data. Future additional studies may validate these findings using single-cell approaches in unrelated individuals across tissues, where there is normal X inactivation.

      We thank the reviewer for their positive assessment of our work. This is a point we have and continue to grapple with. We cannot rule out that the genetic cause of complete skewing may influence tissue-specific XCI.  Moreover, the genetic cause for the non-mosaic XCI is currently unclear and is likely to vary between individuals, which could also result in inter-individual variation in tissue-specific escape. We are currently performing large prospective studies in the tissues of healthy females to specifically address this point.

      Reviewer 3 (Public review):

      There are very few, except that this escape catalogue is limited to 3 donors, based on a single(representative) tissue screen in 285 female donors, mostly using muscle samples. However, if only pituitary samples had been screened, nmXCI-1 would have been missed. Additional donors in the 285 representative samples cross a lower threshold of AE = 0.4. It would be worthwhile to query all tissues of the 285 donors to discover more nmXCI cases, as currently fewer than half of X-linked genes received a call using this very worthwhile approach.

      We thank the reviewer for their positive assessment of our work. Of course, we agree that a tissue-wide screen in all individuals would have been optimal and is a line of research we are currently pursuing. However, the analysis of allele-specific expression in all 5,000 RNA-seq samples is a massive undertaking and was simply not practicable within the time-scale of this study. 

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      Thanks to the authors for an interesting manuscript! I enjoyed reading it and the care that has gone into explaining the analyses and the findings. There are a few recommendations that I have for strengthening the work.

      We thank the reviewer for the nice feedback. Much appreciated.

      (1) I would like to see a genetic analysis of the three individuals, to try and identify the genetic causes of the skewed X inactivation beyond just considering the XIC or translocations. The cause of the highly skewed X inactivation would be of interest to many.

      This is certainly a very interesting avenue of research and one that we are currently focusing on. However, in the current study we simply had too few skewed XCI females to assess this  in an exhaustive manner. To tackle this issue, we have begun a prospective study of healthy females to identify additional non-mosaic females.

      (2) I wonder whether the cause of the skewed XCI may somehow influence the assessment of tissue-specific escape? If there is a problem with X inactivation itself, perhaps escape would also be different, making it appear more constitutive than tissue-specific?

      This is a point we have and continue to grapple with. We cannot rule out that the genetic cause of complete skewing may influence tissue-specific XCI.  Moreover, the genetic cause for the non-mosaic XCI is currently unclear and is likely to vary between individuals, which could result in inter-individual variation in tissue-specific escape.

      (3) Presentation/wording suggestions:

      I think the abstract is likely a bit inaccessible to those outside the field. I am in the X inactivation field, but don't use the term non-mosaic X inactivation, but rather would call it highly skewed, or non-random X inactivation. In my view, it would be simpler for the abstract to call non-mosaic XCI highly skewed XCI instead, or to use more words to ensure it is clear for the reader.

      We agree that the terminology of completely skewed/non-mosaic XCI could be more clearly defined in the abstract and have clarified this. “Using females that are non-mosaic (completely skewed) for X-inactivation (nmXCI) has proven a powerful and natural genetic system for profiling X-inactivation in humans.”

      I would consider calling the always escape genes constitutive escapees, while the variable may be facultative.

      This is something we have also considered and have received differing feedback on. However, we will definitely keep this in mind for future publications.

      Line 132, it would be useful to explain median >0.475 as less than 2.5% of reads coming from the inactive allele here, not just in the methods. Can you also explain why this cutoff was chosen?

      We thank the reviewer for this clarification. A clarification has been added to the main text as suggested.

      The cutoff was applied to account for potential variations in skewing, given that we screened only a single tissue sample per individual. Although nmXCI females are theoretically expected to have 0% of reads originating from the 'inactive' allele, this is not always observed due to (a) technical errors such as PCR or sequencing inaccuracies, or (b) differences in skewing between tissue types.

      Lines 156-160 describe how the heterozygous SNPs were identified in relation to Figure 2. I read these in the methods so that I could understand Figure 1, so I suggest moving this section up.

      We have moved the section as suggested by the reviewer.

      Line 156, consider adding in a sentence to describe what is shown in Figures 2A and B i.e, the overlap of SNPs and spread along the X.

      We have added a sentence describing what is shown in Figures 2A and 2B as suggested by the reviewer.

      Line 217, it would be useful to give the % of genes that show tissue-specific escape, to quantify rare.

      We have added a sentence quantifying ‘rare’ at the suggested line.

      (4) Typos:

      Line 119, missing 'the most' before extensive (and remove an).

      We thank the reviewer for pointing this out. This error has been corrected.

      Reviewer #3 (Recommendations for the authors):

      Some results in the supplementary figures were quite striking. What is going on with DDX3X and ZRSR2? How come total read counts are so different between individuals?

      Indeed, this is a very intriguing observation and one that we have simply failed to understand thus far. We are currently performing a large prospective study to obtain greater number of non-mosaic females and tissues samples. Hopefully, additional observations across females will allow us to gain further insights into the inter-individual behaviour of DDX3X and ZRSR2.   

      One item I would like to see added is some analysis to address the cause of these extremely skewed XCI individuals. The copy number analysis suggests there are some segmental deletions on the X in all three nmXCI cases. Where are these deletions, and do any fall in the region of the X-inactivation centre? Have the authors performed any analysis of potentially deleterious X-linked variants in the WGS or WES data? Why are these donors so skewed? It's interesting that UPIC was still more skewed than the other two.

      The segmental deletions the reviewer points out are not segmental deletions, the same variation in coverage is found in all females we’ve looked at including females with a mosaic XCI (see Author response image 1 below where the same pattern of slightly lower read counts is observed at the same sites in all female samples). No deletions were identified in the XIC region. No analysis was performed of deleterious X-linked variants. Why the donors are so skewed is unknown and intriguing. Indeed, identifying the origin of extreme skewing (including the females in this study) is now the main focus of the group. Whereas UPIC had trisomy 17, which has likely resulted in the observed skewing, we have not yet found a genetic variant that could explain the skewing observed in 13PLJ or ZZPU.

      Author response image 1.

      Copy number as log2 ratio using 500kb bins across the X-chromosome for 3 mosaic XCI females (1QPFJ, OXRO, and RU1J) and 3 nmXCI females, UPIC, nmXCI-1 and nmXCI-2.

      This is not necessary to address with new analyses, but as alluded to above, the authors could screen more than a single representative tissue. And to apply this analysis to larger databases (UK biobank), which the authors may be planning to do already.

      This an avenue of research we are currently investigating. 

      The code is well-documented and accessible. Additional information on the manual reclassification (to deal with inflated binomial P-values) would be helpful. Why not require a minimal threshold for escape (10% of active X allele) in addition to a significant binomial P (inactive X exp. > 2.5% of active)?

      We thank the reviewer for this positive assessment of the code. 

      Indeed, how to define ‘escape’ is a vexed issue, and one we feel has been given undue weight within the field. In reality, studies of escape are often dealing with sparse data (e.g. read depth), few observations (genes and individuals) and substantial amounts of missing data. Thus, it is unlikely that a standard statistical approach will be sensitive and specific across different studies and data types. Similarly, cut-offs, though useful would also need to be adjusted to the data type and quality in any given study.

      Whereas we initially used a significant binomial P-value as our sole test (often quoted as ‘best practice’), this resulted in wide-spread inflation of P-values. Thus, we switched to manually curating the allelic expression status of all 380 genes using the empirical guideline of allelic ratio >0.4 (also a commonly used cut-off) as indicating mono-allelic expression. We considered combining the binomial P-value with the cut-off but felt that this would result in an overly complex definition of escape and would unnecessarily exclude many genes from classification, due to the opposing effects of low/high read depth on the binomial and cut-off approaches respectively.

      Indeed, due to the difficultly of both accurate and objective ‘classification’ of escape that we placed an emphasis on clearly displaying all data for each gene in each individual to allow readers to see all the data on which each classification was based.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:  

      Reviewer #1 (Public review):  

      Summary:  

      This work examines the binding of several phosphonate compounds to a membrane-bound pyrophosphatase using several different approaches, including crystallography, electron paramagnetic resonance spectroscopy, and functional measurements of ion pumping and pyrophosphatase activity. The work attempts to synthesize these different approaches into a model of inhibition by phosphonates in which the two subunits of the functional dimer interact differently with the phosphonate.  

      Strengths:  

      This study integrates a variety of approaches, including structural biology, spectroscopic measurements of protein dynamics, and functional measurements. Overall, data analysis was thoughtful, with careful analysis of the substrate binding sites (for example calculation of POLDOR omit maps).  

      Weaknesses:  

      Unfortunately, the protein did not crystallize with the more potent phosphonate inhibitors. Instead, structures were solved with two compounds with weak inhibitory constants >200 micromolar, which limits the molecular insight into compounds that could possibly be developed into small molecule inhibitors. Likewise, the authors choose to focus the spectroscopy experiments on these weaker binders, missing an opportunity to provide insight into the interaction between more potent binders and the protein. 

      We acknowledge the reviewer concern regarding the choice of weaker inhibitors. We attempted cocrystallization with all available inhibitors, including those with higher potency. However, despite numerous efforts, these potent inhibitors yielded low-resolution crystals, making them unsuitable for detailed structural analysis. Therefore, we chose to focus on the weaker binders, as we were able to obtain high-quality crystal structures for these compounds. This allowed us to perform DEER spectroscopy and monitor conformational TmPPase state ensembles in solution with the added advantage of accurately analysing the data against structural models derived from X-ray crystallography. Using these weaker inhibitors enabled a more precise interpretation of the DEER data, thus providing reliable insights into the conformational dynamics and inhibition mechanism. As suggested by the reviewer, in the revised version, we add new DEER experiments, conditions and analysis on two of the more potent inhibitors (alendronate and pamidronate) to provide additional insight into their interactions. Furthermore, we also implemented additional DEER data on the cytoplasmic side of TmPPase; at a new site we identified (with the advantage of being an endogenous cysteine residue) and spin labelled (C599R1), given the DEER data for the previous T211R1cytoplasmic site were difficult to interpret owing to the highly dynamic nature of this region. The new pair C599R1 yielded high-quality DEER traces and indicated more clearly than T211R1, distance distributions consistent with asymmetry across the sampled conditions.  Again, as suggested by the reviewer, alendronate and pamidronate DEER measurements were also recorded for this site (cytoplasmic side; C599R1) as well as the periplasmic side (525R1).

      In general, the manuscript falls short of providing any major new insight into membrane-bound pyrophosphatases, which are a very well-studied system. Subtle changes in the structures and ensemble distance distributions suggest that the molecular conformations might change a little bit under different conditions, but this isn't a very surprising outcome. It's not clear whether these changes are functionally important, or just part of the normal experimental/protein ensemble variation. 

      We respectfully disagree with the reviewer. The scale of motions particularly seen in solution (and now on a new reliable spin pair (C599R1) located on the cytoplasmic side) correspond to those seen in the full panoply of crystal structures of mPPases. Some proteins undergo very large conformational changes during catalysis – such as the rotary ATPase. This one does not, meaning that the precise motions we describe here are relevant and observed in solution for the first time. Conformational changes in the ensemble, whether large or small, represent essential protein motions which underlie key mPPase catalytic function. These dynamic transitions are extremely challenging to monitor, especially in so many conditions and our DEER spectroscopy data demonstrate the sensitivity and resolution necessary to monitor these subtle changes in equilibria, even if these are only a few Angstroms. For several of the conditions we investigated by DEER in solution, corresponding X-ray structures have been solved, with the derived distances agreeing well with the DEER distributions. This further validates the biological relevance of the structures, and reveals the complete conformational ensemble, intractable using other current approaches. Indeed, some conformational states were previously seen using serial time-resolved X-ray static structures and were consistent with asymmetry.

      The ZLD-bound crystal structure doesn't predict the DEER distances, and the conformation of Na+ binding site sidechains in the ZLD structure doesn't predict whether sodium currents occur. This might suggest that the ZLD structure captures a conformation that does not recapitulate what is happening in solution/ a membrane. 

      We agree with the reviewer that the ZLD-bound crystal structure does not predict the DEER distances. However, we believe this discrepancy arises from the steric bulkiness of ZLD inhibitor, which prevents the closure of the hydrolytic centre. Additionally, the absence of Na+ at the ion gate in the ZLD-bound structure suggests that Na+ transport does not occur, a conclusion further supported by our electrometric measurements. We agree with the reviewer; distances observed in the DEER experiments might represent a potential new conformation in solution, not captured by the static X-ray structure, thereby offering new insights into the dynamic nature of the protein under physiological conditions. This serves to emphasize the complementarity of the DEER approach to Xray crystallography and redoubles the importance of using both techniques. Finally, the static X-ray structures have not captured the asymmetric conformations that must exist to explain half-of-thesites reactivity, where DEER yields distance distributions, across all 16 cases tested here (two mutants with eight conditions each), that are consistent with asymmetry.

      Reviewer #2 (Public review):  

      Summary:  

      Crystallographic analysis revealed the asymmetric conformation of the dimer in the inhibitor-bound state. Based on this result, which is consistent with previous time-resolved analysis, authors verified the dynamics and distance between spin introduced label by DEER spectroscopy in solution and predicted possible patterns of asymmetric dimer.  

      Strengths:  

      Crystal structures with inhibitor bound provide detailed coordination in the binding pocket thus useful information for the mPPase field and maybe for drug development.  

      Weaknesses:  

      The distance information measured by DEER is advantageous for verifying the dynamics and structure of membrane protein in solution. However, regarding T211 data, which, as the authors themselves stated, lacks measurement precision, it is unclear for readers how confident one can judge the conclusion leading from these data for the cytoplasmic side. 

      We thank the reviewer for acknowledging the advantageous use of the DEER methodology for identifying dynamic states of membrane proteins in solution. In our original manuscript, we used two sites in our analysis: S525 (periplasm) and T211 (cytoplasm), in which S525R1 yielded highquality DEER data, while T211R1 yielded weak (or no) visual oscillations, leading to broad distributions for the several conditions tested. In the revised manuscript, we now added a third site at the cytoplasmic side (C599R1 located at TMH14), which yielded high-quality DEER data and comparable to S525R1. Both C599R1 and C525R1 spin pairs generated distance distributions for all 16 conditions (two mutants of eight conditions each) that were described well by the solution-state ensemble adopting a predominantly asymmetric conformation.  

      Furthermore, we have tailored our interpretation of the T211R1 DEER data, and refrain from using the data to draw conclusions about the TmPPase conformational ensemble in the presence of different inhibitors. However, we still opted to include the T211R1 data in the SI because they confirm an important structural feature of mPPase in solution conditions; the intrinsically dynamic behaviour of the loop5-6 where T211 is located. This observation in solution is also consistent with our previous (Kellosalo et al., Science, 2012; Li et al., Nat. Commun, 2016; Vidilaseris et al., Sci. Adv., 2019; Strauss et al., EMBO Rep., 2024) and current X-ray crystallography data. To reiterate, we excluded T211R1 from any analysis relating to mPPase asymmetry and our conclusions were entirely based on the S525R1 and new C599R1 DEER data, which allowed us to monitor both sides on the membrane.  

      The distance information for the luminal site, which the authors claim is more accurate, does not indicate either the possibility or the basis for why it is the ensemble of two components and not simply a structure with a shorter distance than the crystal structure.  

      We thank the reviewer for pointing out this possibility and alternative interpretation of our DEER data. We now provide further analysis to show that our DEER data from both membrane sides reporters are highly consistent with (although they cannot completely exclude) asymmetry and rephrase to be inclusive of other possibilities. Importantly, this additional possibility does not affect the current interpretation of the data in our manuscript. Furthermore, we have removed Fig. 6 from the manuscript, and we now include a direct comparison of the in silico predicted distribution coming from the asymmetric hybrid structure with the 8 conditions tested, for both mutants (i.e. S525R1 and C599R1).

      Reviewer #3 (Public review):  

      Summary:  

      Membrane-bound pyrophosphatases (mPPases) are homodimeric proteins that hydrolyze pyrophosphate and pump H+/Na+ across membranes. They are attractive drug targets against protist pathogens. Non-hydrolysable PPi analogue bisphosphonates such as risedronate (RSD) and pamidronate (PMD) serve as primary drugs currently used. Bisphosphonates have a P-C-P bond, with its central carbon can accommodate up to two substituents, allowing a large compound variability. Here the authors solved two TmPPase structures in complex with the bisphosphonates etidronate (ETD) and zoledronate (ZLD) and monitored their conformational ensemble using DEER spectroscopy in solution. These results reveal the inhibition mechanism of these compounds, which is crucial for developing future small molecule inhibitors.  

      Strengths:  

      The authors show that seven different bisphosphonates can inhibit TmPPase with IC50 values in the micromolar range. Branched aliphatic and aromatic modifications showed weaker inhibition.  

      High-resolution structures for TmPPase with ETD (3.2 Å) and ZLD (3.3 Å) are determined. These structures reveal the binding mode and shed light on the inhibition mechanism. The nature of modification on the bisphosphonate alters the conformation of the binding pocket.  

      The conformational heterogeneity is further investigated using DEER spectroscopy under several conditions.  

      Weaknesses:  

      The authors observed asymmetry in the TmPPase-ELD structure above the hydrolytic center. The structural asymmetry arises due to differences in the orientation of ETD within each monomer at the active site. As a result, loop5-6 of the two monomers is oriented differently, resulting in the observed asymmetry. The authors attempt to further establish this asymmetry using DEER spectroscopy experiments. However, the (over)interpretation of these data leads to more confusion than any further understanding. DEER data suggest that the asymmetry observed in the TmPPase-ELD structure in this region might be funneled from the broad conformational space under the crystallization conditions. 

      We respectfully disagree with the reviewer. The asymmetry was previously established using serial time crystallography (Strauss et al., EMBO Rep, 2024) and biochemical assays (e.g. Malinen et al., Prot. Sci., 2022; Artukka et al., Biochem J, 2018; Luoto et al., PNAS, 2013) and partially seen in one static structure (Vidilaseris et al., Sci Adv 2019). DEER data here also show that the previously proposed asymmetry is also present (and this presence of asymmetry is consistent across all DEER data) within the TmPPase conformational ensemble in solution conditions. Although we cannot rule out the possibility that the TmPPase monomers adopt a metastable intermediate state, in such a case we would expect the distance changes reported by DEER to be symmetric across both membrane sides. However, we observe a symmetry breaking between the cytoplasmic and periplasmic TmPPase sites. Indeed, DEER data yield distance distributions similar to that of the hybrid asymmetric structure under all: apo, +Ca, +Ca/ETD, +ETD, +ZLD, +IDP, +PAM, +ALE conditions.

      DEER data for position T211R1 at the enzyme entrance reveal a highly flexible conformation of loop56 (and do not provide any direct evidence for asymmetry, Figure EV8).

      Please see relevant response above. We acknowledge that T211 is indeed situated on a highly dynamic loop, which is important for gating and our DEER data confirm the high flexibility of this protein region. Given we have not observed dipolar oscillations, leading to broad distributions, we have stated in the original manuscript that we will not establish the presence of any asymmetry in solution on the basis of T211, rather relying on the S525R1 and the new C599R1 sites, for which we have acquired high-quality DEER data, as was also pointed out and has been commented on by all reviewers. We have provided data at the C599R1 position (same cytoplasmic side as 211 for which we have now limited our analysis to a minimum) which further provides evidence for asymmetry, including two new conditions.

      Similarly, data for position S521R1 near the exit channel do not directly support the proposed asymmetry for ETD.  

      The reviewer appears to suggest that we hold the S525R1 DEER data as direct proof of asymmetry; this is combative on the grounds that to directly prove asymmetry would require time-resolved DEER measurements, far beyond the scope of this work. Rather, we have applied DEER measurements to explore whether asymmetry (observed previously via time-resolved X-ray crystallography) is also present (or indeed a possibility) in solution. All our S525R1 and C599R1 DEER data (recorded for eight conditions) are consistent with asymmetry (see also detailed response above).

      Despite the high quality of the data, they reveal a very similar distance distribution. The reported changes in distances are very small (+/- 0.3 nm), which can be accommodated by a change of spin label rotamer distribution alone. Further, these spin labels are located on a flexible loop, thereby making it difficult to directly relate any distance changes to the global conformation

      We thank the reviewer for recognising the high quality of our DEER data for the S525R1 site which we now complement with a new pair on the cytoplasmic facing membrane side (C599R1) with DEER data of comparable quality as for S525R1, where visual oscillations in the raw traces for both spin pairs, as in our case, reportedly lead to highly accurate and reliable distributions, able to separate (in fortuitous cases) helical movements of only a few Angstroms (Peter et al., Nature Comms 13:4396, 2022; Klose et al., Biophys J 120:4842-4858, 2021). The ability of DEER/PELDOR offering near Angstrom resolution was also previously demonstrated by the acquisition and solution of highresolution multi-subunit spin-labelled membrane protein structures (Pliotas at al., PNAS, 2012; Pliotas et al., Nat Struct Mol Biol, 2015; Pliotas, Methods Enzymol, 2017) as well as its ability in detecting small (and of similar to mPPase magnitude) conformational changes in different integral membrane protein systems (Kapsalis et al., Nature Comms, 2019; Kubatova et al., PNAS, 2023; Schmidt et al., JACS, 2024; Lane et al., Structure, 2024; Hett et al., JACS, 2021; Zhao et al., Nature, 2024), occurring under different conditions and/or stimuli in solution and/or lipid environment. The changes here are not below the detection sensitivity of DEER (e.g. ~ 7 Angstroms between the two modal distance extremes (+Ca vs +IDP for S525R1), and with all other conditions showing intermediate changes.  

      We agree with the reviewer that these changes are relatively small, but they are expected for membrane ion pumps. Indeed, none of the mPPase structures show helical movements of greater than half a turn, and that only in helices 6 and 12. There appear to be larger-scale loop closing motions of the 5-6 loop that includes T211, due to the presence of E217 which binds to one of the Mg<sup>2+</sup> ions that coordinate the leaving group phosphate. This is, inter alia, the reason that this loop is so flexible: it cannot order before substrate is bound.  

      The reviewer suggests that the subtle distance shifts detected arise only from changes of label rotamer distribution. However, the concerted nature of the modal distance shifts with respect to multiple different conditions at a single labelling site strongly suggests that preferential rotamer orientations are not the cause. Indeed, for so many spin labels to undergo an arbitrary shift that the modal distance of the entire distribution changes – and in the absence of any conformational change – appears improbable. Here we have the resolution to detect such subtle differences by DEER, given there are unambiguous shifts in our time domain data (i.e. the position of the minimum of the first dipolar oscillation) (Fig 4) and these are reflected in the modal distances in the distributions. We also refrain from performing any quantitative analysis and use qualitative trends in modal distance shifts only; all which support our proposed model of a symmetry breaking across the membrane face. To further belabour this point, we do not quantify the DEER data (for instance through parametric fitting) to extract populations of different conformational states and we appreciate that to do so would be highly prone to error; however we do (and can, we feel without over-interpretation) assert that the modal distances shift.  

      The interpretations listed below are not supported by the data presented:  

      (1) 'In the presence of Ca2+, the distance distribution shifts towards shorter distances, suggesting that the two monomers come closer at the periplasmic side, and consistent with the predicted distances derived from the TmPPase:Ca structure.'

      Problem: This is a far-stretched interpretation of a tiny change, which is not reliable for the reasons described in the paragraph above. 

      While the authors overall agree with the reviewer assessment that ±0.3 nm is a small (not a minor) change, there are literature examples quantifying (or using for quantification) distribution peaks separated by similar Δr. (Kubatova et al., PNAS, 2023; Schmidt et al., JACS, 2024; Hett et al., JACS, 2021; Zhao et al., Nature, 2024). However, the time-domain data clearly indicate the position of the first minimum of the dipolar oscillation shifts to shorter dipolar evolution time. The sensitivity of the time-domain data to subtle changes in dipolar coupling frequency is significantly improved compared to the distance distributions.

      Importantly, we have fitted Gaussians to the experimental distance distributions of 525R1 output by the Comparative Deer Analyzer 2.0 and observed a change in the distribution width in presence of Ca2+, implying the rotameric freedom of the spin label is restricted. However, the CW-EPR for 525R1 indicate that the rotational correlation time of the spin label is highly consistent between conditions (the spectra are almost identical); this cannot be explained simply by rotameric preference of the spin label (as asserted by the reviewer 3), as there is no (further) immobilisation observed from the CW-EPR of apo-state (Figure EV9) to that in presence of Ca2+. Furthermore, in the absence of conformational changes, it is reasonable to assume (and demonstrable from the CW-EPR data) that the rotamer cloud should not significantly change between conditions. However, Gaussian fits of the two extreme cases yielding the longest (i.e., in presence of IDP) and shortest (in presence of ZLD) modal distances for the 525R1 DEER data indicated significant (i.e., above the noise floor after Tikhonov validation) probability density for the IDP condition at 50 Å (P(r) = 0.18). This occurs at four standard deviations above the mean of the Guassian fit to the +ZLD condition, which by random chance should occur with <0.007% probability.  

      As in previous response, the method can detect changes of such magnitude which are not small, but physiologically relevant and expected for integral membrane proteins, such as mPPases. Indeed, even in equal (or more) complex systems such as heptameric mechanosensitive channel proteins DEER provided sub-Angstrom accuracy, when a spin labelled high resolution XRC structure was solved (Pliotas et al., PNAS, 2012; Pliotas et al., Nat Struct Mol Biol, 2015). Despite this being an ideal case where DEER accuracy was experimentally validated another high-resolution structural method on modified membrane protein and is not very common it demonstrates the power of the method, especially when strong oscillations are present in the raw DEER data (as here for mPPase S525R1, and C599R1), even when multiple distances are present, Angstrom resolution is achievable in such challenging protein classes.

      (2) 'Based on the DEER data on the IDP-bound TmPPase, we observed significant deviations between the experimental and the in silico distances derived from the TmPPase:IDP X-ray structure for both cytoplasmic- (T211R1) and periplasmic-end (S525R1) sites (Figure 4D and Figure EV8D). This deviation could be explained by the dimer adopting an asymmetric conformation under the physiological conditions used for DEER, with one monomer in a closed state and the other in an open state.'  

      Problem: The authors are trying to establish asymmetry using the DEER data. Unfortunately, no significant difference is observed (between simulation and experiment) for position 525 as the authors claim (Figure 4D bottom panel). The observed difference for position 112 must be accounted for by the flexibility and the data provide no direct evidence for any asymmetry.  

      Reviewer 3 is incorrect in suggesting that we are trying to prove asymmetry through the DEER data. That is a well-known fact in the literature (e.g. Vidilaseris et al, Sci Adv 2019) where we show (1) that the exit channel inhibitor ATC (i.e. close to S525R1) binds better in solution to the TmPPase:PPi complex than the TmPPase:PPi<sub>2</sub> complex, and (2) that ATC binds in an asymmetric fashion to the TmPPase:IDP<sub>2</sub> complex with just one ATC dimer on one of the exit channels. We merely use the DEER data to support this well-established fact.  

      However, because we agree that the DEER data in presence of IDP does not provide direct proof for asymmetry; particularly for the cytoplasmic facing mutant T211R1, we have refrained from interpreting T211R1 data beyond being a highly dynamic loop region (as evidenced by the broad distributions). As pointed out by the reviewer, the differences in distance distributions between conditions observed for T211R1 likely arise from conformational heterogeneity in solution. Furthermore, we now report DEER data on another new site (C599R1), which is also on the cytoplasmic side and yields high quality DEER data comparable to the S525R1 data (commended for their quality by both the reviewers). The C599R1 measurements show that in all conditions tested, highly similar distributions are observed, inconsistent with the in silico predicted distance distributions from the symmetric X-ray structures, but consistent with an asymmetric hybrid structure (i.e. open-closed) in solution. Importantly, the difference between the fully open (6.8 nm modal distance) and fully closed (4.8 nm modal distance) states of the C599R1 dimer is larger than for the S525R1 dimer pair. Thus, delineating the asymmetric hybrid conformation from the symmetric conformations is more robust.

      (3) 'Our new structures, together with DEER distance measurements that monitor the conformational ensemble equilibrium of TmPPase in solution, provide further solid experimental evidence of asymmetry in gating and transitional changes upon substrate/inhibitor binding.'  

      Problem: See above. The DEER data do not support any asymmetry. 

      We feel that the reviewer comments here are somewhat unfounded. All the DEER data (for 525R1 periplasmic and C599R1 cytoplasmic sites are described, most parsimoniously, using an asymmetric hybrid structure. In particular, the new C599R1 distance distributions are poorly described by the symmetric X-ray crystal structures, with a conserved modal distance of approx. 5.8 nm throughout the tested conditions that aligns nicely with the in silico predictions from the asymmetric hybrid structure. Additionally, all S525R1 and C599R1 data well exceed the relevant criteria of the recent white paper (Schiemann et al., 2021, JACS) from the EPR community to be considered reliably interpretable (strong visual oscillations in the raw traces; signal-to-noise ratio .r.t modulation depth of > 20 in all cases; replicates have been performed and added into the maintext or supplementary; near quantitative labelling efficiency (evidenced by lack of free spin label signal in the CW-EPR spectra); analysed using the CDA (now Figure EV10) to avoid confirmation bias).

      While the DEER data do not prove asymmetry, we do not claim proof of asymmetry in the above sentence. We concede to rephrase the offending sentence above as: “Our new structures, together with DEER distance measurements that monitor the conformational ensemble of TmPPase in solution, do not exclude asymmetry in gating and transitional changes upon substrate/inhibitor binding and are consistent with our proposed model.” We feel that this reframed conjecture of asymmetry is well founded; indeed, comparing all the 16 experimentally derived DEER distance distributions for the 525R1 and 599R1 sites with in-silico modelling performed on the hybridised asymmetric structure (i.e., comprised of one monomer bound to Ca2+ and another bound to IDP) yields overlap coefficients (Islam and Roux, JPC B, 2015) of >0.85. This implies the envelope of the modelled distance distribution is quantitatively inside the envelope of the experimental distance distributions. Thus, the DEER data support asymmetry (previously observed by time-resolved XRC) in solution, and while we appreciate that ideally one would measure time-resolved DEER to directly correlate kinetics of conformational changes within the ensemble to the catalytic cycle of mPPase, (and this is something we aim to do in the future), it is far beyond the scope of this study.

      Indeed, half-of-the-sites reactivity has been demonstrated in at least the following papers

      (Vidilaseris et al, Sci Acv. ,2019, Strauss et al, EMBO Rep. 2024, Malinen et al Prot Sci, 2022, Artukka et al Biochem J, 2018; Luoto et al, PNAS, 2013). Half-of-the sites activity requires asymmetry in the mechanism, and therefore asymmetric motions in the active site (viz 211) and exit channel (viz 525). As mentioned above, we have demonstrated this for other inhibitors (Vidilaseris et al 2019) and as part of a time-resolved experiment (Strauss et al 2024). In fact, given the wealth of evidence showing that the symmetrical crystal structures sample a non- or less-productive conformation of the protein, it would be quixotic to propose the DEER experiments - in solution - do not generate asymmetric conformations. It certainly doesn’t obey Occam’s razor of choosing the simplest possible explanation that covers the data.

      (4) Based on these observations, and the DEER data for +IDP, which is consistent with an asymmetric conformation of TmPPase being present in solution, we propose five distinct models of TmPPase (Figure 7).  

      Problem: Again, the DEER data do not support any asymmetry and the authors may revisit the proposed models. 

      We have redressed the proposed models and limited them to four asymmetric models to clearly illustrate the apo/+Ca/+Ca:ETD-state (model 1) and highlight the distinct binding patterns of various inhibitors (ETD, ZLD and IDP; model 2-4), which result in a variety of closed/open-open states. In this version, we clarify that the proposed models are not solely based on the DEER data but all DEER data recorded for multiple conditions, inhibitors and for two opposite membrane side facing reporters are highly consistent, and are grounded in both current and previously solved structures, with the DEER data providing additional consistency with these models.

      (5) 'In model 2 (Figure 7), one active site is semi-closed, while the other remains open. This is supported by the distance distributions for S525R1 and T211R1 for +Ca/ETD informed by DEER, which agrees with the in silico distance predictions generated by the asymmetric TmPPase:ETD X-ray structure'  

      Problem: Neither convincing nor supported by the data 

      We respectfully disagree with the reviewer. However, owing to the conformational heterogeneity of T211R1, we now exclude T211R1 data from quantitative interpretation of changes to the conformational ensemble. Instead, we include new DEER data from site C599R1, which provides high-quality and convincing data that is consistent with asymmetry at the cytoplasmic face, and inconsistent with in silico distance distributions derived from symmetric X-ray crystal structures. Furthermore, the S525R1 distance distributions for the +ETD (corresponding to +Ca/ETD) and +ZLD conditions were directly compared with both the apo-state distance distribution (corresponding to a fully open, symmetric conformation) and the in silico predicted distributions of the asymmetric hybrid structure (corresponding to an open-closed conformation). Overlap coefficients were calculated (given in the main text) that indicated the +ETD (corresponding to +Ca/ETD) and +ZLD S525R1 distributions were more consistent with the apo-state distance distribution. This suggests that while on the cytosolic face of the membrane, an open-closed conformation is favoured, on the periplasmic face, a symmetric open-open conformation is favoured.

      Recommendations for the authors:  

      Reviewer #1 (Recommendations for the authors):   

      (1) The DEER experiments were performed with the two crystallized inhibitors, ETD and ZLD, along with previously characterized IDP. It would increase the impact of a tighter-binding phosphonate was examined since the inhibitory mechanism of these molecules is of greater interest. 

      We acknowledge the reviewer concern regarding the choice of weaker inhibitors. We chose to focus on the weaker binders, as we were able to obtain high-quality crystal structures for these compounds. This allowed us to perform DEER spectroscopy with the added advantage of accurately analysing the data against structural models derived from X-ray crystallography. In the revised version, we also include results from alendronate and pamidronate, two of the tighter inhibitors, which show similar and consistent results to the others.

      (2) I'm not able to find the concentrations of ETD and ZLD used for the DEER experiments. This information should be added to the Methods section on sample prep for EPR. 

      The information is already mentioned in the Method section on sample preparation for EPR spectroscopy (page 24), where we indicated that the protein aliquots were incubated with a final concentration of 2 mM inhibitors or 10 mM CaCl2 (30 min, RT). However, we recognise that this may not have been sufficiently clear. To clarify, we now explicitly state that the concentration of ETD and ZLD (amongst other inhibitors) used for the DEER experiments is 2 mM.  

      (3) There should be additional detail about the electrometry replicates. Does "triplicate" mean three measurements on the same sensor, three different sensors, and different protein preparations? At a minimum, data should be collected from three different sensors to ensure that the negative results (lack of current) for ETD and ZLD are not due to a failed sensor prep. In addition, Data from the other replicates should be shown in a supplementary figure, either the traces, or in a summary figure. Are the traces shown collected on the same sensor? They could be, in principle, since the inhibitor is washed away after each perfusion. 

      Yes, by 'triplicate', we mean three measurements taken on the same sensor. All traces shown were collected from a single sensor. Thank you for your advice; we now show here additional data from other sensors that display the same pattern. As for the possibility of a failed sensor preparation, this is unlikely since we always ensure the sensor quality with the substrate (PPi) as a positive control after each measurement.

      Author response image 1.

      (4) I'm confused by the NEM modification assay, and I don't think there is enough information in this manuscript for a reader to figure out what is happening. Why is the protein active if an inhibitor is present? I understand that there is a conformational change in the presence of the inhibitor that buries a cysteine, but the inhibitor itself should diminish function, correct? Is the inhibitor removed before testing the function? In addition, it would be clearer if the cysteines that are modified are indicated in the main text. I don't understand what is being shown in Figure Ev2. Shouldn't the accessible cysteines in the apo form be shown? Finally, the sentence "IDP has been reported to prevent the NEM modification..." does not make sense to me. Should the word "by" be removed from this sentence? 

      We apologize for the confusion. Yes, the inhibitors were removed before testing the protein function. In Figure EV2, the accessible cysteines are shown for both the apo and IDP-bound states. As seen, the accessible cysteines in the IDP-bound states are fewer than those in the apo state, meaning fewer cysteines are available for modification. Consequently, more activity is retained when IDP binds due to the reduction in accessible cysteines. We have addressed this in the manuscript (see the method section on the NEM modification assay).

      (5) Why does the model in Figure 7 show the small molecules bound to only one subunit, when they are crystallized in both subunits? 

      We propose that the small molecules bound to the two subunits in the crystal structure is likely a result of substrate inhibition, given the excess inhibitor used during crystallisation (e.g. Artukka, et al., Biochemical Journal, 2018; Vidilaseris, et al., Science Advances, 2022). Our PELDOR data indicate that in solution, the small molecules bound to TmPPase are in an intermediate state between both subunits being closed and both being open, most likely with at least one subunit in an open state. This is also consistent with previous kinetic studies (Anashkin, V. A., et al., International Journal of Molecular Sciences, 22, 2021), which showed that the binding constant of IDP to the second subunit is around 120 times higher than that of the first subunit.

      (6) The authors argue that the two ETDs bound in the two protomers adopt distinct conformations. Can this be further supported, for example, by swapping the position of the two ETDs between the two protomers and calculating a difference map (there should be corresponding negative/positive density if the modelling of the two different conformations is robust)? 

      As per the reviewer suggestion, we swapped the positions of the two ETDs between the protomers and calculated the difference electron density map. This analysis, presented in Figure EV3, reveals corresponding negative and positive electron density peaks, indicating that the ETDs indeed adopt distinct conformations in each protomer, supporting the accuracy of our modeling.

      (7) Are the changes in loop conformation possibly due to crystal packing differences for the two protomers? 

      We examined the crystal packing of the two protomers and found no interactions at the loop regions (red coloured in Author response image 2 below) that could be attributed to crystal packing differences. Therefore, we rule out this possibility.

      Author response image 2.

      (8) Typos:  

      Legend for Figure EV2 cystine - cysteine  

      Page 14, last sentence of the first paragraph: further - further  

      Figure 6 legend: there is no reference to panel B.  

      Thanks for pointing out the typos, now they are fixed.

      Reviewer #2 (Recommendations for the authors):  

      (1) T211 is located on the same loop where ligand/inhibitor-coordinating side chains (E217, D218) are located. It has not been tested whether spin labeling here would affect inhibitor binding. 

      We test all the mutant(s) activity before spin labelling, but not the activity of the spin-labelled mutants. MTSSL spin labels are typically not structurally perturbing. In particular, the T211R1 site that the reviewer is referring to is now not included in our interpretation of conformational changes occurring during mPPase’s functional cycle.

      (2) Why should the spin label be introduced to T211, which is recognized as a flexible region in the crystal structure? Authors should search for suitable residues except for T211 and other residues in this loop to evaluate the cytoplasmic distance. 

      We acknowledge the reviewer’s concern regarding the flexibility of the T211 region for spin labelling. Given the challenges associated with TmPPase, including reduced protein expression, loss of function, or inaccessibility upon spin labelling at certain sites, we have explored alternative residues. After extensive testing, we identified C599 as a suitable site for spin labelling resulting in high-quality DEER data. The results from spin labelling at C599 have been incorporated into the revised manuscript.

      (3) On the other hand, DEER data for S525 is solid, as the authors stated. This residue is located on the luminal side of the enzyme. However, the description of the luminal side structure and the comparison of symmetric/asymmetric dimer in this par are missing in the paper. 

      We thank the viewer for their positive assessment of the S525R1 DEER data. The data for 525 and now also for 599 spin pairs are indeed solid given the strong visual oscillation we observed particularly in such a challenging system.   

      We presented the periplasmic sites in the crystal structure dimer (Figure 4A), highlighting both the symmetrical region and the asymmetric model in Figure 4. In the revised version, we include additional details about this region and our rationale for labeling at position S525.

      (4) The conclusion models (Figure 7) are misleading. In the crystal structure, the 5-6Loop distance between each monomer should be close given the location of the dimer interface, and the actual distance between T211 in the structure (for example, in 5lzq) is about 10A. Nevertheless, the model depicts this distance longer than S525 (40.7A in 5LZQ), which would give a false impression. 

      We would like to apologize for the misleading model. We have now corrected the models to ensure they are consistent with their respective regions in the crystal structures.

      (5) P8 last paragraph  

      It is hard to imagine that in a crystal lattice, the straight inhibitor always binds to monomer A, and the neighboring monomer is always attached to a slightly tilted inhibitor, which causes asymmetry. For example, wouldn't it mean that it would first bind to one of them, which would then affect the neighboring monomer via 5-6 Loop, which would then affect its binding pose? So in this case, the inhibitor did not ARAISE asymmetry, and this is where it is misleading for readers. 

      We apologize for the confusion. What we intended to convey is that the first inhibitor binds to one protomer, which then affects the conformation of the neighbouring monomer, ultimately influencing its binding pose. This is required for half-of-the-sites reactivity, which is well-established in this system. This is reflected in our crystal structure, where we observed asymmetry in the loop 5-6 region and the ETD orientation between the two protomers. We have addressed this in the manuscript accordingly.

      (6) P11 L4 EV10 instead of EV8? 

      Thanks for pointing out. We have corrected it accordingly.

      (7) P11 L5 It is difficult to determine whether the peak is broad or sharp. Should be evaluated quantitatively by showing the half-value width of the peak. This may also be helpful to judge whether the peak is a mixture of two components or a single one. 

      We have taken this analysis out and rephrased the offending sentence. We have also added the FWHM values as the Reviewer suggested, and corresponding standard deviations for the distance distributions (under approximation as Gaussian distribution).   

      (8) Throughout the paper, the topology of the enzyme may be difficult to follow for readers who are not experts in this field. Please indicate the membrane plane's location or a figure's viewpoint in the caption. 

      We acknowledge the importance of making our figures accessible to all readers. In the revised manuscript, we have enhanced the clarity of our figures by explicitly indicating the membrane plane’s location and specifying the viewpoint in each figure caption. For example, we have added annotations such as “Top view of the superposition of chain A (cyan) and chain B (wheat), showing the relative movements (black arrow) of helices. The membrane plane is indicated by dashed lines.”

      (9) Figure 2B Check the color of the helix.  

      IDP and ETD are almost the same color, so it is difficult to see the superposition. It would be easier to understand the reading by, for example, using a lighter or transparent color set only for IDPs.  

      We acknowledge the reviewer concern regarding the colour similarity between the IDP and ETD in Figure 2B, which hinders clear differentiation. To enhance visual distinction, we have adjusted the colour scheme by changing the TmPPase:IDP structure colour to light blue. This modification improves the clarity of the superposition, making the structural differences more discernible.

      (10) Figure 2C Check the coordination state (dotted line), there appears to be coordination between E217Cg and Mg. Also, water that is located near N492 appears to be a bit distant from Mg, why does this act as a ligand? Stereo view or view from different angles, and distance information would help the reader understand the bonding state in more detail.  

      Yes, we confirm that Mg<sup>2+</sup> is coordinated by the oxygen atoms from both the side chain and main chain of residue E217. The water molecule near N492 is not directly coordinated with Mg<sup>2+</sup> but interacts with the O5 atom of one of the phosphate groups in ETD. To enhance clarity, we have updated Figure 2C (and other related figures) to include stereo views.  

      (11) Figure 5A: in the Bottom view (lower left), the symmetric dimer does not look symmetric. Better to view from a 2-fold axis exactly.  

      We have taken this figure out entirely and instead add a direct comparison to the in silico predicted distribution from the asymmetric hybrid structure to all 16 experimental DEER distributions. We have added the symmetric and asymmetric structures to Fig. 4A and view the symmetric structure along the 2-fold axis, as suggested.   

      (12) Figure 5B: Indicate which data is plotted in the caption.  

      As mentioned above, we have taken this figure out, as we felt quantifying two overlapping populations from a single Gaussian was over-interpretation of the data, and at the suggestion of reviewer 3, we have tailored our interpretation here.  

      (13) Figure EV8:  

      Because the authors discuss a lot about their conclusive model based on this data, Figure EV8 should be treated as a main figure, not a supplement. However, this reviewer has serious concerns about the measurement in this figure. Because DEER for T211 is too noisy, I don't see the point in discussing this in detail. For example, in the Ca/ETD data, there is a peak near 50A, but it would be difficult for TM5 to move away from this distance unless the protein unfolds. I do not find it meaningful to discuss using measurement results in which such an impossible distance is detected as a peak.  

      A: Show top view as in Figure 5  

      D: 2nd row dotted line. Regarding the in silico model that is used as a reference to compare the distance information, the distance of 40-50 A for T211 in the Ca-bound form is hard to imagine. PDB 4av6 model shows that T211 is disordered and not visible, but given the position of the TM5 helix, it does not appear to be that different from the IDR binding structure (5LZQ, 10A between two T211). The structures of in silico models are not shown in the figure, as it is only mentioned as modeled in Rossetafold. Please indicate their structures, especially focused on the relative orientation of T211 and S525 in the dimer, which would allow readers to determine the distances.  

      We acknowledge the reviewer’s concerns regarding Figure EV8 and the DEER data for T211R1. Upon re-evaluation, we recognize that the non-oscillating nature of the DEER data for T211R1 leads to broad distributions, indicating increased conformational dynamics, which is expected for a highly dynamic loop. Consequently, we have limited the discussion and interpretation of T211R1 in the revised manuscript and focused more on C599R1.

      Reviewer #3 (Recommendations for the authors):  

      A careful interpretation of the data in view of these limitations and without directly linking to asymmetry could solve the problem of the over-interpretation of the DEER data.  

      We respectfully disagree with the reviewer. Please see our detailed response above.  

      Additional comments:  

      (1) Did the authors use a Cys-less construct for spin labeling and DEER experiments?  

      We utilized a nearly Cys-less construct in which all native cysteines were mutated to serine, except for Cys183, which was retained due to its buried location and functional importance. We then introduced single cysteine mutations for spin labelling. For C599, Ser599 was reverted to cysteine.

      (2) The time data for position T211R1 is too short for most cases (Figure EV8D) for a reliable distance determination. No confidence interval is given for the '+Ca' sample distance distributions.  

      We recorded longer time traces for two of the conditions to better assign the background. We did not use the 211R1 data to reach any conclusions regarding asymmetry, which were based on the 525R1 and the 599R1 data. We now simply include T211R1 data to indicate the high mobility observed at loop5-6. We have added the confidence interval for the +Ca condition.  

      (3) It is recommended to mention the 2+1 artefact obvious at the end of the DEER data. 

      In the methods section, we have mentioned that the “2+1” artefact present at the end of the S525R1, and T211R1 DEER data likely arises from using a 65 MHz offset, rather than an 80 MHz offset (as for the C599R1 data), which avoids significant overlap of the pump and detection pulses. We also mention in the methods section that owing to the intense “2+1” artefact, the decision was made to truncate the artefact away, to minimise the impact on data treatment. As for motivation to use the lower offset of 65 MHz, we did so to maximise the achievable signal-to-noise ratio (SNR), as particularly for the T211R1 data, the detected echo was quite weak. This was further exacerbated by the poor transverse relaxation time observed at that site.  

      (4) Please check the number of significant digits for all the reported values. 

      We have addressed the number of significant digits as requested.

      (5) Please report the mean distances from DEER experiments with the standard deviation or FWHM.

      We have addressed this in the revised manuscript, we report modal distances rather than the mean distances and provide the FWHM and standard deviation.

    1. Author response:

      Reviewer #1 (Public Review):

      In this manuscript, Tran et al. investigate the interaction between BICC1 and ADPKD genes in renal cystogenesis. Using biochemical approaches, they reveal a physical association between Bicc1 and PC1 or PC2 and identify the motifs in each protein required for binding. Through genetic analyses, they demonstrate that Bicc1 inactivation synergizes with Pkd1 or Pkd2 inactivation to exacerbate PKD-associated phenotypes in Xenopus embryos and potentially in mouse models. Furthermore, by analyzing a large cohort of PKD patients, the authors identify compound BICC1 variants alongside PKD1 or PKD2 variants in trans, as well as homozygous BICC1 variants in patients with early-onset and severe disease presentation. They also show that these BICC1 variants repress PC2 expression in cultured cells.

      Overall, the concept that BICC1 variants modify PKD severity is plausible, the data are robust, and the conclusions are largely supported. However, several aspects of the study require clarification and discussion:

      (1) The authors devote significant effort to characterizing the physical interaction between Bicc1 and Pkd2. However, the study does not examine or discuss how this interaction relates to Bicc1's well-established role in posttranscriptional regulation of Pkd2 mRNA stability and translation efficiency.

      The reviewer is correct that the present study has not addressed the downstream consequences of this interaction considering that Bicc1 is a posttranscriptional regulator of Pkd2 (and potentially Pkd1). We think that the complex of Bicc1/Pkd1/Pkd2 retains Bicc1 in the cytoplasm and thus restrict its activity in participating in posttranscriptional regulation. As we do not have yet experimental data to support this model, we have not included this model in the manuscript. Yet, we will update the discussion of the manuscript to further elaborate on the potential mechanism of the Bicc1/Pkd1/Pkd2 complex.

      (2) Bicc1 inactivation appears to downregulate Pkd1 expression, yet it remains unclear whether Bicc1 regulates Pkd1 through direct interaction or by antagonizing miR-17, as observed in Pkd2 regulation. This should be further examined or discussed.

      This is a very interesting comment. The group of Vishal Patel published that PKD1 is regulated by a mir-17 binding site in its 3’UTR (PMID: 35965273). We, however, have not evaluated whether BICC1 participates in this regulation. A definitive answer would require us utilize some of the mice described in above reference, which is beyond the scope of this manuscript. We, however, will revise the discussion to elaborate on this potential mechanism.

      (3) The evidence supporting Bicc1 and ADPKD gene cooperativity, particularly with Pkd1, in mouse models is not entirely convincing, likely due to substantial variability and the aggressive nature of Bpk/Bpk mice. Increasing the number of animals or using a milder Bicc1 strain, such as jcpk heterozygotes, could help substantiate the genetic interaction.

      We have initially performed the analysis using our Bicc1 complete knockout, we previously reported on (PMID 20215348) focusing on compound heterozygotes. Yet, like the Pkd1/Pkd2 compound heterozygotes (PMID 12140187) no cyst development was observed until we sacrificed the mice at P21. Our strain is similar to the above mentioned jcpk, which is characterized by a short, abnormal transcript thought to result in a null allele (PMID: 12682776). We thank the reviewer for pointing use to the reference showing the heterozygous mice show glomerular cysts in the adults (PMID: 7723240). This suggestion is an interesting idea we will investigate. In general, we agree with the reviewer that the better understanding the contribution of Bicc1 to the adult PKD phenotype will be critical. To this end, we are currently generating a floxed allele of Bicc1 that will allow us to address the cooperativity in the adult kidney, when e.g. crossed to the Pkd1<sup>RC/RC</sup> mice. Yet, these experiments are unfortunately beyond the scope of this manuscript.

      Reviewer #2 (Public Review):

      Tran and colleagues report evidence supporting the expected yet undemonstrated interaction between the Pkd1 and Pkd2 gene products Pc1 and Pc2 and the Bicc1 protein in vitro, in mice, and collaterally, in Xenopus and HEK293T cells. The authors go on to convincingly identify two large and non-overlapping regions of the Bicc1 protein important for each interaction and to perform gene dosage experiments in mice that suggest that Bicc1 loss of function may compound with Pkd1 and Pkd2 decreased function, resulting in PKD-like renal phenotypes of different severity. These results led to examining a cohort of very early onset PKD patients to find three instances of co-existing mutations in PKD1 (or PKD2) and BICC1. Finally, preliminary transcriptomics of edited lines gave variable and subtle differences that align with the theme that Bicc1 may contribute to the PKD defects, yet are mechanistically inconclusive.

      These results are potentially interesting, despite the limitation, also recognized by the authors, that BICC1 mutations seem exceedingly rare in PKD patients and may not "significantly contribute to the mutational load in ADPKD or ARPKD". The manuscript has several intrinsic limitations that must be addressed.

      As mentioned above, the study was designed to explore whether there is an interaction between BICC1 and the PKD1/PKD2 and whether this interaction is functionally important. How this translates into the clinical relevance will require additional studies (and we have addressed this in the discussion of the manuscript).

      The manuscript contains factual errors, imprecisions, and language ambiguities. This has the effect of making this reviewer wonder how thorough the research reported and analyses have been.

      We respectfully disagree with the reviewer on the latter interpretation. The study was performed with rigor. We have carefully assessed the critiques raised by the reviewer. Most of the criticisms raised by the reviewer will be easily addressed in the revised version of the manuscript. Yet, none of the critiques raised by the reviewer seems to directly impact the overall interpretation of the data.

      Reviewer #3 (Public Review):

      Summary:

      This study investigates the role of BICC1 in the regulation of PKD1 and PKD2 and its impact on cytogenesis in ADPKD. By utilizing co-IP and functional assays, the authors demonstrate physical, functional, and regulatory interactions between these three proteins.

      Strengths:

      (1) The scientific principles and methodology adopted in this study are excellent, logical, and reveal important insights into the molecular basis of cystogenesis.

      (2) The functional studies in animal models provide tantalizing data that may lead to a further understanding and may consequently lead to the ultimate goal of finding a molecular therapy for this incurable condition.

      (3) In describing the patients from the Arab cohort, the authors have provided excellent human data for further investigation in large ADPKD cohorts. Even though there was no patient material available, such as HUREC, the authors have studied the effects of BICC1 mutations and demonstrated its functional importance in a Xenopus model.

      Weaknesses:

      This is a well-conducted study and could have been even more impactful if primary patient material was available to the authors. A further study in HUREC cells investigating the critical regulatory role of BICC1 and potential interaction with mir-17 may yet lead to a modifiable therapeutic target.

      This is an excellent suggestion. We agree with the reviewer that it would have been interesting to analyze HUREC material from the affected patients. Unfortunately, besides DNA and the phenotypic analysis described in the manuscript neither human tissue nor primary patient-derived cells collected before the two patients with the BICC1 p.Ser240Pro mutation passed away. To address this missing link, we have – as a first pass - generated HEK293T cells carrying the BICC1 p.Ser240Pro variant. While these admittingly are not kidney epithelial cells, they indeed show a reduced level of PC2 expression. These data are shown in the manuscript. We have not yet addressed how this relates to its crosstalk with miR-17.

      Conclusion:

      The authors achieve their aims. The results reliably demonstrate the physical and functional interaction between BICC1 and PKD1/PKD2 genes and their products.

      The impact is hopefully going to be manifold:

      (1) Progressing the understanding of the regulation of the expression of PKD1/PKD2 genes.

      (2) Role of BiCC1 in mir/PKD1/2 complex should be the next step in the quest for a modifiable therapeutic target.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Filamentous fungi are established workhorses in biotechnology, with Aspergillus oryzae as a prominent example with a thousand-year history. Still, the cell biology and biochemical properties of the production strains is not well understood. The paper of the Takeshita group describes the change in nuclear numbers and correlates it to different production capacities. They used microfluidic devices to really correlate the production with nuclear numbers. In addition, they used microdissection to understand expression profile changes and found an increase in ribosomes. The analysis of two genes involved in cell volume control in S. pombe did not reveal conclusive answers to explain the phenomenon. It appears that it is a multi-trait phenotype. Finally, they identified SNPs in many industrial strains and tried to correlate them to the capability of increasing their nuclear numbers.

      The methods used in the paper range from high-quality cell biology, Raman spectroscopy, to atomic force and electron microscopy, and from laser microdissection to the use of microfluidic devices to study individual hyphae.

      This is a very interesting, biotechnologically relevant paper with the application of excellent cell biology. I have only minor suggestions for improvement.

      We sincerely appreciate your fair and positive evaluation of our work. Thank you for your suggestions for improvement. We respond to each of them appropriately.

      Reviewer #2 (Public review):

      Summary:

      In the study presented by Itani and colleagues, it is shown that some strains of Aspergillus oryzae - especially those used industrially for the production of sake and soy sauce - develop hyphae with a significantly increased number of nuclei and cell volume over time. These thick hyphae are formed by branching from normal hyphae and grow faster and therefore dominate the colonies. The number of nuclei positively correlates with the thicker hyphae and also the amount of secreted enzymes. The addition of nutrients such as yeast extract or certain amino acids enhanced this effect. Genome and transcriptome analyses identified genes, including rseA, that are associated with the increased number of nuclei and enzyme production. The authors conclude from their data involvement of glycosyltransferases, calcium channels, and the tor regulatory cascade in the regulation of cell volume and number of nuclei. Thicker hyphae and an increased number of nuclei were also observed in high-production strains of other industrially used fungi such as Trichoderma reesei and Penicillium chrysogenum, leading to the hypothesis that the mentioned phenotypes are characteristic of production strains, which is of significant interest for fungal biotechnology.

      Strengths:

      The study is very comprehensive and involves the application of diverse state-of-the-art cell biological, biochemical, and genetic methods. Overall, the data are properly controlled and analyzed, figures and movies are of excellent quality.

      The results are particularly interesting with regard to the elucidation of molecular mechanisms that regulate the size of fungal hyphae and their number of nuclei. For this, the authors have discovered a very good model: (regular) strains with a low number of nuclei and strains with a high number of nuclei. Also, the results can be expected to be of interest for the further optimization of industrially relevant filamentous fungi.

      Weaknesses:

      There are only a few open questions concerning the activity of the many nuclei in production strains (active versus inactive), their number of chromosomes (haploid/diploid), and whether hyper-branching always leads to propagation of nuclei.

      We are very grateful for your recognition of our findings, the proposed model, and their significance for future applications. We are grateful for the questions, which contribute to a more accurate understanding.

      Our responses to each are provided below. Necessary experiments are in progress.

      Reviewer #3 (Public review):

      Summary:

      The authors seek to determine the underlying traits that support the exceptional capacity of Aspergillus oryzae to secrete enzymes and heterologous proteins. To do so, they leverage the availability of multiple domesticated isolates of A. oryzae along with other Aspergillus species to perform comparative imaging and genomic analysis.

      Strengths:

      The strength of this study lies in the use of multifaceted approaches to identify significant differences in hyphal morphology that correlate with enzyme secretion, which is then followed by the use of genomics to identify candidate functions that underlie these differences.

      Weaknesses:

      There are aspects of the methods that would benefit from the inclusion of more detail on how experiments were performed and data interpreted.

      Overall, the authors have achieved their aims in that they are able to clearly document the presence of two distinct hyphal forms in A. oryzae and other Aspergillus species, and to correlate the presence of the thicker, rapidly growing form with enhanced enzyme secretion. The image analysis is convincing. The discovery that the addition of yeast extract and specific amino acids can stimulate the formation of the novel hyphal form is also notable. Although the conclusions are generally supported by the results, this is perhaps less so for the genetic analysis as it remains unclear how direct the role of RseA and the calcium transporters might be in supporting the formation of the thicker hyphae.

      The results presented here will impact the field. The complexity of hyphal morphology and how it affects secretion is not well understood despite the importance of these processes for the fungal lifestyle. In addition, the description of approaches that can be used to facilitate the study of these different hyphal forms (i.e., stimulation using yeast extract or specific amino acids) will benefit future efforts to understand the molecular basis of their formation.

      We are very grateful for your fair and thoughtful evaluation of our work. We agree that the genetic analysis in the latter part is relatively weaker compared to the imaging analysis in the first half. Rather than a single mutation causing a dramatic phenotypic change, we believe that the accumulation of various mutations through breeding leads to the observed phenotype, making it difficult to clearly demonstrate causality. Since transcriptome and SNP analyses have revealed key pathways and phenotypes, it would be gratifying if these insights could contribute to future applications utilizing filamentous fungi.

    1. Author response:

      (1) General Statements

      As you will see in our attached rebuttal to the reviewers, we have added several new experiments and revised manuscript to fully address their concerns.

      (2) Point-by-point description of the revisions

      Reviewer #1:

      Evidence, reproducibility and clarity

      Summary:

      The manuscript by Yang et al. describes a new CME accessory protein. CCDC32 has been previously suggested to interact with AP2 and in the present work the authors confirm this interaction and show that it is a bona fide CME regulator. In agreement with its interaction with AP2, CCDC32 recruitment to CCPs mirrors the accumulation of clathrin. Knockdown of CCDC32 reduces the amount of productive CCPs, suggestive of a stabilisation role in early clathrin assemblies. Immunoprecipitation experiments mapped the interaction of CCDC42 to the α-appendage of the AP2 complex α-subunit. Finally, the authors show that the CCDC32 nonsense mutations found in patients with cardio-facial-neuro-developmental syndrome disrupt the interaction of this protein to the AP2 complex. The manuscript is well written and the conclusions regarding the role of CCDC32 in CME are supported by good quality data. As detailed below, a few improvements/clarifications are needed to reinforce some of the conclusions, especially the ones regarding CFNDS.

      We thank the referee for their positive comments. In light of a recently published paper describing CCDC32 as a co-chaperone required for AP2 assembly (Wan et al., PNAS, 2024, see reviewer 2), we have added several additional experiments to address all concerns and consequently gained further insight into CCDC32-AP2 interactions and the important dual role of CCDC32 in regulating CME. 

      Major comments:

      (1) Why did the protein could just be visualized at CCPs after knockdown of the endogenous protein? This is highly unusual, especially on stable cell lines. Could this be that the tag is interfering with the expressed protein function rendering it incapable of outcompeting the endogenous? Does this points to a regulated recruitment?

      The reviewer is correct, this would be unusual; however, it is not the case. We misspoke in the text (although the figure legend was correct) these experiments were performed without siRNA knockdown and we can indeed detect eGFP-CCDC32 being recruited to CCPs in the presence of endogenous protein. Nonetheless, we repeated the experiment to be certain (see Author response image 1).  

      Author response image 1.

      Cohort-averaged fluorescence intensity traces of CCPs (marked with mRuby-CLCa) and CCP-enriched eGFPCCDC32(FL).

      (2) The disease mutation used in the paper does not correspond to the truncation found in patients. The authors use an 1-54 truncation, but the patients described in Harel et al. have frame shifts at the positions 19 (Thr19Tyrfs*12) and 64 (Glu64Glyfs*12), while the patient described in Abdalla et al. have the deletion of two introns, leading to a frameshift around amino acid 90. Moreover, to be precisely test the function of these disease mutations, one would need to add the extra amino acids generated by the frame shift. For example, as denoted in the mutation description in Harel et al., the frameshift at position 19 changes the Threonine 19 to a Tyrosine and ads a run of 12 extra amino acids (Thr19Tyrfs*12).

      The label of the disease mutant p.(Thr19Tyrfs12) and p.(Glu64Glyfs12) is based on a 194aa polypeptide version of CCDC32 initiated at a nonconventional start site that contains a 9 aa peptide (VRGSCLRFQ) upstream of the N-terminus we show. Thus, we are indeed using the appropriate mutation site (see: https://www.uniprot.org/uniprotkb/Q9BV29/entry). The reviewer is correct that we have not included the extra 12 aa in our construct; however as these residues are not present in the other CFNDS mutants, we think it unlikely that they contribute to the disease phenotype.  Rather, as neither of the clinically observed mutations contain the 78-98 aa sequence required for AP2 binding and CME function, we are confident that this defect contributed to the disease. Thus, we are including the data on the CCDC32(1-54) mutant, as we believe these results provide a valuable physiological context to our studies. 

      (3) The frameshift caused by the CFNDS mutations (especially the one studied) will likely lead to nonsense mediated RNA decay (NMD). The frameshift is well within the rules where NMD generally kicks in. Therefore, I am unsure about the functional insights of expressing a diseaserelated protein which is likely not present in patients.

      We thank the reviewer for bringing up this concern. However, as shown in new Figure S1, the mutant protein is expressed at comparable levels as the WT, suggesting that NMD is not occurring.

      (4) Coiled coils generally form stable dimers. The typically hydrophobic core of these structures is not suitable for transient interactions. This complicates the interpretation of the results regarding the role of this region as the place where the interaction to AP2 occurs. If the coiled coil holds a stable CCDC32 dimer, disrupting this dimer could reduce the affinity to AP2 (by reduced avidity) to the actual binding site. A construct with an orthogonal dimeriser or a pulldown of the delta78-98 protein with of the GST AP2a-AD could be a good way to sort this issue.

      We were unable to model a stable dimer (or other oligomer) of this protein with high confidence using Alphafold 3.0. Moreover, we were unable to detect endogenous CCDC32 coimmunoprecipitating with eGFP-CCDC32 (Fig. S6C). Thus, we believe that the moniker, based solely on the alpha-helical content of the protein is a misnomer.  We have explained this in the main text.

      Minor comments:

      (1) The authors interchangeably use the term "flat CCPs" and "flat clathrin lattices". While these are indeed related, flat clathrin lattices have been also used to refer to "clathrin plaques". To avoid confusion, I suggest sticking to the term "flat CCPs" to refer to the CCPs which are in their early stages of maturation.

      Agreed. Thank you for the suggestion. We have renamed these structures flat clathrin assemblies, as they do not acquire the curvature needed to classify them as pits, and do not grow to the size that would classify then as plaques. 

      Significance

      General assessment:

      CME drives the internalisation of hundreds of receptors and surface proteins in practically all tissues, making it an essential process for various physiological processes. This versatility comes at the cost of a large number of molecular players and regulators. To understand this complexity, unravelling all the components of this process is vital. The manuscript by Yang et al. gives an important contribution to this effort as it describes a new CME regulator, CCDC32, which acts directly at the main CME adaptor AP2. The link to disease is interesting, but the authors need to refine their experiments. The requirement for endogenous knockdown for recruitment of the tagged CCDC32 is unusual and requires further exploration.

      Advance:

      The increased frequency of abortive events presented by CCDC32 knockdown cells is very interesting, as it hints to an active mechanism that regulates the stabilisation and growth of clathrin coated pits. The exact way clathrin coated pits are stabilised is still an open question in the field.

      Audience:

      This is a basic research manuscript. However, given the essential role of CME in physiology and the growing number of CME players involved in disease, this manuscript can reach broader audiences.

      We thank the referee for recognizing the ‘interesting’ advances our studies have made and for considering these studies as ‘an important contribution’ to ‘an essential process for various physiological processes’ and able ‘to reach broader audiences’. We have addressed and reconciled the reviewer’s concerns in our revised manuscript. 

      Field of expertise of the reviewer:

      Clathrin mediated endocytosis, cell biology, microscopy, biochemistry.

      Reviewer #2:

      Evidence, reproducibility and clarity

      In this manuscript, the authors demonstrate that CCDC32 regulates clathrin-mediated endocytosis (CME). Some of the findings are consistent with a recent report by Wan et al. (2024 PNAS), such as the observation that CCDC32 depletion reduces transferrin uptake and diminishes the formation of clathrin-coated pits. The primary function of CCDC32 is to regulate AP2 assembly, and its depletion leads to AP2 degradation. However, this study did not examine AP2 expression levels. CCDC32 may bind to the appendage domain of AP2 alpha, but it also binds to the core domain of AP2 alpha.

      We thank the reviewer for drawing our attention to the Wan et al. paper, that appeared while this work was under review.  However, our in vivo data are not fully consistent with the report from Wan et al. The discrepancies reveal a dual function of CCDC32 in CME that was masked by complete knockout vs siRNA knockdown of the protein, and also likely affected by the position of the GFP-tag (C- vs N-terminal) on this small protein. Thus:

      -  Contrary to Wan et al., we do not detect any loss of AP2 expression (see new Figure S3A-B) upon siRNA knockdown. Most likely the ~40% residual CCDC32 present after siRNA knockdown is sufficient to fulfill its catalytic chaperone function but not its structural role in regulating CME beyond the AP2 assembly step.  

      - Contrary to Wan et al., we have shown that CCDC32 indeed interacts with intact AP2 complex (Figure S3C and 6B,C) showing that all 4 subunits of the AP2 complex co-IP with full length eGFP-CCDC32. Interestingly, whereas the full length CCDC32 pulls down the intact AP2 complex, co-IP of the ∆78-98 mutant retains its ability to pull down the β2-µ2 hemicomplex, its interactions with α:σ2 are severely reduced.  While this result is consistent with the report of Wan et al that CCDC32 binds to the α:σ2 hemi-complex, it also suggests that the interactions between CCDC32 and AP2 are more complex and will require further studies.

      - Contrary to Wan et al., we provide strong evidence that CCDC32 is recruited to CCPs. Interestingly, modeling with AlphaFold 3.0 identifies a highly probably interaction between alpha helices encoded by residues 66-91 on CCDC32 and residues 418-438 on α. The latter are masked by µ2-C in the closed confirmation of the AP2 core, but exposed in the open confirmation triggered by cargo binding, suggesting that CCDC32 might only bind to membrane-bound AP2.

      Thus, our findings are indeed novel and indicate striking multifunctional roles for CCDC32 in CME, making the protein well worth further study. 

      (1) Besides its role in AP2 assembly, CCDC32 may potentially have another function on the membrane. However, there is no direct evidence showing that CCDC32 associates with the plasma membrane.

      We disagree, our data clearly shows that CCDC32 is recruited to CCPs (Fig. 1B) and that CCPs that fail to recruit CCDC32 are short-lived and likely abortive (Fig. 1C). Wan et al. did not observe any colocalization of C-terminally tagged CCDC32 to CCPs, whereas we detect recruitment of our N-terminally tagged construct, which we also show is functional (Fig. 6F).  Further, we have demonstrated the importance of the C-terminal region of CCDC32 in membrane association (see new Fig. S7).  Thus, we speculate that a C-terminally tagged CCDC32 might not be fully functional. Indeed, SIM images of the C-terminally-tagged CCDC32 in Wan et al., show large (~100 nm) structures in the cytosol, which may reflect aggregation. 

      (2) CCDC32 binds to multiple regions on AP2, including the core domain. It is important to distinguish the functional roles of these different binding sites.

      We have localized the AP2-ear binding region to residues 78-99 and shown these to be critical for the functions we have identified. As described above we now include data that are complementary to those of Wan et al. However, our data also clearly points to additional binding modalities. We agree that it will be important and map these additional interactions and identify their functional roles, but this is beyond the scope of this paper.  

      (3) AP2 expression levels should be examined in CCDC32 depleted cells. If AP2 is gone, it is not surprising that clathrin-coated pits are defective.

      Agreed and we have confirmed this by western blotting (Figure S3A-B) and detect no reduction in levels of any of the AP2 subunits in CCDC32 siRNA knockdown cells. As stated above this could be due to residual CCDC32 present in the siRNA KD vs the CRISPR-mediated gene KO.

      (4) If the authors aim to establish a secondary function for CCDC32, they need to thoroughly discuss the known chaperone function of CCDC32 and consider whether and how CCDC32 regulates a downstream step in CME.

      Agreed. We have described the Wan et al paper, which came out while our manuscript was in review, in our Introduction.  As described above, there are areas of agreement and of discrepancies, which are thoroughly documented and discussed throughout the revised manuscript.  

      (5) The quality of Figure 1A is very low, making it difficult to assess the localization and quantify the data.

      The low signal:noise in Fig. 1A the reviewer is concerned about is due to a diffuse distribution of CCDC32 on the inner surface of the plasma membrane. We now, more explicitly describe this binding, which we believe reflects a specific interaction mediated by the C-terminus of CCDC32; thus the degree of diffuse membrane binding we observe follows: eGFP-CCDC32(FL)> eGFPCCDC32(∆78-98)>eGFP-CCDC32(1-54)~eGFP/background (see new Fig. S7). Importantly, the colocalization of CCDC32 at CCPs is confirmed by the dynamic imaging of CCPs (Fig 1B).

      (6) In Figure 6, why aren't AP2 mu and sigma subunits shown?

      Agreed. Not being aware of CCDC32’s possible dual role as a chaperone, we had assumed that the AP2 complex was intact.  We have now added this data in Figure 6 B,C and Fig. S3C, as discussed above. 

      Page 5, top, this sentence is confusing: "their surface area (~17 x 10 nm<sup>2</sup>) remains significantly less than that required for the average 100 nm diameter CCV (~3.2 x 103 nm<sup>2</sup>)."

      Thank you for the criticism. We have clarified the sentence and corrected a typo, which would definitely be confusing.  The section now reads,  “While the flat CCSs we detected in CCDC32 knockdown cells were significantly larger than in control cells (Fig. 4D, mean diameter of 147 nm vs. 127 nm, respectively), they are much smaller than typical long-lived flat clathrin lattices (d≥300 nm)(Grove et al., 2014). Indeed, the surface area of the flat CCSs that accumulate in CCDC32 KD cells (mean ~1.69 x 10<sup>4</sup> nm<sup>2</sup>) remains significantly less than the surface area of an average 100 nm diameter CCV (~3.14 x 10<sup>4</sup> nm<sup>2</sup>). Thus, we refer to these structures as ‘flat clathrin assemblies’ because they are neither curved ‘pits’ nor large ‘lattices’. Rather, the flat clathrin assemblies represent early, likely defective, intermediates in CCP formation.” 

      Significance

      Overall, while this work presents some interesting ideas, it remains unclear whether CCDC32 regulates AP2 beyond the assembly step.

      Our responses above argue that we have indeed established that CCDC32 regulates AP2 beyond the assembly step. We have also identified several discrepancies between our findings and those reported by Wan et al., most notably binding between CCDC32 and mature AP2 complexes and the AP2-dependent recruitment of CCDC32 to CCPs.  It is possible that these discrepancies may be due to the position of the GFP tag (ours is N-terminal, theirs is C-terminal; we show that the N-terminal tagged CCDC32 rescues the knockdown phenotype, while Wan et al., do not provide evidence for functionality of the C-terminal construct). 

      Reviewer #3: 

      Evidence, reproducibility and clarity (Required): 

      In this manuscript, Yang et al. characterize the endocytic accessory protein CCDC32, which has implications in cardio-facio-neuro-developmental syndrome (CFNDS). The authors clearly demonstrate that the protein CCDC32 has a role in the early stages of endocytosis, mainly through the interaction with the major endocytic adaptor protein AP2, and they identify regions taking part in this recognition. Through live cell fluorescence imaging and electron microscopy of endocytic pits, the authors characterize the lifetimes of endocytic sites, the formation rate of endocytic sites and pits and the invagination depth, in addition to transferrin receptor (TfnR) uptake experiments. Binding between CCDC32 and CCDC32 mutants to the AP2 alpha appendage domain is assessed by pull down experiments. Together, these experiments allow deriving a phenotype of CCDC32 knock-down and CCDC32 mutants within endocytosis, which is a very robust system, in which defects are not so easily detected. A mutation of CCDC32, known to play a role in CFNDS, is also addressed in this study and shown to have endocytic defects.

      We thank the reviewer for their positive remarks regarding the quality of our data and the strength of our conclusions.  

      In summary, the authors present a strong combination of techniques, assessing the impact of CCDC32 in clathrin mediated endocytosis and its binding to AP2, whereby the following major and minor points remain to be addressed: 

      - The authors show that CCDC32 depletion leads to the formation of brighter and static clathrin coated structures (Figure 2), but that these were only prevalent to 7.8% and masked the 'normal' dynamic CCPs. At the same time, the authors show that the absence of CCDC32 induces pits with shorter life times (Figure 1 and Figure 2), the 'majority' of the pits.

      Clarification is needed as to how the authors arrive at these conclusions and these numbers. The authors should also provide (and visualize) the corresponding statistics. The same statement is made again later on in the manuscript, where the authors explain their electron microscopy data. Was the number derived from there? 

      These points are critical to understanding CCDC32's role in endocytosis and is key to understanding the model presented in Figure 8. The numbers of how many pits accumulate in flat lattices versus normal endocytosis progression and the actual time scales could be included in this model and would make the figure much stronger. 

      Thank you for these comments.  We understand the paradox between the visual impression and the reality of our dynamic measurements. We have been visually misled by this in previous work (Chen et al., 2020), which emphasizes the importance of unbiased image analysis afforded to us through the well-documented cmeAnalysis pipeline, developed by us (Aguet et al., 2013) and now used by many others (e.g. (He et al., 2020)). 

      The % of static structures was not derived from electron microscopy data, but quantified using cmeAnalysis, which automatedly provides the lifetime distribution of CCPs. We have now clarified this in the manuscript and added a histogram (Fig. S4) quantifying the fraction of CCPs in lifetime cohorts  <20s, 21-60s, 61-100s, 101-150s and >150s (static). 

      - In relation to the above point, the statistics of Figure 2E-G and the analysis leading there should also be explained in more detail: For example, what are the individual points in the plot (also in Figures 6G and 7G)? The authors should also use a few phrases to explain software they use, for example DASC, in the main text. 

      Each point in these bar graphs represents a movie, where n≥12. These details have been added to the respective figure legend. We have also added a brief description of DASC analysis in the text. 

      -  There are several questions related to the knock-down experiments that need to be addressed:

      Firstly, knock-down of CCDC32 does not seem to be very strong (Figure S2B). Can the level of knock-down be quantified? 

      We have now quantified the KD efficiency. It is ~60%. This turns out to be fortuitous (see responses to reviewer 2), as a recent publication, which came out after we completed our study, has shown by CRISPR-mediated knockout, that CCD32 also plays an essential chaperone function required for AP2 assembly.  We do not see any reduction in AP2 levels or its complex formation under our conditions (see new Supplemental Figure S3), which suggests that the effects of CCDC32 on CCP dynamics are more sensitive to CCDC32 concentration than its roles as a chaperone. Our phenotypes would have been masked by more efficient depletion of CCDC32.  

      In page 6 it is indicated that the eGFP-CCDC32(1-54) and eGFP-CCDC32(∆78-98) constructs are siRNA-resistant. However in Fig S2B, these proteins do not show any signal in the western blot, so it is not clear if they are expressed or simply not detected by the antibody. The presence of these proteins after silencing endogenous CCDC32 needs to be confirmed to support Figures 6 and Figures 7, which critically rely on the presence of the CCDC32 mutants. 

      Unfortunately, the C-terminally truncated CCDC32 proteins are not detected because they lack the antibody epitope, indeed even the ∆78-98 deletion is poorly detected (compare the GFP blot in new S1A with the anti-CCDC32 blot in S1B).  However, these constructs contain the same siRNA-resistance mutation as the full length protein. That they are expressed and siRNA resistant can be seen in Fig. S2A (now Fig. S1A) blotting for GFP.

      In Figures 6 and 7, siRNA knock-down of CCDC32 is only indicated for sub-figures F to G. Is this really the case? If not, the authors should clarify. The siRNA knock-down in Figure 1 is also only mentioned in the text, not in the figure legend. The authors should pay attention to make their figure legends easy to understand and unambiguous. 

      No, it is not the case.  Thank you for pointing out the uncertainty. We have added these details to the Figure legends and checked all Figure legends to ensure that they clearly describe the data shown.  

      - It is not exactly clear how the curves in Figure 3C (lower panel) on the invagination depth were obtained. Can the authors clarify this a bit more? For example, what are kT and kE in Figure 3A? What is I0? And how did the authors derive the logarithmic function used to quantify the invagination depth? In the main text, the authors say that the traces were 'logarithmically transformed'. This is not a technical term. The authors should refer to the actual equation used in the figure. 

      This analysis was developed by the Kirchhausen lab (Saffarian and Kirchhausen, 2008). We have added these details and reference them in the Figure legend and in the text. We also now use the more accurate descriptor ‘log-transformed’.

      - In the discussion, the claim 'The resulting dysregulation of AP2 inhibits CME, which further results in the development of CFNDS.' is maybe a bit too strong of a statement. Firstly, because the authors show themselves that CME is perturbed, but by no means inhibited. Secondly, the molecular link to CFNDS remains unclear. Even though CCDC32 mutants seem to be responsible for CFNDS and one of the mutant has been shown in this study to have a defect in endocytosis and AP2 binding, a direct link between CCDC32's function in endocytosis and CFNDS remains elusive. The authors should thus provide a more balanced discussion on this topic. 

      We have modified and softened our conclusions, which now read that the phenotypes we see likely “contribute to” rather than “cause” the disease.

      - In Figure S1, the authors annotate the presence of a coiled-coil domain, which they also use later on in the manuscript to generate mutations. Could the authors specify (and cite) where and how this coiled-coil domain has been identified? Is this predicted helix indeed a coiled-coil domain, or just a helix, as indicated by the authors in the discussion?

      See response to Reviewer 1, point 4.  We have changed this wording to alpha-helix. The ‘coiled-coil’ reference is historical and unlikely a true reflection of CCDC32 structure. AlphaFold 3.0 predictions were unable to identify with certainly any coiled-coil structures, even if we modelled potential dimers or trimers; and we find no evidence of dimerization of CCDC32 in vivo. We have clarified this in the text.

      Minor comments

      - In general, a more detailed explanation of the microscopy techniques used and the information they report would be beneficial to provide access to the article also to non-expert readers in the field. This concerns particularly the analysis methods used, for example: 

      How were the cohort-averaged fluorescence intensity and lifetime traces obtained? 

      How do the tools cmeAnalysis and DASC work? A brief explanation would be helpful. 

      We have expanded Methods to add these details, and also described them in the main text. 

      - The axis label of Figure 2B is not quite clear. What does 'TfnR uptake % of surface bound' mean? Maybe the authors could explain this in more detail in the figure legend? Is the drop in uptake efficiency also accessible by visual inspection of the images? It would be interesting to see that. 

      This is a standard measure of CME efficiency. 'TfnR uptake % of surface bound' = Internalized TfnR/Surface bound TfnR. Again, images may be misleading as defects in CME lead to increased levels of TfnR on the cell surface, which in turn would result in more Tfn uptake even if the rate of CME is decreased.

      - Figure 4: How is the occupancy of CCPs in the plasma membrane measured? What are the criteria used to divide CCSs into Flat, Dome or Sphere categories? 

      We have expanded Methods to add these details. Based on the degree of invagination, the shapes of CCSs were classified as either: flat CCSs with no obvious invagination; dome-shaped CCSs that had a hemispherical or less invaginated shape with visible edges of the clathrin lattice; and spherical CCSs that had a round shape with the invisible edges of clathrin lattice in 2D projection images. In most cases, the shapes were obvious in 2D PREM images. In uncertain cases, the degree of CCS invagination was determined using images tilted at ±10–20 degrees. The area of CCSs were measured using ImageJ and used for the calculation of the CCS occupancy on the plasma membrane.

      - Figure 5B: Can the authors explain, where exactly the GFP was engineered into AP2 alpha? This construct does not seem to be explained in the methods section. 

      We have added this information. The construct, which corresponds to an insertion of GFP into the flexible hinge region of AP2, at aa649, was first described by (Mino et al., 2020) and shown to be fully functional.  This information has been added to the Methods section.

      - Figure S1B: The authors should indicate the colour code used for the structural model.

      We have expanded our structural modeling using AlphaFold 3.0 in light of the recent publication suggesting the CCDC32 interacts with the µ2 subunit and does not bind full length AP2. These results are described in the text. The color coding now reflects certainty values given by AlphaFold 3.0 (Fig. S6B, D). 

      - The list of primers referred to in the materials and methods section does not exist. There is a Table S1, but this contains different data. The actual Table S1 is not referenced in the main text. This should be done. 

      We apologize for this error. We have now added this information in Table S2.

      Significance (Required):

      In this study, the authors analyse a so-far poorly understood endocytic accessory protein, CCDC32, and its implication for endocytosis. The experimental tool set used, allowing to quantify CCP dynamics and invagination is clearly a strength of the article that allows assessing the impact of an accessory protein towards the endocytic uptake mechanism, which is normally very robust towards mutations. Only through this detailed analysis of endocytosis progression could the authors detect clear differences in the presence and absence of CCDC32 and its mutants. If the above points are successfully addressed, the study will provide very interesting and highly relevant work allowing a better understanding of the early phases in CME with implication for disease. 

      The study is thus of potential interest to an audience interested in CME, in disease and its molecular reasons, as well as for readers interested in intrinsically disordered proteins to a certain extent, claiming thus a relatively broad audience. The presented results may initiate further studies of the so-far poorly understood and less well known accessory protein CCDC32.

      We thank the reviewer for their positive comments on the significance of our findings and the importance of our detailed phenotypic analysis made possible by quantitative live cell microscopy. We also believe that our new structural modeling of CCDC32 and our findings of complex and extensive interactions with AP2 make the reviewers point regarding intrinsically disordered proteins even more interesting and relevant to a broad audience.  We trust that our revisions indeed address the reviewer’s concerns. 

      The field of expertise of the reviewer is structural biology, biochemistry and clathrin mediated endocytosis. Expertise in cell biology is rather superficial.

      References:

      Aguet, F., Costin N. Antonescu, M. Mettlen, Sandra L. Schmid, and G. Danuser. 2013. Advances in Analysis of Low Signal-to-Noise Images Link Dynamin and AP2 to the Functions of an Endocytic Checkpoint. Developmental Cell. 26:279-291.

      Chen, Z., R.E. Mino, M. Mettlen, P. Michaely, M. Bhave, D.K. Reed, and S.L. Schmid. 2020. Wbox2: A clathrin terminal domain–derived peptide inhibitor of clathrin-mediated endocytosis. Journal of Cell Biology. 219.

      Grove, J., D.J. Metcalf, A.E. Knight, S.T. Wavre-Shapton, T. Sun, E.D. Protonotarios, L.D. Griffin, J. Lippincott-Schwartz, and M. Marsh. 2014. Flat clathrin lattices: stable features of the plasma membrane. Mol Biol Cell. 25:3581-3594.

      He, K., E. Song, S. Upadhyayula, S. Dang, R. Gaudin, W. Skillern, K. Bu, B.R. Capraro, I. Rapoport, I. Kusters, M. Ma, and T. Kirchhausen. 2020. Dynamics of Auxilin 1 and GAK in clathrinmediated traffic. J Cell Biol. 219.

      Mino, R.E., Z. Chen, M. Mettlen, and S.L. Schmid. 2020. An internally eGFP-tagged α-adaptin is a fully functional and improved fiduciary marker for clathrin-coated pit dynamics. Traffic. 21:603-616.

      Saffarian, S., and T. Kirchhausen. 2008. Differential evanescence nanometry: live-cell fluorescence measurements with 10-nm axial resolution on the plasma membrane. Biophys J. 94:23332342.

    1. Author Response:

      We sincerely thank the reviewers and the editorial team for their thoughtful and constructive evaluation of our manuscript. We are very pleased that both reviewers and the Reviewing Editor found the work to be compelling and of interest to the community studying membrane-associated condensates. Below we outline our planned revisions in response to the public reviews.

      Reviewer #1

      We appreciate Reviewer #1’s positive evaluation of the study’s significance and the utility of our theoretical framework.

      1. Understandably, the authors used one system to test their theory (ZO-1). However, to establish a theoretical framework, this is sufficient.

      Response: We acknowledge this limitation. While we agree that additional systems would strengthen the generality of our theory, we note that the focus of this work is to introduce and validate a theoretical framework. As the reviewer notes, this is sufficient for establishing the framework. Nonetheless, we are open to further collaborations or future studies to test the model with other systems.

      Reviewer #2

      We are grateful for Reviewer #2’s detailed comments and will address each of the points as follows:

      1. In the theoretical section, what has previously been known, compared to which equations are new, should be made more clear.

      Response: We will revise the theory section to clearly distinguish previously established formulations from novel contributions.

      1. Some assumptions in the model are made purely for convenience and without sufficient accompanying physical justification. E.g., the authors should justify, on physical grounds, why binding rate effects are/could be larger than the other fluxes.

      Response: We will expand the discussion to provide key physical justification, especially to explain why binding rate effects are/could be larger than the other fluxes.

      1. I feel that further mechanistic explanation as to why bulk phase separation widens the regime of surface phase separation is warranted.

      Response: We will elaborate on the mechanism underlying this coupling.

      1. The major advantage of the non-dilute theory as compared with a best parameterized dilute (or homogenous) theory requires further clarification/evidence with respect to capturing the experimental data.

      Response: We will clarify this comparison more explicitly and highlight how the non-dilute model captures key nonlinear behaviors and concentration-dependent adsorption phenomena that the dilute model fails to reproduce.

      1. Discrete (particle-based) molecular modelling could help to delineate the quantitative improvements that the non-dilute theory has over the previous state-of-the-art. Also, this could help test theoretical statements regarding the roles of bulk-phase separation, which were not explored experimentally.

      Response:  We appreciate the suggestion and agree that such modeling would be valuable. However, this is beyond the scope of the current study. We will add a discussion on how discrete simulations could be used to further test our theory in future work.

      1. Discussion of the caveats and limitations of the theory and modelling is missing from the text.

      Response:  We will add a paragraph outlining caveats and limitations of the modelling.

      We believe these changes will significantly improve the clarity and impact of our manuscript, and we thank the reviewers again for their valuable input.

    1. Author response:

      We thank the reviewers for their thoughtful and constructive feedback. As the reviewers noted, dissecting the contributions of Gtr1/2 and Pib2 to TORC1 signaling across diverse nutrient states is a technically and conceptually challenging problem. Indeed, many of the issues raised—including the interpretation of non-canonical TORC1 readouts (e.g., Rps6, Par32), the influence of strain auxotrophy and media composition, and the limitations of phosphoproteomic analysis performed under a single growth condition—underscore the challenges of working with the TORC1 signaling system.

      In response to the reviewers’ comments, we have undertaken a broader and more systematic analysis of TORC1 regulation across defined nitrogen transitions, building directly on the signaling framework established in Figures 6 and 8 of this manuscript. This work, which includes expanded phosphoproteomic profiling and the use of refined genetic tools, supports and extends the key conclusions of Cecil et. al. Specifically, it reinforces the existence of a Pib2-dependent TORC1 output under nitrogen-limited conditions and further clarifies the physiological relevance of the intermediate TORC1 activity state. Due to the scope and depth of this expanded work, we are reporting those findings in a separate publication. Nonetheless, we view the data presented here as a key foundational step in establishing a non-redundant framework for Gtr1/2- and Pib2-dependent control of TORC1.

      We have therefore made minor changes to the manuscript to clarify our use of different growth media and to temper our conclusions where appropriate. These changes, together with the context of ongoing work, should reinforce the value of Cecil et. al. in advancing our understanding of TORC1 and nutrient signaling in eukaryotes.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      In this work Jeong and colleagues focus on exploring the role of the acyltransferase ZDHHC9 in myelinating OLs in particular in the palmitoylation of several myelin proteins. After confirming the specific enrichment of the Zdhhc9 transcript in mouse and human OLs, the authors examine the subcellular localization of the protein in vitro and observed that in comparison with other isoforms, ZDHHC9 localizes at OLs cell bodies and at discrete puncta in the processes. These observations (Figures 1 and 2) led the authors to hypothesize that ZDHHC9 plays an important role in myelination. No gross changes were detected in OL development in Zdhhc9 KO mice and analyses from P28 Zdhhc9 KO mice crossed with Mobp-EGFP reporter mice did not show changes in EGFP+ OL differentiation (Figure 3).

      However, and given the observed subcellular localization of ZDHHC9 in OL processes (Figure 2) and the observation that the percentage of unmyelinated axons is increased in Zdhhc9 KO (Figure 6), early time points to examine the differentiated pools of OLs and their capacity to extend processes/contact axons need to be considered.

      We appreciate this point, but due to the order in which experiments were performed, the ZDHHC9 KO mouse colony that we maintained after initial submission of this work contains homozygous MOBP-EGFP, but not the mT/mG transgene that would be most optimal for the proposed experiment. We hope the reviewer appreciates that it would take considerable time and effort regarding mouse breeding to cross out the MOBP and add back the mT/mG. We nonetheless appreciate the importance of the point raised and therefore examined an earlier developmental time point (P21, 3 weeks) to quantify OLs and NG2+ OPCs. In our updated Fig 3C1-C3, we use Mobp-EGFP mice to show that Zdhhc9 KO does not significantly affect the number of EGFP+ OLs at this time point in the cortex, corpus callosum and spinal cord. We also show that in corpus callosum, Zdhhc9 KO does not significantly affect the number of NG2+ OPCs at this earlier time point (Fig 3D, E). Furthermore, immunostaining to detect BCAS1, a marker of pre-mature OLs, also revealed no qualitative difference with ZDHHC9 loss at P21. We show representative images from these BCAS1 experiments in an updated Fig S3. While these new experiments do not address the morphology of OLs in Zdhhc9 KO, they do provide further evidence that deficits in myelination in young Zdhhc9 KO mice (Figure 6) are not likely due to gross differences in OPC or OL numbers during development.

      Maturation of OL in Zdhhc9 KO was examined by crossing Zdhhc9 KO with Pdgfra-CreER;R26- EGFP and following the newly EGFP-labelled OPCs following tamoxifen administration. No changes in the numbers of EGFP+ OL were detected. The authors concluded that the loss of ZDHHC9 does not alter oligodendrogenesis in either the young or mature CNS. The authors observed defects in Zdhhc9 KO OL protrusions that they attributed to abnormal OL membrane expansion (Fig 4 and 5). Can they show evidence for this?

      This is an important point, and we appreciate the opportunity to explain the reasoning behind our initial statement more fully, while noting that other explanations are possible. Fig 5B (an Imaris-assisted reconstruction using the EGFP cell fill/morphology marker) highlights large spheroid-like distensions along OL processes. We reason that these spheroids are enclosed by the OL lipid membrane because if the membrane were ruptured, the EGFP signal would likely diffuse. This in turn suggests that the caliber of the OL process at the position of the spheroid is grossly abnormal i.e. the membrane has hyper-expanded. Given that OL membrane growth during myelination extends in two directions, i.e., spiral growth to the axonal surface and longitudinal growth along the axon, it is possible that spheroid-like structures are formed by uneven myelin growth. We recognize that we cannot yet conclude whether and how spheroid formation might be linked to the myelination deficit that we observe in Zdhhc9 KO mice. However, defining the subcellular mechanism for spheroid formation may provide further insights into this issue. We have therefore largely retained the original statement but have added the reasoning above to our revised Discussion.

      The authors report that Zdhhc9 KO primary and secondary branches in OL were longer, some contained spheroid-like swellings and the OL protrusion complexity was higher. However, these data is partially contradictory to what they show in OL differentiation experiments in vitro (Fig 7). There is also no evidence for increased membrane expansion in Zdhhc9 knockdown myelin forming cells in culture. How to reconcile this? 

      We appreciate the reviewer’s interest in this issue. Several non-mutually exclusive factors could account for the differences in OL morphology in vitro versus in vivo caused by Zdhhc9 loss. First, morphology in vivo may well be influenced by the axons and/or other extrinsic components around each OL that are not present in our primary cultures. Second, OL growth in vivo is highly 3-dimensional, whereas growth in culture is largely 2-dimensional – it may be difficult to support formation of spheroids (by definition, a 3-dimensional structure) in the latter situation. Finally, Zdhhc9 is absent in vivo from the beginning of development until the time points examined, whereas in our cultured OL experiments, Zdhhc9 shRNA is virally delivered to OPC cultures at DIV2 and likely acutely affects Zdhhc9 expression predominantly in committed OLs (following the switch to differentiation medium at DIV3). These differences may also affect the ability of other PATs or, potentially, palmitoylation-independent subcellular processes, to compensate for Zdhhc9 loss. We have more fully explained these points in our revised Discussion. 

      Reviewer #2 (Public Review):

      This study provides an in-depth exploration of the impact of X-linked ZDHHC9 gene mutations on cognitive deficits and epilepsy, with a particular focus on the expression and function of ZDHHC9 in myelin-forming oligodendrocytes (OLs). These findings offer crucial insights into understanding ZDHHC9-related X-linked intellectual disability (XLID) and shed light on the regulatory mechanisms of palmitoylation in myelination. The experimental design and analysis of results are convincing, providing a valuable reference for further research in this field. However, upon careful review, I believe the article still needs further improvement and supplementation in the following aspects:

      (1) Regarding the subcellular localization experiment of ZDHHC9 mutants in OL, it is currently limited to in vitro cultured OL, lacking validation in vivo OL or myelin sheath. Additionally, it is necessary to investigate whether the abnormal subcellular localization of ZDHHC9 mutants affects their enzyme activity and palmitoylation modification of substrate proteins.

      This is an important point but is technically challenging to address in vivo as it would likely require delivery of AAV to express ZDHHC9wt and XLID mutants specifically in OLs, preferably in the absence of endogenous ZDHHC9. We hope the reviewers would agree that this experiment is beyond the scope of the current study. However, we did compare the ability of ZDHHC9wt and XLID mutants to palmitoylate MBP, and to autopalmitoylate (sometimes used as a surrogate measure of PAT activity) in transfected heterologous cells. Although we recognize that this over-expression system is less physiological than a native OL, it has the benefit of being able to readily compare transfected wt vs mutant forms of ZDHHC9 with minimal contribution from endogenous ZDHHC9. Intriguingly, using this system, we found that autopalmitoylation activity of the XLID ZDHHC9-P150S mutant does not differ significantly from that of ZDHHC9wt, and that this mutant is still capable of palmitoylating MBP. Moreover, the R96W mutant, while impaired in autopalmitoylation, still palmitoylated MBP approximately 50% as effectively as ZDHHC9wt in our cell-based assay. These findings suggest that ZDHHC9-P150S and, probably, ZDHHC9-R96W mutants might still be able to palmitoylate substrates in OLs if they were properly localized. This possibility in turn suggests that impaired subcellular targeting in addition to, or instead of, impaired catalytic activity, may be a key factor in certain cases of ZDHHC9-associated XLID. We have expanded our Figure 8 (new panels 8E-G) to show these additional experiments and have summarized the conclusions above in our revised Discussion. We thank the reviewer for suggesting that we further investigate this issue.

      (2) The experimental period (P21+21 days) using genetic labeling to track the development of myelinating cells may not be long enough. It is recommended to extend the observation time and analyze at more time points to more comprehensively reflect the impact of Zdhhc9 KO.

      We appreciate this point from the reviewer but, regrettably, we did not maintain the PdgfraCreER; R26-EGFP; Zdhhc9 KO mouse line and hope the reviewer appreciates that it would take considerable time and effort to rederive this line and then perform the suggested extended time course experiments. However, we note for the reviewer that our preliminary studies did not reveal any effect of Zdhhc9 KO on the number of MOBP-EGFP+ OLs in 6-month-old mice (not shown), consistent with a model in which Zdhhc9 loss does not affect OPC-OL commitment per se.

      (3) The author speculates that Zdhhc9 may regulate myelination by affecting the membrane localization of specific myelin proteins, but lacks direct experimental evidence to support this. It is suggested to detect the expression and distribution of relevant proteins in the myelin of Zdhhc9 KO mice.

      We share the reviewer’s interest in this point but realized that it is more technically challenging to address than might be initially thought. The main protein we would implicate and seek to test is MBP, but we already found that there is no gross change in MBP distribution in vivo in Zdhhc9 KO mice (Fig 3A). However, an anti-MBP antibody recognizes all forms of MBP, not just the specific splice variants whose palmitoylation is affected by ZDHHC9 loss. Specifically assessing nanoscale distribution of these splice variants would require a way (e.g. anti-MBP splice form-specific antibodies that are compatible with immuno-EM) to distinguish these variants from other, non-palmitoylated forms of MBP. Although such an antibody could be an important tool, we hope the reviewers would agree that developing and characterizing such a reagent is beyond the scope of the current study.

      We do, however, note that the lack of gross change in MBP distribution and levels in Zdhhc9 KO mice is consistent with the relatively mild phenotype of these mice, compared with shiverer (shi/shi) mice, in which MBP is completely lost. In shiverer, CNS compact myelin is almost absent (PMID: 671037; PMID: 88695; PMID: 460693) and, as the name suggests, mice display a shivering gait, and exhibit seizures and early death. In contrast, Zdhhc9 mice show only subtle behavioral deficits (PMID: 29944857). These differences are all consistent with a model in which Zdhhc9 KO mice, despite their significantly reduced MBP palmitoylation (Fig 8) have grossly normal distribution and levels of MBP when all splice variants are assessed (Fig 3, Fig 8). It is not inconceivable that Zdhhc9 KO mice have a nanoscale change in the distribution of MBP, particularly of specific palmitoylated splice variants, within myelin that profoundly affects myelin ultrastructure, without grossly altering MBP distribution. However, an alternative and not mutually exclusive possibility is that aberrant palmitoylation of other Zdhhc9 substrates accounts for, or contributes to, the abnormalities in myelin at the ultrastructural level. Addressing this issue would require a multi-pronged approach, not just to assess palmitoylation and distribution of such proteins in Zdhhc9 KO, but also to test whether they are direct Zdhhc9 substrates, in order to rule out indirect effects. We hope reviewers would agree that this is best left to a separate study. However, in our revised Discussion we now summarize what can be inferred regarding Zdhhc9-dependent effects on total and splicevariant specific distribution and levels of MBP.  

      (4) Although the article mentions the association of Zdhhc9 with intellectual disabilities, it does not involve behavioral analysis of Zdhhc9 KO mice. It is recommended to supplement some behavioral experimental data to support the important role of Zdhhc9 in maintaining normal cognitive function, enhancing the clinical relevance of the article.

      We appreciate this point from the reviewer. The behavior of the same ZDHHC9 KO mouse line that we used was reported in PMID: 31747610 and in PMID: 29944857. In the former study, Zdhhc9 KO mice were reported to display seizures reminiscent of phenotypes in human patients with ZDHHC9 mutation. The latter study assessed performance of Zddhc9 KO mice in several tasks that test cognitive function. Specifically the KO mice were reported to display “altered behaviour in the open-field test, elevated plus maze and acoustic startle test that is consistent with a reduced anxiety level; a reduced hang time in the hanging wire test that suggests underlying hypotonia but which may also be linked to reduced anxiety [and] deficits in the Morris water maze test of hippocampal-dependent spatial learning and memory.”. We have incorporate these findings in our revised Discussion, where we summarize how these phenotypes are common, not just to human patients with ZDHHC9 mutation, but also to other human neurodevelopmental conditions and mouse models in which ID is a common feature.

      (5) For the abnormal myelination observed in Zdhhc9 KO mice, including unmyelinated large-diameter axons and excessively myelinated small-diameter axons, the article lacks indepth research and explanation on the exact mechanism and mode of action of ZDHHC9 in regulating myelination.

      We share the reviewer’s interest in this point but again note that gaining definitive insights into this issue is far from trivial. Convincing evidence of a causative mechanism would require an exhaustive identification of ZDHHC9 in vivo substrates, followed by point mutation of substrate palmitoylation site(s) to determine the extent to which palmitoylation of such protein(s) phenocopies ZDHHC9 loss. Nonetheless, it is possible to break this question down and to summarize what we do and do not know. For example, our experiments in cultured OLs show that ZDHHC9 loss causes call-autonomous deficits in morphological maturation of these cells. We also know that ZDHHC9 loss results in impaired palmitoylation of MBP, a direct substrate for ZDHHC9. Moreover, loss of ZDHHC9 at Golgi outposts in OLs (a phenotype observed with several XLID-associated mutant forms of ZDHHC9, even those with no significant loss of catalytic activity) correlates with intellectual disability. Together, these findings are consistent with a model in which ZDHHC9 action at OL Golgi outposts is critical for normal myelination. However, it is yet to be determined whether the key substrates of ZDHHC9 include MBP, other palmitoyl-proteins that are key constituents of CNS myelin, or proteins whose palmitoylation is important for myelin protein trafficking and targeting. Another non-mutually exclusive possibility is that ZDHHC9 acts at Golgi outposts but indirectly, for example to drive the expression of myelin protein genes. Future experiments, including but not limited to palmitoyl-proteomics in ZDHHC9 (OL-specific) KO mice, will be needed to provide more definitive insights into this issue. We have expanded our Discussion of links between ZDHHC9 mutation and impaired myelination to summarize the above points.

      (6) The function of ZDHHC9 in OL may be related to the Golgi apparatus, but its exact role in these structures is still unclear. It is suggested to discuss in more detail the role of ZDHHC9 in the Golgi apparatus in the discussion section.

      We appreciate this point, which we considered as related to point (5) above. In our revised Discussion we highlight how ZDHHC9 action at Golgi outposts may involve direct palmitoylation of myelin proteins, palmitoylation of proteins that direct myelin proteins to the myelin membrane and/or activation of gene expression programs that serve to drive myelination. We further note that these possibilities are not mutually exclusive.

      (7) More experimental support and in-depth research are needed on the detailed mechanism of how ZDHHC9 and Golga7 cooperatively regulate MBP palmitoylation, and how this decrease in palmitoylation level leads to myelination defects.

      This is another important point – our new experiments suggest that, although some XLID mutations markedly affect ZDHHC9’s ability to palmitoylate MBP, others do not, yet all of the mutant forms fail to localize to Golgi outposts. These findings are consistent with a model in which the subcellular location at which ZDHHC9 palmitoylates MBP, and potentially other substrates, is critical for normal myelination. Interestingly, despite their marked differences in basal catalytic activity (as assessed by autopalmitoylation), wt and all XLID forms of ZDHHC9 appear to show enhanced activity (measured by both auto- and MBP palmitoylation) in the presence of ZDHHC9, suggesting that the association with Golga7 (which also localizes to Golgi outposts) is central to ZDHHC9 activity. This model is also highly consistent with the biased expression of Golga7 in OLs, compared to other CNS cell types (Fig 1E, 1F). Moreover, XLID-associated mutant forms of ZDHHC9 also show reduced protein stability and are impaired in their ability to form complexes with Golga7 (also known as Golgi Complex Protein 16kDa; GCP16; PMID: 37035671). Failure of ZDHHC9 XLID mutants to localize to Golgi outposts may thus be due to aberrant trafficking of mutant ZDHHC9 per se, but may also involve impaired association/stabilization of ZDHHC9/Golga7 complexes at these locations. Again, it is possible that either or both of these mechanisms, which are not mutually exclusive, contribute to impaired MBP palmitoylation and/or myelination deficits. We summarize these points in our revised Discussion.

      In summary, it is recommended that the authors address the above issues through additional experiments and improved discussions to further strengthen the credibility and clinical relevance of the article.

      Recommendations for the authors:  

      Reviewer #1 (Recommendations For The Authors):

      No gross changes were detected in OL development in Zdhhc9 KO mice and analyses from P28 Zdhhc9 KO mice crossed with Mobp-EGFP reporter mice did not show changes in EGFP+ OL differentiation (Figure 3). However, and given the observed subcellular localization of ZDHHC9 in OL processes (Figure 2) and the observation that the percentage of unmyelinated axons is increased in Zdhhc9 KO (Figure 6), ***early time points to examine the differentiated pools of OLs and their capacity to extend processes/contact axons need to be considered***.

      We appreciate this point, but due to the order in which experiments were performed, the ZDHHC9 KO mouse colony that we maintained after initial submission of this work contains homozygous MOBP-EGFP, but not the mT/mG transgene that would be most optimal for the proposed experiment. We hope the reviewer appreciates that it would take considerable time and effort regarding mouse breeding to cross out the MOBP and add back the mT/mG. We nonetheless appreciate the importance of the point raised and therefore examined an earlier developmental time point (P21, 3 weeks) to quantify OLs and NG2+ OPCs. In our updated Fig 3C1-C3, we use Mobp-EGFP mice to show that Zdhhc9 KO does not significantly affect the number of EGFP+ OLs at this time point in the cortex, corpus callosum and spinal cord. We also show that in corpus callosum, Zdhhc9 KO does not significantly affect the number of NG2+ OPCs at this earlier time point (Fig 3D, E). Furthermore, immunostaining to detect BCAS1, a marker of pre-mature OLs, also revealed no qualitative difference with ZDHHC9 loss at P21. We show representative images from these BCAS1 experiments in an updated Fig S3. While these new experiments do not address the morphology of OLs in Zdhhc9 KO, they do provide further evidence that deficits in myelination in young Zdhhc9 KO mice (Figure 6) are not likely due to gross differences in OPC or OL numbers during development.

      The authors observed defects in Zdhhc9 KO OL protrusions that they attributed to abnormal OL membrane expansion (Fig 4 and 5). Can they show evidence for this?

      This is an important point, and we appreciate the opportunity to explain the reasoning behind our initial statement more fully, while noting that other explanations are possible. Fig 5B (an Imaris-assisted reconstruction using the EGFP cell fill/morphology marker) highlights large spheroid-like distensions along OL processes. We reason that these spheroids are enclosed by the OL lipid membrane because if the membrane were ruptured, the EGFP signal would likely diffuse. This in turn suggests that the caliber of the OL process at the position of the spheroid is grossly abnormal i.e. the membrane has hyper-expanded. Given that OL membrane growth during myelination extends in two directions, i.e., spiral growth to the axonal surface and longitudinal growth along the axon, it is possible that spheroid-like structures are formed by uneven myelin growth. We recognize that we cannot yet conclude whether and how spheroid formation might be linked to the myelination deficit that we observe in Zdhhc9 KO mice.

      However, defining the subcellular mechanism for spheroid formation may provide further insights into this issue. We have therefore largely retained the original statement but have added the reasoning above to our revised Discussion.

      The authors report that Zdhhc9 KO primary and secondary branches in OL were longer, some contained spheroid-like swellings and the OL protrusion complexity was higher. However, these data is partially contradictory to what they show in OL differentiation experiments in vitro (Fig 7). There is also no evidence for increased membrane expansion in Zdhhc9 knockdown myelin forming cells in culture. How do they reconcile these different findings?

      We appreciate the reviewer’s interest in this issue. Several non-mutually exclusive factors could account for the differences in OL morphology in vitro versus in vivo caused by Zdhhc9 loss. First, morphology in vivo may well be influenced by the axons and/or other extrinsic components around each OL that are not present in our primary cultures. Second, OL growth in vivo is highly 3-dimensional, whereas growth in culture is largely 2-dimensional – it may be difficult to support formation of spheroids (by definition, a 3-dimensional structure) in the latter situation. Finally, Zdhhc9 is absent in vivo from the beginning of development until the time points examined, whereas in our cultured OL experiments, Zdhhc9 shRNA is virally delivered to OPC cultures at DIV2 and likely acutely affects Zdhhc9 expression predominantly in committed OLs (following the switch to differentiation medium at DIV3). These differences may also affect the ability of other PATs or, potentially, palmitoylation-independent subcellular processes, to compensate for Zdhhc9 loss. We have more fully explained these points in our revised Discussion. 

      Page 7: "The OL processes in this culture condition correspond to large lipid-rich membranous sheets that form spiral membrane expansion on axons in vivo (49)." At which stage are authors referring to? OL processes are extended in culture before membrane formation and this is not clear here. In a 3-days differentiation culture, most OLs have not yet formed a myelin sheath (eg., Figure 2 in Zuchero et al., 2015, Dev Cell).

      We appreciate the reviewer highlighting this point. We first note that our oligodendrocyte (OL) culture conditions differ from the immunopanning method used by Zuchero et al., 2015 (original reference (Emery and Dugas, 2013)), which may affect the time course and progression of OL process elaboration and/or myelin sheath formation. We further note that in our cultures most EGFP+ processes are also MBP+ at the time point examined (strictly 3 days plus 9 hours post-differentiation). It thus seems likely that these MBP+ structures largely correspond to the MBP+ wrapping sheaths that occur in vivo, so we have therefore retained our original statement but have added this further explanation.

      Minor: Figure 6 (Legend): Time points should be indicated throughout the panels.

      We have added this information as requested

      Reviewer 2 Recommendations for the Authors:

      (1) Regarding the subcellular localization experiment of ZDHHC9 mutants in OL, it is currently limited to in vitro cultured OL, lacking validation in vivo OL or myelin sheath. Additionally, it is necessary to investigate whether the abnormal subcellular localization of ZDHHC9 mutants affects their enzyme activity and palmitoylation modification of substrate proteins.

      We thank the reviewer for raising this point. New data in our revised Figure 8 compares autopalmitoylation (sometimes used as a surrogate measure of PAT activity) of ZDHHC9wt and XLID mutants, and their ability to palmitoylate MBP in transfected cells. Intriguingly, we found that autopalmitoylation activity of the ZDHHC9-P150S mutant does not differ significantly from that of ZDHHC9wt, and that this mutant is still capable of palmitoylating MBP. Moreover, the R96W mutant, while impaired in autopalmitoylation, still palmitoylated MBP approximately 50% as effectively as ZDHHC9wt in our cell-based assay. These findings suggest that ZDHHC9-P150S and, probably, ZDHHC9-R96W mutants might still be able to palmitoylate substrates in OLs if they were properly localized. This possibility in turn suggests that impaired subcellular targeting in addition to, or instead of, impaired catalytic activity, may be a key factor in certain cases of ZDHHC9-associated XLID. We have expanded our Figure 8 to show these new experiments and have summarized the conclusions above in our revised Discussion. We thank the reviewer for suggesting that we further investigate this issue.

      (2) The experimental period (P21+21 days) using genetic labeling to track the development of myelinating cells may not be long enough. It is recommended to extend the observation time and analyze at more time points to more comprehensively reflect the impact of Zdhhc9 KO.

      We appreciate this point from the reviewer but, regrettably, we did not maintain the PdgfraCreER; R26-EGFP; Zdhhc9 KO mouse line and hope the reviewer appreciates that it would take considerable time and effort to rederive this line and then perform the suggested extended time course experiments. However, we note for the reviewer that our preliminary studies did not reveal any effect of Zdhhc9 KO on the number of MOBP-EGFP+ OLs in 6-month-old mice (not shown), consistent with a model in which Zdhhc9 loss does not affect OPC-OL commitment per se.

      (3) The author speculates that Zdhhc9 may regulate myelination by affecting the membrane localization of specific myelin proteins, but lacks direct experimental evidence to support this. It is suggested to detect the expression and distribution of relevant proteins in the myelin of Zdhhc9 KO mice.

      We share the reviewer’s interest in this point but realized that it is more technically challenging to address than might be initially thought. The main protein we would implicate and seek to test is MBP, but we already found that there is no gross change in MBP distribution in vivo in Zdhhc9 KO mice (Fig 3A). However, an anti-MBP antibody recognizes all forms of MBP, not just the specific splice variants whose palmitoylation is affected by ZDHHC9 loss. Specifically assessing nanoscale distribution of these splice variants would require a way (e.g. am anti-MBP splice form-specific antibody that is compatible with immuno-EM) to distinguish these variants from other, non-palmitoylated forms of MBP. Although such an antibody could be an important tool we hope the reviewers would agree that developing and characterizing such a reagent is beyond the scope of the current study.

      We do, however, note that the lack of gross change in MBP distribution and levels in Zdhhc9 KO mice is consistent with the relatively mild phenotype of these mice, compared with shiverer (shi/shi) mice, in which MBP is completely lost. In shiverer, CNS compact myelin is almost absent (PMID: 671037; PMID: 88695; PMID: 460693) and, as the name suggests, mice display a shivering gait, and exhibit seizures and early death. In contrast, Zdhhc9 mice show only subtle behavioral deficits (PMID: 29944857). These differences are all consistent with a model in which Zdhhc9 KO mice, despite their significantly reduced MBP palmitoylation (Fig 8) have grossly normal distribution and levels of MBP when all splice variants are assessed (Fig 3, Fig 8). It is not inconceivable that Zdhhc9 KO mice have a nanoscale change in the distribution of MBP, particularly of specific palmitoylated splice variants, within myelin that profoundly affects myelin ultrastructure, without grossly altering MBP distribution. However, an alternative and not mutually exclusive possibility is that aberrant palmitoylation of other

      Zdhhc9 substrates accounts for, or contributes to, the abnormalities in myelin at the ultrastructural level. Addressing this issue would require a multi-pronged approach, not just to assess palmitoylation and distribution of such proteins in Zdhhc9 KO, but also to test whether they are direct Zdhhc9 substrates, in order to rule out indirect effects. We hope reviewers would agree that this is best left to a separate study. However, in our revised Discussion we now summarize what can be inferred regarding Zdhhc9-dependent effects on total and splicevariant specific distribution and levels of MBP.  

      (4) Although the article mentions the association of Zdhhc9 with intellectual disabilities, it does not involve behavioral analysis of Zdhhc9 KO mice. It is recommended to supplement some behavioral experimental data to support the important role of Zdhhc9 in maintaining normal cognitive function, enhancing the clinical relevance of the article.

      We appreciate this point from the reviewer. The behavior of the same ZDHHC9 KO mouse line that we used was reported in PMID: 31747610 and in PMID: 29944857. In the former study, Zdhhc9 KO mice were reported to display seizures reminiscent of phenotypes in human patients with ZDHHC9 mutation. The latter study assessed performance of Zddhc9 KO mice in several tasks that test cognitive function. Specifically the KO mice were reported to display “altered behaviour in the open-field test, elevated plus maze and acoustic startle test that is consistent with a reduced anxiety level; a reduced hang time in the hanging wire test that suggests underlying hypotonia but which may also be linked to reduced anxiety [and] deficits in the Morris water maze test of hippocampal-dependent spatial learning and memory.”. We have incorporate these findings in our revised Discussion, where we summarize how these phenotypes are common, not just to human patients with ZDHHC9 mutation, but also to other human neurodevelopmental conditions and mouse models in which ID is a common feature.

      (5) For the abnormal myelination observed in Zdhhc9 KO mice, including unmyelinated large-diameter axons and excessively myelinated small-diameter axons, the article lacks indepth research and explanation on the exact mechanism and mode of action of ZDHHC9 in regulating myelination.

      We share the reviewer’s interest in this point but again note that gaining definitive insights into this issue is far from trivial. Convincing evidence of a causative mechanism would require an exhaustive identification of ZDHHC9 in vivo substrates, followed by point mutation of substrate palmitoylation site(s) to determine the extent to which palmitoylation of such protein(s) phenocopies ZDHHC9 loss. Nonetheless, it is possible to break this question down and to summarize what we do and do not know. For example, our experiments in cultured OLs show that ZDHHC9 loss causes call-autonomous deficits in morphological maturation of these cells. We also know that ZDHHC9 loss results in impaired palmitoylation of MBP, a direct substrate for ZDHHC9. Moreover, loss of ZDHHC9 at Golgi outposts in OLs (a phenotype observed with several XLID-associated mutant forms of ZDHHC9, even those with no significant loss of catalytic activity) correlates with intellectual disability. Together, these findings are consistent with a model in which ZDHHC9 action at OL Golgi outposts is critical for normal myelination. However, it is yet to be determined whether the key substrates of ZDHHC9 include MBP, other palmitoyl-proteins that are key constituents of CNS myelin, or proteins whose palmitoylation is important for myelin protein trafficking and targeting. Another non-mutually exclusive possibility is that ZDHHC9 acts at Golgi outposts but indirectly, for example to drive the expression of myelin protein genes. Future experiments, including but not limited to palmitoyl-proteomics in ZDHHC9 (OL-specific) KO mice, will be needed to provide more definitive insights into this issue. We have expanded our Discussion of links between ZDHHC9 mutation and impaired myelination to summarize the above points.

      (6) The function of ZDHHC9 in OL may be related to the Golgi apparatus, but its exact role in these structures is still unclear. It is suggested to discuss in more detail the role of ZDHHC9 in the Golgi apparatus in the discussion section.

      We appreciate this point, which we considered as related to point (5) above. In our revised Discussion we highlight how ZDHHC9 action at Golgi outposts may involve direct palmitoylation of myelin proteins, palmitoylation of proteins that direct myelin proteins to the myelin membrane and/or activation of gene expression programs that serve to drive myelination. We further note that these possibilities are not mutually exclusive.

      (7) More experimental support and in-depth research are needed on the detailed mechanism of how ZDHHC9 and Golga7 cooperatively regulate MBP palmitoylation, and how this decrease in palmitoylation level leads to myelination defects.

      This is another important point – our new experiments suggest that, although some XLID mutations markedly affect ZDHHC9’s ability to palmitoylate MBP, others do not, yet all of the mutant forms fail to localize to Golgi outposts. These findings are consistent with a model in which the subcellular location at which ZDHHC9 palmitoylates MBP, and potentially other substrates, is critical for normal myelination. Interestingly, despite their marked differences in basal catalytic activity (as assessed by autopalmitoylation), wt and all XLID forms of ZDHHC9 appear to show enhanced activity (measured by both auto- and MBP palmitoylation) in the presence of ZDHHC9, suggesting that the association with Golga7 (which also localizes to Golgi outposts) is central to ZDHHC9 activity. This model is also highly consistent with the biased expression of Golga7 in OLs, compared to other CNS cell types (Fig 1E, 1F). Moreover, XLID-associated mutant forms of ZDHHC9 also show reduced protein stability and are impaired in their ability to form complexes with Golga7 (also known as Golgi Complex Protein 16kDa; GCP16; PMID: 37035671). Failure of ZDHHC9 XLID mutants to localize to Golgi outposts may thus be due to aberrant trafficking of mutant ZDHHC9 per se, but may also involve impaired association/stabilization of ZDHHC9/Golga7 complexes at these locations. Again, it is possible that either or both of these mechanisms, which are not mutually exclusive, contribute to impaired MBP palmitoylation and/or myelination deficits. We summarize these points in our revised Discussion.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #2 (Public review):

      This manuscript determines how PA28g, a proteasome regulator that is overexpressed in tumors, and C1QBP, a mitochondrial protein for maintaining oxidative phosphorylation that plays a role in tumor progression, interact in tumor cells to promote their growth, migration and invasion. Evidence for the interaction and its impact on mitochondrial form and function was provided although it is not particularly strong.

      The revised manuscript corrected mislabeled data in figures and provides more details in figure legends. Misleading sentences and typos were corrected. However, key experiments that were suggested in previous reviews were not done, such as making point mutations to disrupt the protein interactions and assess the consequence on protein stability and function. Results from these experiments are critical to determine whether the major conclusions are fully supported by the data.

      The second revision of the manuscript included the proximity ligation data to support the PA28g-C1QBP interaction in cells. However, the method and data were not described in sufficient detail for readers to understand. The revision also includes the structural models of the PA28g-C1QBP complex predicted by AlphaFold. However, the method and data were not described with details for readers to understand how this structural modeling was done, what is the quality of the resulting models, and the physical nature of the protein-protein interaction such as what kind of the non-covalent interactions exist in the interface of the protein complexes. Furthermore, while the interactions mediated by the protein fragments were tested by pull-down experiments, the interactions mediated by the three residues were not tested by mutagenesis and pull-down experiments. In summary, the revision was improved, but further improvement is needed.

      Thank you very much for your comments.

      (1) Based on your suggestion, we predicted the possible interaction sites using AlphaFold 3 and found that mutations in amino acids 76 and 78 of C1QBP affect the interaction with PA28γ (Revised Appendix Figure 1J). Subsequently, pulldown experiment also found that after mutating the amino acids at the two aforementioned sites (T76A, G78N), C1QBP that could bind to PA28γ decreased (Revised Figure 1J). The above results confirm that PA28γ could interacts with C1QBP, in a manner dependent on the N-terminus of C1QBP. These findings are now included in the revised manuscript “In addition, we employed AlphaFold 3 to perform energy minimization and predict hydrogen bonds between the C1QBP N-terminus (amino acids 1-167) and the PA28γ protein interaction region. The results suggest that the T76 and G78 residues of C1QBP may be key contributors to the interaction. Consistently, coimmunoprecipitation analysis demonstrated that mutations at these sites (C1QBPT76A and C1QBPG78N) significantly reduced the binding ability to PA28γ (Fig. 1J and Appendix Fig. 1J)”, specifically in results section. We believe this additional validation strengthens the robustness of our findings.

      (2) According to your suggestion, we have added a description of the results of PLA in the figure legend (Revised Figure 1C) and the method of PLA in the appendix file (Revised Appendix file, Part “Proximity Ligation Assay”). The revised text reads as follows: (C) PLA image of UM1 cells shows the interaction between C1QBP and PA28γ in both cytoplasm and nucleus (red fluorescence).

      (3) In the light of your suggestion, we have enriched the description of AlphaFold 3 analysis in the appendix file (Revised Appendix file, Page 10-11). The revised text reads as follows:

      “Prediction and Analysis of Protein Interactions

      Protein Sequence Retrieval and Structure Prediction

      The protein sequences of C1QBP and PA28γ were obtained from the AlphaFold Protein Structure Database. Structural predictions of the protein-protein interaction between C1QBP and PA28γ were conducted using AlphaFold 3. The plDDT (predicted local distance difference test) values were utilized to assess the confidence of the predicted models. Models with a plDDT score above 70 were considered confident, while those with a score above 90 were categorized as very high confidence. These values were annotated in the figures to indicate the reliability of the structural predictions.”

      “Protein Preparation and Structure Optimization

      The best-scored model for the C1QBP-PA28γ interaction predicted by AlphaFold 3 was selected for further analysis. The model was imported into MOE 2022 (Molecular Operating Environment) software for protein preparation. This process included the removal of water molecules and other heteroatoms, followed by the addition of hydrogen atoms to the structure. This step was essential for optimizing the protein’s 3D conformation and ensuring the correctness of the protonation states at physiological pH.”

      “Energy Minimization and Hydrogen Bond Prediction

      The protein structure was subjected to energy minimization using the Amber10: EHT (Effective Hamiltonian Theory) force field, with R-field 1: 80 settings to refine the model’s geometry. The minimization process was performed to optimize the protein’s internal energy and ensure stable conformation, followed by calculation of hydrogen bond interactions. The interaction energies and hydrogen bonds were analyzed to identify potential binding sites and stabilize the predicted protein-protein complex.”

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1:

      The authors sought to examine the associations between child age, reports of parent-child relationship quality, and neural activity patterns while children (and also their parents) watched a movie clip. Major methodological strengths include the sample of 3-8 year-old children in China (rare in fMRI research for both age range and non-Western samples), use of a movie clip previously demonstrated to capture theory of mind constructs at the neural level, measurement of caregiver-child neural synchrony, and assessment of neural maturity. Results provide important new information about parent-child neural synchronization during this movie and associations with reports of parent-child relationship quality. The work is a notable advance in understanding the link between the caregiving context and the neural construction of theory of mind networks in the developing brain.

      We are grateful for the reviewer’s generous and thoughtful summary of our work. We particularly appreciate the recognition of the methodological strengths—including the rare developmental sample, culturally diverse context, and use of naturalistic, theory of mind-relevant stimuli—as well as the importance of integrating neural synchrony and relational variables. The reviewer’s comments affirm the core motivation behind this study: to advance our understanding of how the caregiving environment shapes the neurodevelopment of social cognition in early childhood. We have taken all specific suggestions seriously and hope the revised manuscript more clearly communicates these contributions.

      We appreciate that the authors wanted to show support for a mediational mechanism. However, we suggest that the authors drop the structural equation modeling because the data are cross-sectional so mediation is not appropriate. Other issues include the weak justification of including the parent-child neural synchronization as part of parenting.... it could just as easily be a mechanism of change or driven by the child rather than a component of parenting behavior. The paper would be strengthened by looking at associations between selected variables of interest that are MOST relevant to the imaging task in a regression type of model. Furthermore, the authors need to be more explicit about corrections for multiple comparisons throughout the manuscript; some of the associations are fairly weak so claims may need to be tempered if they don't survive correction.

      Thanks for feedback on the use of SEM in our study. We recognize the limitations of using SEM to infer mediation with cross-sectional data and acknowledge that longitudinal designs are better suited for such analyses. However, our goal was not to establish causality but to explore potential pathways linking parenting, personal traits, and Theory of Mind (ToM) behavior to social cognition outcomes. SEM allowed us to simultaneously examine the relationships among these latent constructs, providing a cohesive framework for understanding the interplay of these factors. That said, we understand your concern and are willing to revise the manuscript to de-emphasize causal interpretations of the SEM findings.

      We thank the reviewer for raising the corrections for multiple comparisons. We confirm that all correlation analyses reported in the manuscript have been corrected for multiple comparisons using the False Discovery Rate (FDR) procedure. In the revised manuscript, we now explicitly indicate FDR correction for all relevant p-values to ensure clarity and transparency. Where this information was previously missing, we have corrected the oversight and clearly labeled the results as FDR-corrected or uncorrected where appropriate. Additionally, we have carefully reviewed our interpretation of all reported associations. For any results that were close to the significance threshold, we have tempered our claims and now describe them as a marginally significant association to avoid overstating our findings.

      The corresponding changes have been made on Discussion section of the revised manuscript.

      Reverse correlation analysis is sensible given what prior developmental fMRI studies have done. But reverse correlation analysis may be more prone to overfitting and noise, and lacks sensitivity to multivariate patterns. Might inter-subject correlation be useful for *within* the child group? This would minimize noise and allow for non-linear patterns to emerge.

      We appreciate the reviewer’s thoughtful suggestion regarding potential limitations of reverse correlation analysis. While we agree that inter-subject correlation (ISC) within the child group may be useful in other contexts, our primary goal in using reverse correlation was not to identify temporally distributed or multivariate response patterns, but rather to isolate specific events within the naturalistic stimulus that reliably evoke Theory of Mind (ToM) and Social Pain-related responses in adults—who possess more stable and mature neural signatures. These adult-derived events serve as anchors for subsequent developmental comparisons and provide a principled way to define timepoints of interest that are behaviorally and theoretically meaningful.

      Using reverse correlation in adults allows us to identify canonical ToM and Social Pain events in a data-driven yet hypothesis-informed manner. We then examine how children’s neural responses to these same events vary with age, neural maturity, and dyadic synchrony. This approach is consistent with prior work in developmental social neuroscience (e.g., Richardson et al., 2018) and offers a valid framework for identifying interpretable social-cognitive events in naturalistic stimuli.

      We have now clarified the rationale for using adult-based reverse correlation in the revised manuscript and explicitly stated its advantages for identifying targeted ToM and Social Pain content in the stimulus.

      The corresponding changes have been made on pages 17 of the revised manuscript.

      “We employed reverse correlation analysis in adults to identify discrete events within the movie that elicited reliable neural responses across participants in ToM and SPM networks.

      The events of adults were chosen for this analysis due to the relative stability and maturity of their social brain responses, allowing for robust detection of canonical ToM and social pain-related moments. These events, once identified, served as stimulus-locked timepoints for subsequent analyses in the child cohort. This approach enables us to examine how children's responses to well-characterized, socially meaningful events vary with age and parent-child dyadic dynamics.”

      No learning effects or temporal lagged effects are tested in the current study, so the results do not support the authors' conclusions that the data speak to Bandura's social learning theory. The authors do mention theories of biobehavioral synchrony in the introduction but do not discuss this framework in the discussion (which is most directly relevant to the data). The data can also speak to other neurodevelopmental theories of development (e.g.,neuroconstructivist approaches), but the authors do not discuss them. The manuscript would benefit from significantly revising the framework to focus more on biobehavioral synchrony data and other neurodevelopmental approaches given the prior work done in this area rather than a social psychology framework that is not directly evaluated.

      We appreciate the reviewer’s thoughtful and constructive feedback. We agree that the current study does not directly test mechanisms central to Bandura’s social learning theory, such as observational learning over time or behavioral modeling. In light of this, we have significantly revised the theoretical framing of the manuscript to focus more directly on the biobehavioral synchrony framework, which more accurately reflects the dyadic neural measures employed in this study and is better supported by our findings.

      Specifically, we have expanded the Discussion to contextualize our findings in terms of biobehavioral synchrony, emphasizing how inter-subject neural synchronization may reflect coordinated parent-child engagement and emotional attunement. We have also incorporated insights from neurodevelopmental and neuroconstructivist models, acknowledging that social cognitive development is shaped by dynamic interactions between neural maturation and environmental input over time.

      Although we continue to briefly reference Bandura’s theory to situate our findings within broader social-cognitive frameworks, we have clearly delineated the boundaries of what our data can support and have tempered previous claims. These changes are intended to better align our conceptual framing with the empirical evidence and relevant theoretical models.

      The corresponding changes have been made on pages 11-12 of the revised manuscript.

      “Insights into mechanisms of Neuroconstructivist Perspectives and Bandura’s social learning theory

      Our findings align with a neuroconstructivist perspective, which conceptualizes brain development as an emergent outcome of reciprocal interactions between biological constraints and context-specific environmental inputs. Rather than presuming fixed traits or linear maturation, this perspective highlights how neural circuits adaptively organize in response to experience, gradually supporting increasingly complex cognitive functions49. It offers a particularly powerful lens for understanding how early caregiving environments modulate the maturation of social brain networks.

      Building on this framework, the present study reveals that moment-to-moment neural synchrony between parent and child, especially during emotionally salient or socially meaningful moments, is associated with enhanced Theory of Mind performance and reduced dyadic conflict. This suggests that beyond age-dependent neural maturation, dyadic neural coupling may serve as a relational signal, embedding real-time interpersonal dynamics into the child’s developing neural architecture [1] . Our data demonstrate that children’s brains are not merely passively maturing, but are also shaped by the relational texture of their lived experiences—particularly interactions characterized by emotional engagement and joint attention. Importantly, this adds a new dimension to neuroconstructivist theory: it is not simply whether the environment shapes development, but how the quality of interpersonal input dynamically calibrates neural specialization. Interpersonal variation leaves detectable signatures in the brain, and our use of neural synchrony as a dyadic metric illustrates one potential pathway through which caregiving relationships exert formative influence on the developing social brain.

      The contribution of this work lies not in reiterating the interplay of nature and nurture, but in specifying the mechanistic role of interpersonal neural alignment as a real-time, context-sensitive developmental input. Neural synchrony between parent and child may function as a form of relationally grounded, temporally structured experience that tunes the child’s social brain toward contextually relevant signals. Unlike generalized enrichment, this form of neural alignment is inherently personalized and contingent—features that may be especially potent in shaping social cognitive circuits during early childhood.

      Although our study was not designed to directly examine learning mechanisms such as imitation or reinforcement, the findings can be viewed as broadly consistent with social learning theory. Bandura's theory posits that human behavior is shaped by observational learning and modeling from others in one's environment [2-4]. According to Bandura, children acquire social cognitive skills by observing and interacting with their parents and other significant figures in their environment. This dynamic interplay shapes their ability to understand and predict the behavior of others, which is crucial for the development of ToM and other social competencies.”

      References

      (1) Hughes, C. et al. Origins of individual differences in theory of mind: From nature to nurture? Child development 76, 356-370 (2005).

      (2) Koole, S. L. & Tschacher, W. Synchrony in psychotherapy: A review and an integrative framework for the therapeutic alliance. Frontiers in psychology 7, 862 (2016).

      (3) Liu, D., Wellman, H. M., Tardif, T. & Sabbagh, M. A. Theory of mind development in Chinese children: a meta-analysis of false-belief understanding across cultures and languages. Developmental Psychology 44, 523 (2008).

      (4) Frith, U. & Frith, C. D. Development and neurophysiology of mentalizing. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 358, 459-473 (2003).

      The significance and impact of the findings would be clearer if the authors more clearly situated the findings in the context of (a) other movie and theory of mind fMRI task data during development; and (b) existing data on parent-child neural synchrony (often uses fNIRS or EEG). What principles of brain and social cognition development do these data speak to? What is new?

      We thank the reviewer for this thoughtful comment. In response, we have revised the Discussion section to more clearly situate our findings within two key literatures: (a) fMRI studies examining Theory of Mind using movie-based and traditional task paradigms across development, and (b) research on parent-child neural synchrony. We now articulate more explicitly how our findings advance current understanding of the neural architecture of social cognition in childhood, and how they contribute new insights into the relational processes shaping brain function. These revisions clarify the conceptual and empirical novelty of our study, particularly in its use of naturalistic fMRI, simultaneous child-parent dyads, and integration of neural maturity with interpersonal synchrony.

      The corresponding changes have been made on pages 12 of the revised manuscript.

      “Our findings contribute to and extend prior research using fMRI paradigms to investigate ToM development in children.  Previous work has shown that these networks become increasingly specialized and differentiated throughout childhood [1-3]. The current study extends these findings by demonstrating that the development of social brain networks is a gradual process that continues beyond the preschool years and is related to children's chronological age. This finding is consistent with behavioral research indicating that ToM and social abilities continue to develop and refine throughout middle childhood and adolescence [4]. Importantly, we move beyond prior work by combining reverse correlation with naturalistic stimuli to isolate discrete, behaviorally meaningful events (e.g., mental state attribution, social rejection) and relate children’s brain responses to adult patterns and social outcomes. This event-level analysis in a dyadic context offers greater ecological and interpretive precision than traditional block or condition-based designs. Our study provides novel evidence for the neural underpinnings of this protracted development, suggesting that the functional maturation of social brain networks may support the continued acquisition and refinement of social cognitive skills.

      In parallel, our study builds on and extends a growing body of work on parent-child neural synchrony, much of which has relied on fNIRS or EEG hyperscanning to demonstrate interpersonal alignment during communication, shared attention, or cooperative tasks [5-7]. While these modalities offer fine temporal resolution, they are limited in spatial precision and typically focus on surface-level cortical regions such as the prefrontal cortex. By contrast, our naturalistic fMRI approach enables the examination of deep and distributed brain networks—specifically those supporting social cognition—within child-parent dyads during emotionally and cognitively rich scenarios. Intriguingly, we found that neural synchronization during movie viewing was higher in child-mother dyads compared to child-stranger dyads.”

      Reference

      (1) Jacoby, N., Bruneau, E., Koster-Hale, J. & Saxe, R. Localizing Pain Matrix and Theory of Mind networks with both verbal and non-verbal stimuli. Neuroimage 126, 39-48 (2016).

      Astington, J. W. & Jenkins, J. M. A longitudinal study of the relation between language and theory-of-mind development. Developmental Psychology 35, 1311 (1999).

      (2) Carter, E. J. & Pelphrey, K. A. School-aged children exhibit domain-specific responses to biological motion. Social Neuroscience 1, 396-411 (2006).

      (3) Cantlon, J. F., Pinel, P., Dehaene, S. & Pelphrey, K. A. Cortical representations of symbols, objects, and faces are pruned back during early childhood. Cerebral Cortex 21, 191-199 (2011).

      (4) Im-Bolter, N., Agostino, A. & Owens-Jaffray, K. Theory of mind in middle childhood and early adolescence: Different from before? Journal of experimental child psychology 149, 98-115 (2016).

      (5) Deng, X. et al. Parental involvement affects parent-adolescents brain-to-brain synchrony when experiencing different emotions together: an EEG-based hyperscanning study. Behavioural brain research 458, 114734 (2024).

      (6) Miller, J. G. et al. Inter-brain synchrony in mother-child dyads during cooperation: an fNIRS hyperscanning study. Neuropsychologia 124, 117-124 (2019).

      (7) Nguyen, T., Bánki, A., Markova, G. & Hoehl, S. Studying parent-child interaction with hyperscanning. Progress in brain research 254, 1-24 (2020).

      There is little discussion about the study limitations, considerations about the generalizability of the findings, and important next steps and future directions. What can the data tell us, and what can it NOT tell us?

      We appreciate the reviewer’s recommendation to elaborate on the study’s limitations, generalizability, and future directions. In response, we have added a dedicated section to the Discussion that critically addresses these considerations. We acknowledge the cross-sectional nature of the study, the modest sample size, and the use of a single stimulus context as key limitations. We also clarify the inferences that can be drawn from our data and what remains speculative. Finally, we outline specific future research directions.

      The corresponding changes have been made on pages 13-14 of the revised manuscript.

      “While leveraging a naturalistic movie-viewing paradigm allowed us to study children's spontaneous neural responses during a semi-structured yet engaging task, dedicated experimental designs are still needed to make stronger inferences about the cognitive processes involved. Additionally, our region-of-interest approach precluded examination of whole-brain networks; future work could explore developmental changes in broader functional circuits. The cross-sectional nature of our study is a further limitation, as it cannot definitively establish the causal directions of the observed relationships. Longitudinal designs tracking children's brain development and social cognitive abilities over time would help clarify whether early parenting impacts later neural maturation and behavioral outcomes, or vice versa. Our sample was restricted to mother-child dyads, leaving open questions about potential differences in father-child relationships and gender effects on parenting neurobiology. Larger and more diverse samples would enhance the generalizability of the findings.

      Several future directions emerge from this research. First, combining naturalistic neuroimaging with structured cognitive tasks could elucidate the specific mental processes underlying children's neural responses during movie viewing. Examining how these processes relate to real-world social behavior would further bridge neurocognitive function and ecological validity. Longitudinal studies beginning in infancy could chart the developmental trajectories of parent-child neural synchrony and their impact on long-term social outcomes. Such work could also explore sensitive periods when parenting may be most influential on social brain maturation. Finally, expanding this multimodal approach to clinical populations like autism could yield insights into atypical social cognitive development and inform tailored intervention strategies targeting parent-child relationships and neural plasticity.”

      To evaluate associations between child neural activity patterns during the movie AND parent-child synchronization patterns AND other variables such as parent-child communication and theory of mind behavior, it seems like a robust approach could be to examine whether similar synchronization patterns are associated with similar scores on different variables. Would allow for non-linear and multivariate associations.

      We greatly appreciate the reviewer’s thoughtful suggestion regarding the use of similarity-based or multivariate analyses to assess whether dyads with similar neural synchronization profiles also exhibit similar scores on behavioral or relational variables. We agree that this type of analysis—such as representational similarity analysis (RSA) or inter-subject pattern similarity—offers a powerful framework for capturing non-linear and multivariate associations, and could provide deeper insights into shared neurobehavioral patterns across participants. However, the analytic logic of similarity-based approaches typically requires the availability of comparable measures across individuals or dyads (e.g., child A and child B must both have measures of brain activity, behavior, and environment). In the present study, our focus was on the child as the behavioral and developmental target, and we did not collect parallel behavioral or cognitive variables from the parent side (e.g., adult Theory of Mind ability, emotional traits, parenting style questionnaires beyond dyadic reports). As a result, it was not feasible to construct pairwise similarity matrices across dyads that include both neural synchrony and matched behavioral dimensions from both individuals.

      Instead, our study was designed to examine how child-level outcomes (e.g., Theory of Mind performance, social functioning) are associated with (a) the child’s neural responses to specific social events, and (b) the degree of neural synchronization with their mother, as a marker of relational engagement. The analytical emphasis, therefore, remained on within-child variation, modulated by the quality of the parent-child interaction.

      Were there associations between parent-child neural synchronization and child age? What was the association between neural maturity and parent-child neural synchronization

      We thank the reviewer for raising this important point regarding associations between parent-child neural synchronization (ISS), child age, and neural maturity.

      As reported in the original manuscript, we did not observe significant correlations between parent-child ISS and child age for either the Theory of Mind (ToM) or Social Pain Matrix (SPM) networks (all ps > 0.1). Additionally, we conducted additional analysis, we found no significant correlations between ISS and neural maturity (Author response image 1, r = 0.2503, p = 0.1533).

      These findings indicate that parent-child neural synchronization in this naturalistic viewing context is not simply explained by age-related maturation or children's neural maturity level. Instead, ISS may predominantly reflect real-time interpersonal engagement or relational dynamics rather than individual developmental trajectories or neural maturity.

      Author response image 1.

      Scatterplot showing the association between parent-child inter-subject synchronization (ISS) and neural maturity, averaged across the Theory of Mind (ToM) and Social Pain Matrix (SPM) networks. Each point represents one dyad. No significant correlation was observed between ISS and neural maturity (r = 0.2503, p = 0.1533, suggesting that interpersonal neural synchronization and individual neural maturation may reflect dissociable aspects of social brain development.

      The rationale for splitting the ages into 3 groups is unclear and creates small groups that could be more prone to spurious associations. Why not look at age continuously?

      We thank the reviewer for raising this important point. We fully agree that analyzing age as a continuous variable is statistically more robust and minimizes concerns about spurious associations due to arbitrary groupings.

      To clarify, all primary statistical models—including correlational analyses—treated age as a continuous variable, and our core developmental inferences are based on these continuous-age findings.

      In addition to these analyses, we included age group comparisons as a supplementary approach, guided by both theoretical considerations and visual inspection of the data. Specifically, we aimed to explore whether functional differentiation between social brain networks (e.g., ToM and SPM) might begin to emerge non-linearly or earlier than expected, particularly in the youngest children. Such early neural divergence may not be well-captured by linear trends alone. The grouped analysis allowed us to illustrate that network differentiation was already observable in children under age 5, suggesting that certain aspects of social brain organization may emerge earlier than classically assumed.

      We have now clarified this rationale in the revised manuscript and emphasized that the group-based analysis was used solely to highlight developmental shifts that may not follow a linear pattern, and not for formal hypothesis testing.

      The corresponding changes have been made on pages 9 of the revised manuscript.

      “While our primary analyses treated age as a continuous variable, we also performed exploratory group-based comparisons to probe for potential non-linear developmental shifts in social brain network organization. This approach revealed that the differentiation between ToM and SPM networks was already present in the youngest group (ages 3–4), suggesting that early neural specialization may begin prior to the age at which ToM behavior is reliably observed. These group-level observations provide complementary evidence to the continuous analyses and may inform future work examining sensitive periods or early markers of social brain development.”

      Tables would be improved if they were more professionally formatted (e.g., names of the variables rather than variable abbreviation codes).

      We appreciate the reviewer’s suggestion to improve the clarity and professionalism of our tables. In the revised manuscript, we have reformatted all tables to include full variable names rather than abbreviations or coded labels, and we ensured consistency in terminology across the manuscript text, tables, and figure legends. We have also added explanatory footnotes where needed to clarify any derived or composite measures. We hope these revisions improve the accessibility and readability of the results for a broader audience

      Reviewer #2:

      Summary:

      This study investigates the impact of mother-child neural synchronization and the quality of parent-child relationships on the development of Theory of Mind (ToM) and social cognition. Utilizing a naturalistic fMRI movie-viewing paradigm, the authors analyzed inter-subject neural synchronization in mother-child dyads and explored the connections between neural maturity, parental caregiving, and social cognitive outcomes. The findings indicate age-related maturation in ToM and social pain networks, emphasizing the importance of dyadic interactions in shaping ToM performance and social skills, thereby enhancing our understanding of the environmental and intrinsic influences on social cognition.

      Strengths:

      This research addresses a significant question in developmental neuroscience, by linking social brain development with children's behaviors and parenting. It also uses a robust methodology by incorporating neural synchrony measures, naturalistic stimuli, and a substantial sample of mother-child dyads to enhance its ecological validity. Furthermore, the SEM approach provides a nuanced understanding of the developmental pathways associated with Theory of Mind (ToM).

      We appreciate the positive evaluation and valuable comments of the reviewer. According to the reviewer`s comments, we have revised the manuscript thoroughly to address the concerns raised by the reviewer. A point-by-point response to each of the issues raised by the reviewer has been made. We believe that the revision of our manuscript has now been significantly improved.

      Upon reviewing the introduction, I feel that the first goal - developmental changes of the social brain and its relation to age - seems somewhat distinct from the other two goals and the main research question of the manuscript. The authors might consider revising this section to enhance the overall coherence of the manuscript. Additionally, the introduction lacks a clear background and rationale for the importance of examining age-related changes in the social brain.

      We thank the reviewer for this thoughtful observation. In response, we have revised the Introduction to better integrate the developmental aspect of the social brain with the broader research aims. We now explicitly link age-related changes in social brain organization to the emergence of social cognitive abilities and highlight why early childhood (ages 3–8) represents a particularly formative period. This revision clarifies that our first aim—examining functional specialization and neural maturity in Theory of Mind (ToM) and Social Pain Matrix (SPM) networks—serves as a developmental foundation for understanding how dyadic influences, such as neural synchrony and caregiving quality, shape children’s social cognition.

      We have also improved the rationale for examining age-related change, drawing on key literature in developmental neuroscience to show how the early emergence and specialization of social brain networks provide a necessary context for interpreting interpersonal neural dynamics.

      The corresponding changes have been made on pages 3 of the revised manuscript.

      “These findings suggest that the development of specialized brain regions for reasoning about others' mental states and physical sensations is a gradual process that continues throughout childhood.

      Understanding how these networks differentiate with age is essential not only for mapping typical brain development, but also for contextualizing the role of environmental influences. By establishing normative patterns of neural maturity and differentiation, we can better interpret how relational experiences—such as caregiver-child synchrony and parenting quality—modulate these trajectories. Thus, our first goal provides a developmental anchor that grounds our investigation of interpersonal and environmental contributions to social brain function.”

      The manuscript uses both "mother-child" and "parent-child" terminology. Does this imply that only mothers participated in the fMRI scans while fathers completed the questionnaires? If so, have the authors considered the potential impact of parental roles (father vs. mother)?

      We thank the reviewer for raising this important point regarding terminology and parental roles. To clarify, all participating caregivers in the current study were biological mothers, and all behavioral questionnaires were also completed by these same mothers. No fathers were included in this study. We have revised the manuscript throughout to consistently use the term “mother-child” when referring to the specific dyads in our sample.

      We also appreciate the opportunity to elaborate on the rationale for including only mothers. Prior research has shown that maternal and paternal influences on child development are not interchangeable, and that the neural correlates of caregiving behaviors differ between mothers and fathers. For example, studies have demonstrated distinct patterns of brain activation during social and emotional processing in mothers versus fathers (Abraham et al., 2014; JE Swain et al., 2014). Given these differences, we deliberately focused on mother-child dyads to maintain neurobiological consistency in our analysis and reduce variance associated with heterogeneous caregiving roles. We now clarify this rationale in the revised Methods and Discussion sections.

      The corresponding changes have been made on pages 14 of the revised manuscript.

      “We chose to focus exclusively on mother-child dyads in this study based on prior evidence suggesting distinct neural and behavioral caregiving profiles between mothers and fathers [1-2], allowing us to maintain role consistency and reduce variability in dyadic interactions.

      Our sample was restricted to mother-child dyads, leaving open questions about potential differences in father-child relationships and gender effects on parenting neurobiology [1]. Larger and more diverse samples would enhance the generalizability of the findings.”

      Reference:

      (1) Swain, J. E. et al. Approaching the biology of human parental attachment: Brain imaging, oxytocin and coordinated assessments of mothers and fathers. Brain research 1580, 78-101 (2014).

      (2) Abraham, E. et al. Father's brain is sensitive to childcare experiences. Proceedings of the National Academy of Sciences 111, 9792-9797 (2014).

      There is inconsistent usage of the terms ISC and ISS in the text and figures, both of which appear to refer to synchronization derived from correlation analysis. It would be beneficial to maintain consistency throughout the manuscript.

      We thank the reviewer for highlighting the inconsistent use of “ISC” and “ISS” in the original manuscript. We agree that clarity and consistency in terminology are essential. In response, we have revised the manuscript to consistently use “ISS” (inter-subject synchronization) throughout the text, figures, tables, and legends.

      Of the 50 dyads, 16 were excluded due to data quality issues, which constitutes a significant proportion. It would be helpful to know whether these excluded dyads exhibited any distinctive characteristics. Providing information on demographic or behavioral differences-such as Theory of Mind (ToM) performance and age range between the excluded and included dyads would enhance the assessment of the findings' generalizability.

      We thank the reviewer for this important observation. We agree that understanding the characteristics of excluded participants is essential for assessing the generalizability of the findings.

      In response, we conducted comparative analyses between included and excluded dyads (N = 34 included; N = 16 excluded) on key demographic and behavioral variables, including child age, gender, and Theory of Mind (ToM) performance. These analyses revealed no significant differences between groups on any of these measures (ps > 0.1), suggesting that data exclusion due to quality issues (e.g., excessive motion, incomplete scans) did not introduce systematic bias.

      We have now added this information to the Results and Methods sections of the manuscript.

      The corresponding changes have been made on pages 6 and 17 of the revised manuscript.

      “Of the 50 initial mother-child dyads recruited, 16 were excluded due to excessive head motion (n = 11), incomplete scan sessions (n = 3), or technical issues during data acquisition (n = 2). The final sample consisted of 34 dyads. To assess potential bias introduced by data exclusion, we compared included and excluded dyads on child age, gender, and Theory of Mind performance. No significant differences were found across these variables (all ps > 0.1), suggesting that the analytic sample was demographically representative of the full cohort.

      Comparison between included and excluded dyads revealed no significant differences in child age (t = 1.23, p = 0.24), ToM scores (t = -0.54, p = 0.59), or sex distribution (χ² < 0.01, p = 0.98), indicating that data exclusion did not bias the sample in a systematic way.”

      The article does not adhere to the standard practice of using a resting state as a baseline for subtracting from task synchronization. Is there a rationale for this approach? Not controlling for a baseline may lead to issues, such as whether resting state synchronization already differs between subjects with varying characteristics.

      We thank the reviewer for raising this important methodological point. We agree that controlling for baseline synchronization, such as using a resting-state scan as a comparison, can help disambiguate whether task-induced synchrony reflects genuine stimulus-driven coupling or baseline differences across individuals or dyads.

      In the present study, we focused on inter-subject synchronization (ISS) during naturalistic movie viewing, a task condition that has been widely used in previous developmental and social neuroscience research to assess shared neural engagement. We did not include a resting-state scan in the current protocol due to time constraints and the young age of our participants (ages 3–8), as longer scanning sessions often result in increased motion and reduced data quality in pediatric populations. Moreover, many prior studies using ISS in naturalistic paradigms have similarly focused on task-driven synchrony without subtracting a resting baseline (e.g., Hasson et al., 2004; Nguyen et al., 2020; Reindl et al., 2018).

      That said, we acknowledge that baseline neural synchrony across dyads may vary depending on individual or relational characteristics (e.g., temperament, arousal, attentional style), and this remains an important question for future research. In the revised Discussion, we now explicitly note the absence of a resting-state baseline as a limitation and highlight the need for future studies to examine how resting and task-based ISS may interact, particularly in the context of child-caregiver dyads.

      The corresponding changes have been made on page 13 of the revised manuscript.

      “Another limitation of the current design is the lack of a resting-state baseline for inter-subject synchronization. While our focus was on synchronization during naturalistic social processing, we cannot determine whether individual differences in ISS reflect purely task-induced coupling or are partially shaped by trait-level synchrony present at rest. Including both resting and task conditions in future work would allow for stronger inferences about stimulus-specific versus baseline-driven synchronization, especially in relation to interpersonal factors such as relationship quality or social responsiveness.”

      The title of the manuscript suggests a direct influence of mother-child interactions on children's social brain and theory of mind. However, the use of structural equation modeling (SEM) may not fully establish causal relationships. It is possible that the development of children's social brain and ToM also enhances mother-child neural synchronization. The authors should address this alternative hypothesis of the potential bidirectional relationship in the discussion and exercise caution regarding terms that imply causality in the title and throughout the manuscript.

      We appreciate the reviewer’s careful attention to issues of causality in our manuscript. We agree that our cross-sectional design limits causal inference, and that the use of structural equation modeling (SEM) in this context does not allow for conclusions about directional or mechanistic pathways. In response, we have revised the Discussion to explicitly acknowledge these limitations, and now include an expanded section on the potential for bidirectional or co-constructed processes, consistent with neuroconstructivist frameworks.

      We have also tempered the interpretation of our SEM findings, avoiding causal language throughout the manuscript and clarifying that our analyses are exploratory and associational in nature. We hope that these changes provide a more cautious and developmentally grounded interpretation of the data.

      With regard to the title, we respectfully chose to retain the original wording, as we believe it captures the thematic focus and central research question of the paper—namely, the potential role of mother-child interaction in the development of children’s social brain and Theory of Mind. While we understand the reviewer’s concern, we note that the interpretation of this phrasing is contextualized within the manuscript, which now includes clear qualifications regarding the limits of causal inference. We have taken care to ensure that no claims of unidirectional causality are made in the body of the paper.

      The corresponding changes have been made on pages 11- 12 of the revised manuscript.

      “Our findings align with a neuroconstructivist perspective, which conceptualizes brain development as an emergent outcome of reciprocal interactions between biological constraints and context-specific environmental inputs. Rather than presuming fixed traits or linear maturation, this perspective highlights how neural circuits adaptively organize in response to experience, gradually supporting increasingly complex cognitive functions54. It offers a particularly powerful lens for understanding how early caregiving environments modulate the maturation of social brain networks.

      Building on this framework, the present study reveals that moment-to-moment neural synchrony between parent and child, especially during emotionally salient or socially meaningful moments, is associated with enhanced Theory of Mind performance and reduced dyadic conflict. This suggests that beyond age-dependent neural maturation, dyadic neural coupling may serve as a relational signal, embedding real-time interpersonal dynamics into the child’s developing neural architecture. Our data demonstrate that children’s brains are not merely passively maturing, but are also shaped by the relational texture of their lived experiences—particularly interactions characterized by emotional engagement and joint attention. Importantly, this adds a new dimension to neuroconstructivist theory: it is not simply whether the environment shapes development, but how the quality of interpersonal input dynamically calibrates neural specialization. Interpersonal variation leaves detectable signatures in the brain, and our use of neural synchrony as a dyadic metric illustrates one potential pathway through which caregiving relationships exert formative influence on the developing social brain.

      The contribution of this work lies not in reiterating the interplay of nature and nurture, but in specifying the mechanistic role of interpersonal neural alignment as a real-time, context-sensitive developmental input. Neural synchrony between parent and child may function as a form of relationally grounded, temporally structured experience that tunes the child’s social brain toward contextually relevant signals. Unlike generalized enrichment, this form of neural alignment is inherently personalized and contingent—features that may be especially potent in shaping social cognitive circuits during early childhood.

      The cross-sectional nature of our study is a further limitation, as it cannot definitively establish the causal directions of the observed relationships. Longitudinal designs tracking children's brain development and social cognitive abilities over time would help clarify whether early parenting impacts later neural maturation and behavioral outcomes, or vice versa.”

      I would appreciate more details about the 14 Theory of Mind (ToM) tasks, which could be included in supplemental materials. The authors score them on a scale from 0 to 14 (each task 1 point); however, the tasks likely vary in difficulty and should carry different weights in the total score (for example, the test and the control questions should have different weights). Many studies have utilized the seven tasks according to Wellman and Liu (2004), categorizing them into "basic ToM" and "advanced ToM." Different components of ToM could influence the findings of the current study, which should be further examined by a more in-depth analysis.

      We thank the reviewer for raising this important point regarding the structure and scoring of the Theory of Mind (ToM) tasks. We will provide a detailed description of all 14 tasks in the Supplemental Materials, including their content, targeted mental state concepts (e.g., beliefs, desires, intentions), and design features (e.g., test/control items, task format).

      We fully agree that ToM tasks differ in complexity, and in principle, a weighted or component-based scoring approach (e.g., distinguishing basic and advanced ToM) could offer greater interpretive value. However, in our study design, tasks were administered in a fixed sequence from lower to higher difficulty, and testing was terminated if the child was unable to successfully complete three consecutive tasks. This approach is developmentally appropriate for younger children but results in non-random missingness for more advanced tasks—particularly among children at the lower end of the age range (3–4 years).

      Given this adaptive task structure, re-scoring using weighted or subscale-based approaches would introduce systematic bias, as children who struggled with early items were not administered more complex ones. As a result, a full breakdown by task type (e.g., basic vs. advanced ToM) would only reflect a restricted subsample and would not be comparable across the full cohort. For this reason, we retained the unit-weighted total ToM score as the most developmentally valid and comparable metric across participants.

      Reviewer #3:

      Summary:

      The article explores the role of mother-child interactions in the development of children's social cognition, focusing on Theory of Mind (ToM) and Social Pain Matrix (SPM) networks. Using a naturalistic fMRI paradigm involving movie viewing, the study examines relationships among children's neural development, mother-child neural synchronization, and interaction quality. The authors identified a developmental pattern in these networks, showing that they become more functionally distinct with age. Additionally, they found stronger neural synchronization between child-mother pairs compared to child-stranger pairs, with this synchronization and neural maturation of the networks associated with the mother-child relationship and parenting quality.

      Strengths:

      This is a well-written paper, and using dyadic fMRI and naturalistic stimuli enhances its ecological validity, providing valuable insights into the dynamic interplay between brain development and social interactions. However, I have some concerns regarding the analysis and interpretation of the findings. I have outlined these concerns below in the order they appear in the manuscript, which I hope will be helpful for the revision.

      We appreciate the reviewer’s thoughtful and constructive summary of the manuscript. The concerns raised regarding aspects of the analysis and interpretation have been carefully considered. Detailed point-by-point responses are provided below, along with descriptions of the corresponding revisions made to improve the clarity, precision, and interpretive caution of the manuscript.

      Given the importance of social cognition in this study, please cite a foundational empirical or review paper on social cognition to support its definition. The current first citation is primarily related to ASD research, which may not fully capture the broader context of social cognition development.

      We thank the reviewer for this helpful suggestion. We agree that a broader, foundational reference is more appropriate for introducing the concept of social cognition. In response, we have revised the Introduction to include a widely cited theoretical or review paper on social cognition to provide a more general developmental context.

      The corresponding changes have been made on pages 3 of the revised manuscript.

      “Social cognition, defined as the ability to interpret and predict others' behavior based on their beliefs and intentions and to interact in complex social environments and relationships is a crucial aspect of human development [1-2]”

      (1) Adolphs, R. The social brain: neural basis of social knowledge. Annual review of psychology 60, 693-716 (2009).

      (2) Frith, C. D. & Frith, U. Mechanisms of social cognition. Annual review of psychology 63, 287-313 (2012).

      It is standard practice to report the final sample size in the Abstract and Introduction, rather than the initial recruited sample, as high attrition rates are common in pediatric studies. For example, this study recruited 50 mother-child dyads, and only 34 remained after quality control. This information is crucial for interpreting the results and conclusions. I recommend reporting the final sample size in the abstract and introduction but specifying in the Methods that an additional 16 mother-child dyads were initially recruited or that 50 dyads were originally collected.

      We thank the reviewer for this helpful recommendation. In the original version of the manuscript, the Abstract and Introduction referenced the total number of dyads recruited (N = 50). In line with standard reporting practices and to ensure clarity regarding the analytic sample, we have now revised both the Abstract and Introduction to report the final sample size (N = 34). The full recruitment and exclusion details—including the number of dyads removed due to excessive motion or technical issues—are now clearly described in the Methods section.

      The corresponding changes have been made on pages 1 and 4 of the revised manuscript.

      In the "Neural maturity reflects the development of the social brain" section, the authors report the across-network correlation for adults, finding a negative correlation between ToM and SPM. However, the cross-network correlations for the three child groups are not reported. The statement that "the two networks were already functionally distinct in the youngest group of children we tested" is based solely on within-network positive correlations, which does not fully demonstrate functional distinctness. Including cross-network correlations for the child groups would strengthen this conclusion.

      We thank the reviewer for this insightful comment. We agree that within-network correlations alone do not fully establish functional distinctness, particularly in early development. To more directly test whether the ToM and SPM networks were already differentiated in children, we have now included the cross-network correlations between the two networks for each of the three age groups in the revised manuscript. These findings support and strengthen our original claim that the ToM and SPM networks are functionally dissociable even in early childhood, and we have revised the relevant Results sections accordingly to reflect this.

      The corresponding changes have been made on page 7 of the revised manuscript.

      “In children, each network also exhibited positive correlations within-network and negative correlations across networks (within-ToM correlation M(s.e.) = 0.31(0.04); within-SPM correlation M(s.e.) = 0.29(0.04); across-network M(s.e.) = −0.09 (0.02).

      In the Pre-junior group only (3-4 years old children, n = 12), both ToM and SPM networks had positive within-network correlations (within-ToM correlation M (s.e.) = 0.29(0.06); within-SPM correlation M(s.e.) = 0.23(0.05), across-network M(s.e.) = −0.05(0.02)).”

      The ROIs for the ToM and SPM networks are defined based on previous literature, applying the same ROIs across all age groups. While I understand this is a common approach, it's important to note that this assumption may not fully hold, as network architecture can evolve with age. The functional ROIs or components of a network might shift, with regions potentially joining or exiting a network or changing in size as children develop. For instance, Mark H. Johnson's interactive specialization theory suggests that network composition may adapt over developmental stages. Although the authors follow the approach of Richardson et al. (2018), it would be beneficial to discuss this limitation in the Discussion. An alternative approach would be to apply data-driven analysis to justify the selection of the ROIs for the two networks.

      We thank the reviewer for this thoughtful and theoretically grounded comment.  In our study, we followed the approach of Richardson et al. (2018), using a priori ROIs defined from adult meta-analyses and ToM/SPM task studies. This approach facilitates comparison with prior work and provides anatomical consistency across participants. However, we fully agree that applying adult-defined ROIs to pediatric populations involves important assumptions about the stability of network architecture across development, which may not fully hold in early childhood.

      We have now addressed this limitation more explicitly in the revised Discussion, emphasizing that the fixed-ROI approach may not capture the dynamic reorganization of social brain networks during development.

      The corresponding changes have been made on pages 13 of the revised manuscript.

      “Moreover, the ROIs used to define the ToM and SPM networks were based on meta-analyses and task studies primarily conducted with adults. While this approach promotes comparability with existing literature, it assumes that the spatial organization of these networks is stable across age groups. However, theories of interactive specialization suggest that the composition and boundaries of functional networks may undergo reorganization during development, with regions potentially entering or exiting networks based on experience and maturational processes. As a result, the current analysis may not fully capture age-specific functional architecture, particularly in younger children. Future studies using data-driven or age-appropriate parcellation methods could provide more precise characterizations of how social brain networks are constructed and differentiated throughout childhood.”

      The current sample size (N = 34 dyads) is a limitation, particularly given the use of SEM, which generally requires larger samples for stable results. Although the model fit appears adequate, this does not guarantee reliability with the current sample size. I suggest discussing this limitation in more detail in the Discussion.

      We thank the reviewer for highlighting the limitations of applying structural equation modeling (SEM) with a relatively modest sample size. We agree that SEM generally benefits from larger samples to ensure model stability and parameter reliability, and that satisfactory model fit does not guarantee robustness in small-sample contexts.

      In the revised Discussion, we now more clearly acknowledge that the use of SEM in the current study is exploratory in nature, and that all results should be interpreted with caution due to potential sample size-related constraints. The model was constructed to provide an integrated view of the observed associations rather than to establish definitive pathways. We have also added a note that future research with larger samples and longitudinal designs will be needed to validate and extend the proposed model.

      The corresponding changes have been made on pages 13 of the revised manuscript.

      “In addition, the modest sample size (N = 34 dyads) presents limitations for the application of structural equation modeling (SEM), which typically requires larger samples for stable estimation and generalizable inferences. While the model fit was acceptable, the results should be interpreted as exploratory and hypothesis-generating, rather than confirmatory. Future studies with larger, independent samples will be important for validating the structure and directionality of the proposed relationships”

      Based on the above comment, I believe that conclusions regarding the relationship between social network development, parenting, and support for Bandura's theory should be tempered. The current conclusions may be too strong given the study's limitations.

      We thank the reviewer for this important and balanced observation. We agree that the conclusions drawn from the current study should reflect the exploratory nature of the analyses, as well as the methodological limitations, including the modest sample size and cross-sectional design.

      In response, we have revised the Conclusion sections to use more cautious, associative language when describing the observed relationships among social brain development, parenting factors, and Theory of Mind outcomes. In particular, we have tempered statements regarding support for Bandura’s social learning theory, clarifying that while our findings are consistent with social learning frameworks, the data do not allow for direct tests of modeling or observational learning mechanisms.

      We hope these revisions help clarify the scope of the findings and improve the conceptual rigor of the manuscript.

      The corresponding changes have been made on pages 14 of the revised manuscript.

      “Our study provides novel evidence that children's social cognitive development may be shaped by the intricate interplay between environmental influences, such as parenting, and biological factors, such as neural maturation. Our findings contribute to a growing understanding of the factors associated with social cognitive development and suggest the potential importance of parenting in this process. Specifically, the study points to the possible role of the parent-child relationship in supporting the development of social brain circuitry and highlights the relevance of family-based approaches for addressing social difficulties. The observed neural synchronization between parent and child, which was associated with relationship quality, underscores the potential significance of positive parental engagement in fostering social cognitive skills. Future longitudinal and clinical research can build on this multimodal approach to further clarify the neurobehavioral mechanisms underlying social cognitive development. Such research may help inform more effective strategies for promoting healthy social functioning and mitigating social deficits through targeted family-based interventions.”

      The SPM (pain) network is associated with empathic abilities, also an important aspect of social skills. It would be relevant to explore whether (or explain why) SPM development and child-mother synchronization are (or are not) related to parenting and the parent-child relationship.

      We thank the reviewer for this thoughtful and important comment regarding the role of the Social Pain Matrix (SPM) network in social cognition and empathy. We agree that this network represents a critical component of social-cognitive development and is theoretically linked to affective processing and interpersonal understanding.

      We would like to clarify that in our existing analyses—already included in the original submission and detailed in the Supplemental Results—SPM network measures showed similar significant associations with behavioral outcomes than the ToM network. These outcomes included children's performance on ToM tasks as well as broader measures of social functioning. We have added more discussion in the supplementary results.

      “To further investigate the specificity of our findings, we conducted additional control analyses focusing on the individual components of the social brain networks examined in our study: the Theory of Mind (ToM) and Social Pain Matrix (SPM) networks.

      When analyzing these networks separately, we found significant correlations between neural maturity and age, as well as between inter-subject synchronization (ISS) and parent-child relationship quality for both the ToM and SPM networks individually (Fig. S1). Specifically, neural maturity within each network was positively correlated with age, indicating that both networks undergo maturation during childhood. Similarly, ISS within each network was negatively correlated with parent-child conflict scores, suggesting that both networks contribute to the observed relationship between neural synchrony and parent-child relationship quality.

      These results highlight the importance of considering the social brain as an integrated system, where the ToM and SPM networks work in concert to support social cognitive development. While each network shows age-related maturation and sensitivity to parent-child relationship quality, their combined functioning appears to be crucial for predicting broader social cognitive outcomes.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      Astrocytes are known to express neuroligins 1-3. Within neurons, these cell adhesion molecules perform important roles in synapse formation and function. Within astrocytes, a significant role for neuroligin 2 in determining excitatory synapse formation and astrocyte morphology was shown in 2017. However, there has been no assessment of what happens to synapses or astrocyte morphology when all three major forms of neuroligins within astrocytes (isoforms 1-3) are deleted using a well characterized, astrocyte specific, and inducible cre line. By using such selective mouse genetic methods, the authors here show that astrocytic neuroligin 1-3 expression in astrocytes is not consequential for synapse function or for astrocyte morphology. They reach these conclusions with careful experiments employing quantitative western blot analyses, imaging and electrophysiology. They also characterize the specificity of the cre line they used. Overall, this is a very clear and strong paper that is supported by rigorous experiments. The discussion considers the findings carefully in relation to past work. This paper is of high importance, because it now raises the fundamental question of exactly what neuroligins 1-3 are actually doing in astrocytes. In addition, it enriches our understanding of the mechanisms by which astrocytes participate in synapse formation and function. The paper is very clear, well written and well illustrated with raw and average data.

      Comments on revisions:

      My previous comments have been addressed. I have no additional points to make and congratulate the authors.

      Thank you for your acceptance.

      Reviewer #2 (Public Review):

      In the present manuscript, Golf et al. investigate the consequences of astrocyte-specific deletion of Neuroligin (Nlgn) family cell adhesion proteins on synapse structure and function in the brain. Decades of prior research had shown that Neuroligins mediate their effects at synapses through their role in the postsynaptic compartment of neurons and their transsynaptic interaction with presynaptic Neurexins. More recently, it was proposed for the first time that Neuroligins expressed by astrocytes can also bind to presynaptic Neurexins to regulate synaptogenesis (Stogsdill et al. 2017, Nature). However, several aspects of the model proposed by Stogsdill et al. on astrocytic Neuroligin function conflict with prior evidence on the role of Neuroligins at synapses, prompting Golf et al. to further investigate astrocytic Neuroligin function in the current study. Using postnatal conditional deletion of Nlgn1-3 specifically from astrocytes in mice, Golf et al. show that virtually no changes in the expression of synaptic proteins or in the properties of synaptic transmission at either excitatory or inhibitory synapses are observed. Moreover, no alterations in the morphology of astrocytes themselves were found. To further extend this finding, the authors additionally analyzed human neurons co-cultured with mouse glia lacking expression of Nlgn1-4. No difference in excitatory synaptic transmission was observed between neurons cultured in the present of wildtype vs. Nlgn1-4 conditional knockout glia. The authors conclude that while Neuroligins are indeed expressed in astrocytes and are hence likely to play some role there, this role does not include any direct consequences on synaptic structure and function, in direct contrast to the model proposed by Stogsdill et al.

      Overall, this is a strong study that addresses a fundamental and highly relevant question in the field of synaptic neuroscience. Neuroligins are not only key regulators of synaptic function, they have also been linked to numerous psychiatric and neurodevelopmental disorders, highlighting the need to precisely define their mechanisms of action. The authors take a wide range of approaches to convincingly demonstrate that under their experimental conditions, Nlgn1-3 are efficiently deleted from astrocytes in vivo, and that this deletion does not lead to major alterations in the levels of synaptic proteins or in synaptic transmission at excitatory or inhibitory synapses, or in the morphology of astrocytes. While the co-culture experiments are somewhat more difficult to interpret due to lack of a control for the effect of wildtype mouse astrocytes on human neurons, they are also consistent with the notion that deletion of Nlgn1-4 from astrocytes has no consequences for the function of excitatory synapses. Together, the data from this study provide compelling and important evidence that, whatever the role of astrocytic Neuroligins may be, they do not contribute substantially to synapse formation or function under the conditions investigated.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      The authors have fully addressed my concerns, and have in particular conducted a very elegant and compelling analysis of the degree of deletion of astrocytic Nlgn1-3/4 in their models. This greatly strengthens the main claims of their study and the fundamental nature of their conclusions for the field of synapse biology.

      I am somewhat less convinced by the newly added experiment to investigate deletion of Nlgns1-4 from glia in glia-neuron co-cultures. The authors provide no evidence to show that either WT or cKO glia have any effect on synapse formation or function in human neurons, and therefore, the current lack of a difference could equally result from the fact that both WT and cKO glia were non-functional altogether. The authors cite two studies to state that human neurons do not form synapses in the absence of astrocytes, Zhang et al. 2013 and Huang et al. 2017, but neither seem to be listed in the references (unless Zhang et al. 2014 was meant), making it difficult to assess the relevance of these data. However, since the data on astrocytic Nlgn1-3 deletion in vivo are compelling on their own, I do not see the co-culture experiment as essential for the main conclusions of the study.

      Minor comment:

      Please add the information on the strain background of the mice to the methods section of the manuscript. Strain background can have a significant impact on many aspects of neuronal function, and this information is therefore essential for the interpretation of potential differences to other studies.

      We deeply apologize for forgetting to include the two important references mentioned by the reviewer in the reference list. We understand that the reviewer as a result could not assess the validity of our statement that co-culture of glia is required for efficient synapse formation by human neurons that are induced from ES or iPS cells. Note that this conclusion does not postulate that all synapse formation requires glia, since the cited papers demonstrate that human neurons induced by our protocol still form scarce synapses without glia. This observation has been confirmed in many different experiments that were performed after the data presented in the cited papers. As a result of this extensive prior documentation that human neurons produced by forced expression of Ngn2 require coculture of glia for efficient synapse formation, we do not feel that we need to repeat this basic characterization of our culture system again to validate multiple previous papers and hope the reviewer will concur. We have additionally added the relevant mouse strain information to the methods section.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review):

      The experimental rigor and design of the noctural IOP experiments was weak with low n values and differing methods of IOP measurement (conscious versus anesthetized). The same method of IOP measurement needs to be used for all measurements to make any conclusions on the circadian patterns of IOP in each condition.

      One of the goals of our study was to confirm the results from the Patel et al (2021; PMID33853948) study, which in which nocturnal IOP measurements were conducted in anesthetized mice and diurnal IOP measurements in awake animals but we agree with both Reviewers that IOP should be measured under identical experimental conditions. Parenthetically, the number of animals per each treatment paradigm in the original version (N = 4) was sufficient to produce statistical significance for diurnal control vs diurnal TGFB, and diurnal control vs nocturnal control conditions.

      To address the comment, we generated an additional cohort of TGFb2-expressing mice (N = 6) in which nocturnal and diurnal measurements were performed in awake animals. The results are shown in the revised Figure 6. Similar to the anesthetized cohort, the diurnal IOP in Lv-TGFB2 mice was statistically indistinguishable from the nocturnal value, indicating that TGFB2-induced OHT is not additive to physiological (circadian) OHT. The TRPV4-dependence of ocular hypertension induced by physiological and pathological methods suggests that the channel functions as a final common mechanism for ocular hypertension.

      Reviewer #2 (Public review):

      Figure 1A-C. Often there is a difference between the massage (message?, op. authors) and transcript data. I recommend the authors to confirm with qPCR data with another mode of protein measurements.

      We are not sure we understand the Reviewer’s comment regarding the “difference between the message and transcript data” but note that the mRNA data shown in panels A & B are confirmatory of previously published transcriptomic and proteomic screens (eg, Fleenor et al., IOVS 2006; Bollinger et al., IOVS 2011;  Callaghan et al., Scientific Reports 2022; Li et al., Current Eye Research 2022 etc) and were included to show that the transcriptional response of canonical SMAD and pro-fibrotic genes unfolds as predicted from previous work. With regard to TRPV4 signaling, we expand transcriptomic data with protein analysis (Western blots) and functional analyses (measurements of TRPV4-mediated current and calcium imaging). Transcriptomic, protein expression, electrophysiological and imaging experiments revealed a remarkable consistency in TGFB2-dependence of gene (Fig. 1C) and protein expression (Fig. 1D), transmembrane current (Fig. 3C) and intracellular calcium (Fig. 2).

      Parenthetically, we attempted to get a sense for the TGFB2-dependence of Piezo1 protein expression by conducting Western blots with multiple antibodies and experimental conditions. These efforts were unsuccessful, presumably due to the complexity (30-40 TM domains) and large molecular weight (280-300 kDa) of the protein. We note, however, that Piezo1 signaling cannot account for the observed OHT given that studies by us and others  (Yarishkin et al., 2021, PMID: 33226641 and Zhu et al., 2021; PMID: 33532718) associated Piezo1 signaling with facility increases. The revised m/s reads: “The suppression of outflow facility by Piezo1 inhibitors applied under in vitro and in vivo conditions (39, 81) instead suggests that Piezo1 opposes the hypertensive functions of TRPV4.” The preprint by Redmon et al. (bioRxiv 2024, PMID 39041037) expands the TRPV4-dependence of OHT to microbead-induced, steroid-induced and nocturnal models of OHT to indicate that TRPV4 functions as a universal driver of elevated IOP.  We reiterate this in the revised Discussion.

      Does direct TRPV4 activation also induce the expression of these markers? Does inhibition of TRPV4, after TGF-β treatment, prevent the expression of these markers? Is TRPV4 acting downstream of this response?

      A RNASeq study conducted by us (Rudzitis et al., under review) suggests that the agonist GSK101 has minimal effect on the fibrotic and canonical pathways shown in panels A and B. These data are beyond the scope of the present study. They will be published elsewhere, however, we include the data associated with genes depicted in panels A and B for the reviewer at the end of this Response.

      We conducted an additional series of experiments to test whether TGFB2-induced upregulation of the TRPV4 and Piezo1 genes is itself TRPV4-dependent. As shown in the new SFig. 1, upregulation of the two genes is unaffected by TRPV4 inhibition.

      Figure 1D. Beta tubulin is not a membrane marker. Having staining of b tubulin in membrane fraction shows contamination from the cytoplasm. Does the overall expression also increase?

      b-tubulin associates with the plasma membrane by binding to integral membrane proteins in the plasma and organellar membranes through palmitoylation and attachment to linker proteins and as an integral component of exocytotic vesicles (Wolff, BBA 2009; Hogerheide et al., PNAS 2017). The protein is often used as a loading control for the TRPV4 protein (please see https://www.cellsignal.com/products/primary-antibodies/trpv4-antibody/65893; Grove et al., Science Signaling 2019 and Moore et al., PNAS 2013).  Parenthetically, our RNASeq studies did not find modulation of b-tubulin expression by TGFβ2 [CNR and DK, unpublished observations].

      We examined the overall (cytosolic and membrane) TRPV4 expression and observed, similarly to the membrane fraction alone (Figure 2), upregulation following cytokine stimulation:

      Author response image 1.

      Western blot, total protection extract from control and TGFb2-treated TM cells [Alomone antibody].

      These results in our estimation do not add to the overall narrative and were not included into the paper.

      Figure 4A: it is not very clear. I recommend including a zoom image or better resolution image.

      We include a whole-page image as the new SFigure 4.

      Figure 5B and 6B. Why there is a difference between groups in pre-injection panel. As Figure 5A, in pre-injection, there is no difference between LV-TGFβ and LV-control while in 5B there is a significant difference between these groups.

      We revised Figure Legends to clarify that “pre-injection” in Figures 5B and 6B refers to IOP measurements before the intracameral injection of HC-06  not pre-injection of lentiviral constructs.

      Discussion section. Line 279: "TRPV4 channels in cells treated with TGFβ2 are likely to be constitutively active" ... needs to be discussed further.

      We rewrote the paragraph to clarify that TRPV4 is a thermosensitive channel that is expected to be constitutively active at the incubator temperature:

      “The effectiveness of TRPV4 inhibition in suppressing TGFB2-induced contractility (Fig. 4) is consistent with constitutive activation of TRPV4 channels in incubator-cultured cells.  TRPV4 is a thermosensitive channel (Q10 ~10). Mouse TRPV4 is activated by physiological temperatures (Chung et al., 2003; Shibasaki et al., 2007) with peak activation between ~34 - 37oC (Guler et al., 2003). The several-fold increase in functional expression of the channel in TGFB2-treated cells (Fig. 2) would be expected to promote tonic influx of Ca2+ and Ca2+-dependent cellular signaling. The abrogation of the contractile response in the presence of HC-06 indicates that TRPV4-mediated Ca2+ influx represents the principal source of calcium that drives the contractile response. Consistent with this, supplementation with the agonist GSK101 was sufficient to evoke TM contraction (Fig. 4B).”

      Line 280: "The residual contractility in HC-06-treated cells may reflect TGFβ2-mediated contributions from Piezo1." Piezo1 has a low threshold for mechanosensitivity. How do the authors discuss the observation that, in the presence of Piezo1, TRPV4 has a more prominent mechanosensory function? Is this tied to TGFβ signalling?

      This is an interesting question. Our macroscopic and single channel recordings of Piezo1 activity in TM cells recapitulate the time course published in the original Coste et al. (2010) study, showing the channel inactivates within 10-100 msec (Yarishkin et al., 2021). Thus, it is likely that the channel is largely inactivated during chronic ocular hypertension. Indeed, it has been suggested that resting membrane tension alone may be sufficient to inactivate Piezo1 (Lewis and Grandl, 2015), with cells grown on stiff substrates (e.g., under our experimental conditions) experiencing almost complete Piezo1 inactivation. We propose that the primary function of Piezo channels may be to sense and transduce transient mechanical loading. The remarkable IOP-lowering effectiveness of TRPV4 antagonists and knockdown indicates that - in contrast to Piezo1 - TRPV4 activation is sustained.  

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The complete strain name for the Trpv4-/- mice are missing.

      Corrected.

      The layout for Figure 6 is confusing as HC-06 was only used in panels B and C but the labels are above panel A.

      Corrected.

      Reviewer #2 (Recommendations for the authors):

      Only two mice were used for the noctural IOP experiments. Justification for retreating the same mice in opposite eyes and counting it as n=4 is not rigorous or justified.

      The number of mice investigated in the original submission was four. In Week 1, two mice underwent PBS injections and 2 two mice were treated with HC-06. After the baseline was re-established in Week 2, the treatments were reversed.

      We supplemented these numbers with an additional cohort of 6 mice, with identical results re: nocturnal vs diurnal IOP. These data are presented in the revised Figure 6.

      Why are daytime IOPs measured in awake mice but noctural IOP's measured in isoflurane anesthetized mice? Anesthesia is well known to effect IOP and using two different methods could alter the results, especially when comparing between the groups. This could be why you did not see a noctural rise in the TGFB injected eyes. The same method needs to be used for all measurements to make any conclusions on the circadian patterns of IOP in each condition.

      This is a good point, please see our response above.

    1. Author response:

      Reviewer #1:

      Point 1

      Not many weaknesses, but probably validation at more enhancers could have made the paper stronger.

      We experimentally validated two sets of enhancers from two distinct tissues and observed similar effects. While this supports the idea that the TEAD-tissue-specific TF interaction we observe is not restricted to a single tissue, we agree that testing additional enhancers from a third tissue would strengthen our conclusions. We will acknowledge in the discussion that including a third tissue could provide additional support for the generality of our findings.

      Reviewer #2:

      Point 1

      The authors propose a mechanism of a TF trio (TEAD - CHD4 - tissue-specific TFs). However, only one validation experiment checked CHD4. CHD4 binding was not mentioned at all in the other cases.

      Indeed, CHD4 binding was experimentally validated at only one enhancer. This was a deliberate decision based on two key considerations:

      (1) Consistent functional response across enhancers: We tested multiple enhancers (n =8) for functional response to the TEAD+YAP and GATA4/6 combination. All enhancers tested exhibited the same trend—attenuation of GATA-mediated activation upon co-expression of TEAD or TEAD/YAP. This consistent pattern supports a shared mechanism across these elements.

      (2) Substantial prior evidence supporting CHD4 recruitment by both GATA4 and YAP: Specifically, CHD4 recruitment by GATA4 has been described in the context of cardiovascular development[1], and CHD4 can also be recruited by TEAD coactivator YAP2. Furthermore, published genomic occupancy data from embryonic heart tissue show widespread co-binding of GATA4, TEAD, and CHD4[1,3], including at most of the cardiac enhancers we functionally tested (4 out of 5).

      Given the consistent enhancer responses and the supporting literature and genomic data indicating TEAD-CHD4 co-occupancy, we chose to validate CHD4 binding at a representative enhancer as a proof of concept.

      We will clarify this rationale in the revised manuscript to better address this concern.

      Reviewer #2:

      Point 2

      The authors integrated E12.5 TEAD binding with E11.5 acetylation data, and it would be important to show that this experimental approach is valid or otherwise qualify its limitations.

      We will provide additional evidence in support of this approach in the revised manuscript or alternatively acknowledge its limitations.

      Reviewer #2:

      Point 3

      Motif co-occurrence analysis was extended to claiming TF interactions without further validation.

      We thank the reviewer for pointing out this important distinction. We reviewed the manuscript and identified seven instances where TF interactions were mentioned. Four of these correctly refer to previously established protein-protein interactions. For the remaining instances, we will adjust the wording to reflect the level of evidence, e.g.  describe combinatorial binding based on motif co-occurrence, rather than implying direct interaction.

      Reviewer #3:

      Point 1

      Much of this manuscript focuses on confirming transcription factor relationships that have been reported previously. For example, it is well known that GATA4 interacts with MEF2 in the ventricle. There are limited new or unexpected associations discussed and tested.

      We thank the reviewer for this important observation and see the recurrence of known interactions, such as GATA4-MEF2, not as a drawback, but as an important validation of our methodology.

      The identification of novel TF-TF combinations was geared toward uncovering shared regulatory principles across diverse human developmental tissues. While analysing 13 heterogeneous embryonic tissues introduced limitations, such as cellular complexity that may obscure rare interactions, it also allowed the identification of robust, recurrent patterns across tissues.  Indeed, using this approach, we identified the widespread combinatorial effect of TEAD in partnership with lineage-specific TFs, which is explored more in depth in the manuscript.

      Another main goal of the study was to develop and demonstrate a generalizable strategy for identifying combinatorial TF binding patterns that underlie tissue-specific gene regulation. Given the inherent heterogeneity of the embryonic organs analysed, the approach is naturally biased toward recovering the most prevalent, and often well-characterized, TF combinations. While we fully acknowledge this limitation, we believe that the ability to robustly recover well-established TF partnerships across multiple organs provides a valuable proof of concept. The next step will be to apply this strategy to single-cell RNA datasets, in order to define TF relationships at higher resolution, for example, resolving associations down to specific family members that cooperate within distinct lineages or cell types, and identifying less frequent or underrepresented TF-TF relationships.

      In this context, we believe that our strategy has successfully highlighted shared enhancer logic and offers a framework for future high-resolution dissection of TF cooperativity at the single-cell level. The rationale for analysing heterogeneous tissues, along with its limitations, will be addressed in the revised version.

      Reviewer #3:

      Point 2

      Embryonic tissues are highly heterogeneous, limiting the utility of the bulk ChIP-seq employed in these analyses. Does the cellular heterogeneity explain the discrepancy between TEAD binding and histone acetylation? Similarly, how does conservation between species affect the TF predictions?

      We thank the reviewer for raising these important points. We acknowledge the limitations of using bulk ChIP-seq data in the context of complex embryonic tissues (see also previous point). We cannot exclude that the discrepancy between TEAD binding and histone acetylation is an effect of cellular heterogeneity. Indeed, we mention in the results “Our ventricle-specific enhancers were sampled at a single time point and likely represent enhancers that are selectively active in different cell types and developmental stages, given the heterogeneity of cell types in the ventricle”. The limitation of bulk ChIP-seq will be addressed in the discussion. In the specific case of the enhancers selected for validation, the binding site sequences are conserved between species, suggesting that the cis-regulatory activity is likely to be similar in both.

      Reviewer #3:

      Point 3

      Some of the interpretations should also be fleshed out a bit more to clarify the advantage of the analyses presented here. For example, if Gata4 and Foxa2 transcripts are expressed during different stages of development, then it's likely that (as stated by the authors) these motifs are not used during the same stage of development. But examining the flanking regions wasn't necessary to make that statement. This type of conclusion seems tangential to the benefit of this analysis, which is to understand which TFs work together in a single organ at a single time point.

      We appreciate the reviewer’s comment and the opportunity to clarify our interpretation. The reviewer refers to the finding that GATA4 and FOXA2 motifs are flanked by different sets of motifs in liver enhancers, suggesting that these TFs operate within distinct regulatory contexts.

      Our aim was not to state that GATA4 and FOXA2 do not function simultaneously—this can indeed be inferred from their non-overlapping expression patterns. Rather, we intended to highlight the potential of our approach, even when applied to bulk data, to resolve distinct regulatory modules that may act in different subpopulations of cells or developmental windows within the same tissue.

      We will revise the relevant section of the manuscript to make this interpretative point clearer.

      Reviewer #3:

      Point 4

      This manuscript hinges on luciferase assays whose results can be difficult to translate to complex gene regulation networks. Many motifs are often clustered together, which makes designing experiments at endogenous loci important in studies such as this one.

      We agree with the Reviewer that luciferase assays represent an oversimplified model of gene regulation and do not fully capture the complexity of endogenous regulatory networks. We will explicitly acknowledge this limitation in the discussion.

      Mutagenesis of TEAD and tissue-specific TF motifs at endogenous loci would provide more conclusive evidence. However, our goal was to test the generality of TEAD effect across multiple enhancers and tissues. Despite its limitations, a luciferase-based assay was the most feasible approach, as an endogenous strategy would not have allowed us to assess a broader set of enhancers efficiently. Additionally, the presence of recurrent motifs and the potential functional redundancy among enhancers targeting the same gene can complicate the interpretation of single-locus perturbations.

      References

      (1) Robbe ZL, Shi W, Wasson LK, Scialdone AP, Wilczewski CM, Sheng X, et al. CHD4 is recruited by GATA4 and NKX2-5 to repress noncardiac gene programs in the developing heart. Genes Dev. 2022 Apr 1;36(7–8):468–82.

      (2) Kim M, Kim T, Johnson RL, Lim DS. Transcriptional Co-repressor Function of the Hippo Pathway Transducers YAP and TAZ. Cell Rep. 2015 Apr;11(2):270–82.

      (3) Akerberg BN, Gu F, VanDusen NJ, Zhang X, Dong R, Li K, et al. A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers. Nat Commun. 2019 Oct 28;10(1):4907.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews: 

      Reviewer #1 (Public Review): 

      Summary: 

      The authors state the study's goal clearly: "The goal of our study was to understand to what extent animal individuality is influenced by situational changes in the environment, i.e., how much of an animal's individuality remains after one or more environmental features change." They use visually guided behavioral features to examine the extent of correlation over time and in a variety of contexts. They develop new behavioral instrumentation and software to measure behavior in Buridan's paradigm (and variations thereof), the Y-maze, and a flight simulator. Using these assays, they examine the correlations between conditions for a panel of locomotion parameters. They propose that inter-assay correlations will determine the persistence of locomotion individuality.

      Strengths: 

      The OED defines individuality as "the sum of the attributes which distinguish a person or thing from others of the same kind," a definition mirrored by other dictionaries and the scientific literature on the topic. The concept of behavioral individuality can be characterized as: 

      (1) a large set of behavioral attributes, 

      (2) with inter-individual variability, that are 

      (3) stable over time. 

      A previous study examined walking parameters in Buridan's paradigm, finding that several parameters were variable between individuals, and that these showed stability over separate days and up to 4 weeks (DOI: 10.1126/science.aaw718). The present study replicates some of those findings and extends the experiments from temporal stability to examining the correlation of locomotion features between different contexts.

      The major strength of the study is using a range of different behavioral assays to examine the correlations of several different behavior parameters. It shows clearly that the inter-individual variability of some parameters is at least partially preserved between some contexts, and not preserved between others. The development of highthroughput behavior assays and sharing the information on how to make the assays is a commendable contribution.

      We thank the reviewer for his exceptionally kind assessment of our work!

      Weaknesses: 

      The definition of individuality considers a comprehensive or large set of attributes, but the authors consider only a handful. In Supplemental Fig. S8, the authors show a large correlation matrix of many behavioral parameters, but these are illegible and are only mentioned briefly in Results. 

      We have now uploaded a high-resolution PDF to the Github Address: https://github.com/LinneweberLab/Mathejczyk_2024_eLife_Individuality/blob/main/S8.pdf, and this is also mentioned in the figure legend for Fig. S8

      Why were five or so parameters selected from the full set? How were these selected? 

      The five parameters (% of time walked, walking speed, vector strength, angular velocity, and centrophobicity) were selected because they describe key aspects of the investigated behaviors that can be compared directly across assays. Importantly, several parameters we typically use (e.g., Linneweber et al., 2020) cannot be applied under certain conditions, such as darkness or the absence of visual cues. Furthermore, these five parameters encompass three critical aspects of navigation across standard visual behavioral arenas: (1) The “exploration” category is characterized by parameters describing the fly’s activity. (2) Parameters related to “attention” reflect heightened responses to visual cues, but unlike commonly used metrics such as angle or stripe deviations (e.g., Coulomb, 2012; Linneweber et al., 2020), they can also be measured in absence of visual cues and are therefore suitable for cross-assay comparisons. (3) The parameter “centrophobicity,” used as a potential indicator of anxiety, is conceptually linked to the open-field test in mice, where the ratio of wall-to-open-field activity is frequently calculated as a measurement of anxiety (see for example Carter, Sheh, 2015, chapter 2. https://www.sciencedirect.com/book/9780128005118/guide-to-researchtechniques-in-neuroscience). Admittedly, this view is frequently challenged in mice, but it has a long history which is why we use it.

      Do the correlation trends hold true across all parameters? For assays in which only a subset of parameters can be directly compared, were all of these included in the analysis, or only a subset? 

      As noted above, we only included a subset of parameters in our final analysis, as many were unsuitable for comparison across assays while still providing valuable assayspecific information which are important to relate these results to previous publications.

      The correlation analysis is used to establish stability between assays. For temporal retesting, "stability" is certainly the appropriate word, but between contexts, it implies that there could be 'instability'. Rather, instead of the 'instability' of a single brain process, a different behavior in a different context could arise from engaging largely (or entirely?) distinct context-dependent internal processes, and have nothing to do with process stability per se. For inter-context similarities, perhaps a better word would be "consistency". 

      Thank you for this suggestion. During the preparation of the manuscript, we indeed frequently alternated between the terms “stability” and “consistency.” And decided to go with “stability” as the only descriptor, to keep it simple. We now fully agree with the reviewer’s argument and have replaced “stability” by “consistency” throughout the current version of the manuscript in order to increase clarity and coherence.

      The parameters are considered one by one, not in aggregate. This focuses on the stability/consistency of the variability of a single parameter at a time, rather than holistic individuality. It would appear that an appropriate measure of individuality stability (or individuality consistency) that accounts for the high-dimensional nature of individuality would somehow summarize correlations across all parameters. Why was a multivariate approach (e.g. multiple regression/correlation) not used? Treating the data with a multivariate or averaged approach would allow the authors to directly address 'individuality stability' and analyses of single-parameter variability stability.

      We agree with the reviewer that a multivariate analysis adds clear advantages in terms of statistical power, in addition to our chosen approach. On one hand, we believe that the simplicity of our initial analysis, both for correlational and mean data, makes easy for readers to understand and reproduce our data. While preparing the previous version of the manuscript we were skeptical since more complex analyses often involve numerous choices, which can complicate reproducibility. For instance, a recent study in personality psychology (Paul et al., 2024) highlighted the risks of “forking paths” in statistical analysis, showing that certain choices of statistical methods could even reverse findings—a concern mitigated by our simplistic straightforward approach. Still, in preparation of this revised version of the manuscript, we accepted the reviewer’s advice and reanalyzed the data using a generalized linear model. This analysis nicely recapitulates our initial findings and is now summarized in a single figure (Fig. 9).

      The correlation coefficients are sometimes quite low, though highly significant, and are deemed to indicate stability. For example, in Figure 4C top left, the % of time walked at 23{degree sign}C and 32{degree sign}C are correlated by 0.263, which corresponds to an R2 of 0.069 i.e. just 7% of the 32{degree sign}C variance is predictable by the 23{degree sign}C variance. Is it fair to say that a 7% determination indicates parameter stability? Another example: "Vector strength was the most correlated attention parameter... correlations ranged... to -0.197," which implies that 96% (1 - R2) of Y-maze variance is not predicted by Buridan variance. At what level does an r value not represent stability?

      We agree that this is an important question. Our paper clearly demonstrates that individuality always plays a role in decision-making (and, in this context, any behavioral output can be considered a decision). However, the non-linear relationship between certain situations and the individual’s behavior often reduces the predictive value (or correlation) across contexts, sometimes quite drastically.

      For instance, temperature has a relatively linear effect on certain behavioral parameters, leading to predictable changes across individuals. As a result, correlations across temperature conditions are often similar to those observed across time within the same situation. In contrast, this predictability diminishes when comparing conditions like the presence or absence of visual stimuli, the use of different arenas, or different modalities.

      For this reason, we believe that significance remains the best indicator for describing how measurable individuality persists, even across vastly different situations.

      The authors describe a dissociation between inter-group differences and interindividual variation stability, i.e. sometimes large mean differences between contexts, but significant correlation between individual test and retest data. Given that correlation is sensitive to slope, this might be expected to underestimate the variability stability (or consistency). Is there a way to adjust for the group differences before examining the correlation? For example, would it be possible to transform the values to in-group ranks prior to correlation analysis?  

      We thank the reviewer for this suggestion, and we have now addressed this point. To account for slope effects, we have now introduced in-group ranks for our linear model computation (see Fig. 9). 

      What is gained by classifying the five parameters into exploration, attention, and anxiety? To what extent have these classifications been validated, both in general and with regard to these specific parameters? Is the increased walking speed at higher temperatures necessarily due to an increased 'explorative' nature, or could it be attributed to increased metabolism, dehydration stress, or a heat-pain response? To what extent are these categories subjective?

      We agree that grouping our parameters into traits like exploration, attention, and anxiety always includes subjective decisions. The classification into these three categories is even considered partially controversial in the mouse specific literature, which uses the term “anxiety” in similar experiments (see for exampler Carter, Sheh, 2015, chapter 2 . https://www.sciencedirect.com/book/9780128005118/guide-to-research-techniquesin-neuroscience). Nevertheless, we believe that readers greatly benefit from these categories, since they make it easier to understand (beyond mathematical correlations) which aspects of the flies’ individuality can be considered consistent across situations. Furthermore, these categories serve as a bridge to compare insight from very distinct models.

      The legends are quite brief and do not link to descriptions of specific experiments. For example, Figure 4a depicts a graphical overview of the procedure, but I could not find a detailed description of this experiment's protocol.

      We assume the reviewer is referring to Figure 3a. The detailed experimental protocol can be found in the Materials and Methods section under Setup 2: IndyTrax Multi-Arena Platform. We have now clarified this in the mentioned figure legend.

      Using the current single-correlation analysis approach, the aims would benefit from rewording to appropriately address single-parameter variability stability/consistency (as distinct from holistic individuality). Alternatively, the analysis could be adjusted to address the multivariate nature of individuality, so that the claims and the analysis are in concordance with each other.

      The reviewer raises an important point about hierarchies within the concept of animal individuality or personality. We agree that this is best addressed by first focusing on single behavioral traits/parameters and then integrating several trait properties into a cohesive concept of animal personality (holistic individuality). To ensure consistency throughout the text, we have now thoroughly reviewed the entire manuscript clearly distinguish between single-parameter variability stability/consistency and holistic individuality/personality.

      The study presents a bounty of new technology to study visually guided behaviors. The GitHub link to the software was not available. To verify the successful transfer of open hardware and open-software, a report would demonstrate transfer by collaboration with one or more other laboratories, which the present manuscript does not appear to do. Nevertheless, making the technology available to readers is commendable.

      We have now uploaded all codes and materials to GitHub and made them available as soon as we received the reviewers’ comments. All files and materials can be accessed at https://github.com/LinneweberLab/Mathejczyk_2024_eLife_Individuality, which is now frequently mentioned throughout the revised manuscript.

      The study discusses a number of interesting, stimulating ideas about inter-individual variability, and presents intriguing data that speaks to those ideas, albeit with the issues outlined above.

      While the current work does not present any mechanistic analysis of inter-individual variability, the implementation of high-throughput assays sets up the field to more systematically investigate fly visual behaviors, their variability, and their underlying mechanisms. 

      We thank the reviewer again for the extensive and constructive feedback.

      Reviewer #2 (Public Review): 

      Summary: 

      The authors repeatedly measured the behavior of individual flies across several environmental situations in custom-made behavioral phenotyping rigs.

      Strengths: 

      The study uses several different behavioral phenotyping devices to quantify individual behavior in a number of different situations and over time. It seems to be a very impressive amount of data. The authors also make all their behavioral phenotyping rig design and tracking software available, which I think is great and I'm sure other folks will be interested in using and adapting it to their own needs.

      We thank the reviewer for highlighting the strengths of our study.

      Weaknesses/Limitations: 

      I think an important limitation is that while the authors measured the flies under different environmental scenarios (i.e. with different lighting and temperature) they didn't really alter the "context" of the environment. At least within behavioral ecology, context would refer to the potential functionality of the expressed behaviors so for example, an anti-predator context, a mating context, or foraging. Here, the authors seem to really just be measuring aspects of locomotion under benign (relatively low-risk perception) contexts. This is not a flaw of the study, but rather a limitation to how strongly the authors can really say that this demonstrates that individuality is generalized across many different contexts. It's quite possible that rank order of locomotor (or other) behaviors may shift when the flies are in a mating or risky context. 

      We agree with the reviewer that the definition of environmental context can differ between fields and that behavioral context is differently defined, particularly in ecology. Nevertheless, we highlight that our alternations of environmental context are highly stereotypic, well-defined, and unbiased from any interpretation (we only modified what we stated in the experimental description without designing a specific situation that might be again perceived individually differently. E.g., comparing a context with a predator and one without might result in a binary response because one fraction of the tested individuals might perceive the predator in the predator situation, and the other half does not. 

      The analytical framework in terms of statistical methods is lacking. It appears as though the authors used correlations across time/situations to estimate individual variation; however, far more sophisticated and elegant methods exist. The paper would be a lot stronger, and my guess is, much more streamlined if the authors employ hierarchical mixed models to analyse these data these models could capture and estimate differences in individual behavior across time and situations simultaneously. Along with this, it's currently unclear whether and how any statistical inference was performed. Right now, it appears as though any results describing how individuality changes across situations are largely descriptive (i.e. a visual comparison of the strengths of the correlation coefficients?). 

      The reviewer raises an important point, also raised by reviewer #1. On one hand, we agree with both reviewers that a more aggregated analysis has clear advantages like more statistical power and has the potential to streamline our manuscript, which is why we added such an analysis (see below). On the other hand, we would also like to defend the initial approach we took, since we think that the simplicity of the analysis for both correlational and mean data is easy to understand and reproduce. More complex analyses necessarily include the selection of a specific statistical toolbox by the experimenters and based on these decisions, different analyses become less comparable and more and more complicated to reproduce, unless the entire decision tree is flawlessly documented. For instance, a recent personality psychology paper investigated the relationship between statistical paths within the decision tree (forking analysis) and their results, leading to very surprising results (Paul et al., 2024), since some paths even reversed their findings. Such a variance in conclusions is hardly possible with the rather simplistic and easily reproducible analysis we performed. One of the major strengths of our study is the simple experimental design, allowing for rather simple and easy to understand analyses.

      We nevertheless took the reviewer’s advice very seriously and reanalyzed the data using a generalized linear model, which largely recapitulated the findings of our previously performed “low-tech” analysis in a single figure (Fig. 9).

      Another pretty major weakness is that right now, I can't find any explicit mention of how many flies were used and whether they were re-used across situations. Some sort of overall schematic showing exactly how many measurements were made in which rigs and with which flies would be very beneficial. 

      We apologize for this inconvenience. A detailed overview of male and female sample sizes has been listed in the supplemental boxplots next to the plots (e.g, Fig S6). Apparently, this was not visible enough. Therefore, we have now also uniformly added the sample sizes to the main figure legends.

      I don't necessarily doubt the robustness of the results and my guess is that the author's interpretations would remain the same, but a more appropriate modeling framework could certainly improve their statistical inference and likely highlight some other cool patterns as these methods could better estimate stability and covariance in individual intercepts (and potentially slopes) across time and situation.

      As described above, we have now added the suggested analyses. We hope that the reviewer will appreciate the new Fig. 9, which, in our opinion, largely confirms our previous findings using a more appropriate generalized linear modelling framework.

      Reviewer #3 (Public Review): 

      This manuscript is a continuation of past work by the last author where they looked at stochasticity in developmental processes leading to inter-individual behavioural differences. In that work, the focus was on a specific behaviour under specific conditions while probing the neural basis of the variability. In this work, the authors set out to describe in detail how stable the individuality of animal behaviours is in the context of various external and internal influences. They identify a few behaviours to monitor (read outs of attention, exploration, and 'anxiety'); some external stimuli (temperature, contrast, nature of visual cues, and spatial environment); and two internal states (walking and flying).

      They then use high-throughput behavioural arenas - most of which they have built and made plans available for others to replicate - to quantify and compare combinations of these behaviours, stimuli, and internal states. This detailed analysis reveals that:

      (1) Many individualistic behaviours remain stable over the course of many days. 

      (2) That some of these (walking speed) remain stable over changing visual cues. Others (walking speed and centrophobicity) remain stable at different temperatures.

      (3) All the behaviours they tested failed to remain stable over the spatially varying environment (arena shape).

      (4) Only angular velocity (a readout of attention) remains stable across varying internal states (walking and flying).

      Thus, the authors conclude that there is a hierarchy in the influence of external stimuli and internal states on the stability of individual behaviours.

      The manuscript is a technical feat with the authors having built many new highthroughput assays. The number of animals is large and many variables have been tested - different types of behavioural paradigms, flying vs walking, varying visual stimuli, and different temperatures among others. 

      We thank the reviewer for this extraordinary kind assessment of our work!

      Recommendations for the authors:  

      Reviewing Editor (Recommendations For The Authors): 

      While appreciating the effort and quality of the work that went into this manuscript, the reviewers identified a few key points that would greatly benefit this work.

      (1) Statistical methods adopted. The dataset produced through this work is large, with multiple conditions and comparisons that can be made to infer parameters that both define and affect the individualistic behaviour of an animal. Hierarchical mixed models would be a more appropriate approach to handle such datasets and infer statistically the influence of different parameters on behaviours. We recommend that the authors take this approach in the analyses of their data.

      (2) Brevity in the text. We urge the authors to take advantage of eLife's flexible template and take care to elaborate on the text in the results section, the methods adopted, the legends, and the guides to the legends embedded in the main text. The findings are likely to be of interest to a broad audience, and the writing currently targets the specialist.

      Reviewer #2 (Recommendations For The Authors): 

      I want to start by saying this seems like a really cool study! It's an impressive amount of work and addressing a pretty basic question that is interesting (at least I think so!)

      We thank the reviewer again for this assessment!

      That said, I would really strongly recommend the authors embrace using mixed/hierarchical models to analyze their data. They're producing some really impressive data and just doing Pearson correlation coefficients across time points and situations is very clunky and actually losing out on a lot of information. The most up-todate, state-of-the-art are mixed models - these models can handle very complex (or not so complex) random structures which can estimate variance and importantly, covariance, in individual intercepts both over time and across situations. I actually think this could add some really cool insights into the data and allow you to characterize the patterns you're seeing in far more detail. It's datasets exactly like this that are tailormade for these complex variance partitioning models! 

      As mentioned before, we have now adopted a more appropriate GLM-based data analysis (see above).

      Regardless of which statistical methods you decide to use, please explicitly state in your methods exactly what analyses you did. That is completely lacking now and was a bit frustrating. As such, it's completely unclear whether or how statistical inference was performed. How did you do the behavioral clustering? 

      We apologize that these points were not clearly represented in the previous version of the manuscript. We have now significantly extended the methods section to include a separate paragraph on the statistical methods used, in order to address this critique and hope that the revised version is clear now.

      Also, I could not for the life of me figure out how many flies had been measured. Were they reused across the situation? Or not?

      We reused the same flies across situations whenever possible. However, having one fly experience all assays consecutively was not feasible due to their fragility. Instead, individual flies were exposed to at least 2 of the 3 groups of assays used here: in the Indytrax setup ,  the Buridan arenas and variants thereof, and the virtual arenas Hence, we have compared flies across entirely different setups, but the number of times flies can be retested is limited (as otherwise, sample sizes will drop over time, and the flies will have gone through too many experimental alternations). To make this more clear, we have elaborated on this point in the main text, and we added group sample sizes to figure legends r.

      What are these "groups" and "populations" that are referred to in the results (e.g. lines 384, 391, 409)?

      We apologize for using these two terms somewhat interchangeably without proper introduction/distinction. We have now made this more clear in at the beginning of the results in the main text, by focusing on the term ‘group’. By ‘group’ we refer to the average of all individuals tested in the same situation. Sample sizes in the figure legends now indicate group/population sizes to make this clearer.

      Some of the rationale for the development of the behavioral rigs would have actually been nice to include in the intro, rather than in the results.

      This rationale is introduced at the beginning of the last paragraph of the introduction. We hope that this now becomes clear in the revised version of the manuscript.

      Reviewer #3 (Recommendations For The Authors): 

      This manuscript would do well to take advantage of eLife's flexible word limit. I sense that it has been written in brevity for a different journal but I would urge the authors to revisit this and unpack the language here - in the text, in the figure legends, in references to the figures within the text. The way it's currently written, though not misleading, will only speak to the super-specialist or the super-invested :). But the findings are nice, and it would be nice to tailor it to a broader audience.

      We appreciate this suggestion. Initially, we were hoping that we had described our results as clearly and brief as possible. We apologize if that was not always the case. The comments and requests of all three reviewers now led to a series of additions to both main text and methods, leading to a significantly expanded manuscript. We hope that these additons are helpful for the general, non-expert audience.

    1. Author response:

      The following is the authors’ response to the original reviews

      Overview of changes in the revision

      We thank the reviewers for the very helpful comments and have extensively revised the paper. We provide point-by-point responses below and here briefly highlight the major changes:

      (1) We expanded the discussion of the relevant literature in children and adults.

      (2) We improved the contextualization of our experimental design within previous reinforcement studies in both cognitive and motor domains highlighting the interplay between the two.

      (3) We reorganized the primary and supplementary results to better communicate the findings of the studies.

      (4) The modeling has been significantly revised and extended. We now formally compare 31 noise-based models and one value-based model and this led to a different model from the original being the preferred model. This has to a large extent cleaned up the modeling results. The preferred model is a special case (with no exploration after success) of the model proposed in Therrien et al. (2018). We also provide examples of individual fits of the model, fit all four tasks and show group fits for all, examine fits vs. data for the clamp phases by age, provide measures of relative and absolute goodness of fit, and examine how the optimal level of exploration varies with motor noise.

      Reviewer #1 (Public review):

      Summary:

      Here the authors address how reinforcement-based sensorimotor adaptation changes throughout development. To address this question, they collected many participants in ages that ranged from small children (3 years old) to adulthood (1 8+ years old). The authors used four experiments to manipulate whether binary and positive reinforcement was provided probabilistically (e.g., 30 or 50%) versus deterministically (e.g., 100%), and continuous (infinite possible locations) versus discrete (binned possible locations) when the probability of reinforcement varied along the span of a large redundant target. The authors found that both movement variability and the extent of adaptation changed with age.

      Thank you for reviewing our work. One note of clarification. This work focuses on reinforcementbased learning throughout development but does not evaluate sensorimotor adaptation. The four tasks presented in this work are completed with veridical trajectory feedback (no perturbation).

      The goal is to understand how children at different ages adjust their movements in response to reward feedback but does not evaluate sensorimotor adaptation. We now explain this distinction on line 35.

      Strengths:

      The major strength of the paper is the number of participants collected (n = 385). The authors also answer their primary question, that reinforcement-based sensorimotor adaptation changes throughout development, which was shown by utilizing established experimental designs and computational modelling.

      Thank you.

      Weaknesses:

      Potential concerns involve inconsistent findings with secondary analyses, current assumptions that impact both interpr tation and computational modelling, and a lack of clearly stated hypotheses.

      (1) Multiple regression and Mediation Analyses.

      The challenge with these secondary analyses is that:

      (a) The results are inconsistent between Experiments 1 and 2, and the analysis was not performed for Experiments 3 and 4,

      (b) The authors used a two-stage procedure of using multiple regression to determine what variables to use for the mediation analysis, and

      (c)The authors already have a trial-by-trial model that is arguably more insightful.

      Given this, some suggested changes are to:

      (a) Perform the mediation analysis with all the possible variables (i.e., not informed by multiple regression) to see if the results are consistent.

      (b) Move the regression/mediation analysis to Supplementary, since it is slightly distracting given current inconsistencies and that the trial-by-trial model is arguably more insightful.

      Based on these comments, we have chosen to remove the multiple regression and mediation analyses. We agree that they were distracting and that the trial-by-trial model allows for differentiation of motor noise from exploration variability in the learning block.

      (2) Variability for different phases and model assumptions:

      A nice feature of the experimental design is the use of success and failure clamps. These clamped phases, along with baseline, are useful because they can provide insights into the partitioning of motor and exploratory noise. Based on the assumptions of the model, the success clamp would only reflect variability due to motor noise (excludes variability due to exploratory noise and any variability due to updates in reach aim). Thus, it is reasonable to expect that the success clamps would have lower variability than the failure clamps (which it obviously does in Figure 6), and presumably baseline (which provides success and failure feedback, thus would contain motor noise and likely some exploratory noise).

      However, in Figure 6, one visually observes greater variability during the success clamp (where it is assumed variability only comes from motor noise) compared to baseline (where variability would come from: (a) Motor noise.

      (b) Likely some exploratory noise since there were some failures.

      (c) Updates in reach aim.

      Thanks for this comment. It made us realize that some of our terminology was unintentionally misleading. Reaching to discrete targets in the Baseline block was done to a) determine if participants could move successfully to targets that are the same width as the 100% reward zone in the continuous targets and b) determine if there are age dependent changes in movement precision. We now realize that the term Baseline Variability was misleading and should really be called Baseline Precision.

      This is an important distinction that bears on this reviewer's comment. In clamp trials, participants move to continuous targets. In baseline, participants move to discrete targets presented at different locations. Clamp Variability cannot be directly compared to Baseline Precision because they are qualitatively different. Since the target changes on each baseline trial, we would not expect updating of desired reach (the target is the desired reach) and there is therefore no updating of reach based on success or failure. The SD we calculate over baseline trials is the endpoint variability of the reach locations relative to the target centers. In success clamp, there are no targets so the task is qualitatively different.

      We have updated the text to clarify terminology, expand upon our operational definitions, and motivate the distinct role of the baseline block in our task paradigm (line 674).

      Given the comment above, can the authors please:

      (a) Statistically compare movement variability between the baseline, success clamp, and failure clamp phases.

      Given our explanation in the previous point we don't think that comparing baseline to the clamp makes sense as the trials are qualitatively different.

      (b) The authors have examined how their model predicts variability during success clamps and failure clamps, but can they also please show predictions for baseline (similar to that of Cashaback et al., 2019; Supplementary B, which alternatively used a no feedback baseline)?

      Again, we do not think it makes sense to predict the baseline which as we mention above has discrete targets compared to the continuous targets in the learning phase.

      (c) Can the authors show whether participants updated their aim towards their last successful reach during the success clamp? This would be a particularly insightful analysis of model assumptions.

      We have now compared 31 models (see full details in next response) which include the 7 models in Roth et al. (2023). Several of these model variants have updating even after success with so called planning noise). We also now fit the model to the data that includes the clamp phases (we can't easily fit to success clamp alone as there are only 10 trials). We find that the preferred model is one that does not include updating after success.

      (d) Different sources of movement variability have been proposed in the literature, as have different related models. One possibility is that the nervous system has knowledge of 'planned (noise)' movement variability that is always present, irrespective of success (van Beers, R.J. (2009). Motor learning is optimally tuned to the properties of motor noise. Neuron, 63(3), 406-417). The authors have used slightly different variations of their model in the past. Roth et al (2023) directly Rill compared several different plausible models with various combinations of motor, planned, and exploratory noise (Roth A, 2023, "Reinforcement-based processes actively regulate motor exploration along redundant solution manifolds." Proceedings of the Royal Society B 290: 20231475: see Supplemental). Their best-fit model seems similar to the one the authors propose here, but the current paper has the added benefit of the success and failure clamps to tease the different potential models apart. In light of the results of a), b), and c), the authors are encouraged to provide a paragraph on how their model relates to the various sources of movement variability and ther models proposed in the literature.

      Thank you for this. We realized that the models presented in Roth et al. (2023) as well as in other papers, are all special cases of a more general model. Moreover, in total there are 30 possible variants of the full model so we have now fit all 31 models to our larger datasets and performed model selection (Results and Methods). All the models can be efficiently fit by Kalman smoother to the actual data (rather than to summary statistics which has sometimes been done). For model selection, we fit only the 100 learning trials and chose the preferred model based on BIC on the children's data (Figure 5—figure Supplement 1). After selecting the preferred model we then refit this model to all trials including the clamps so as to obtain the best parameter estimates.

      The preferred model was the same whether we combined the continuous and discrete probabilistic data or just examin d each task separately either for only the children or for the children and adults combined. The preferred model is a pecial case (no exploration after success) of the one proposed in Therrien et al. (2018) and has exploration variability (after failure) and motor noise with full updating with exploration variability (if any) after success. This model differs from the model in the original submission which included a partial update of the desired reach after exploration this was considered the learning rate. The current model suggests a unity learning rate.

      In addition, as suggested by another reviewer, we also fit a value-based model which we adapted from the model described in Giron et al. (2023). This model was not preferred.

      We have added a paragraph to the Discussion highlighting different sources of variability and links to our model comparison.

      (e) line 155. Why would the success clamp be composed of both motor and exploratory noise? Please clarify in the text

      This sentence was written to refer to clamps in general and not just success clamps. However, in the revision this sentence seemed unnecessary so we have removed it.

      (3) Hypotheses:

      The introduction did not have any hypotheses of development and reinforcement, despite the discussion above setting up potential hypotheses. Did the authors have any hypotheses related to why they might expect age to change motor noise, exploratory noise, and learning rates? If so, what would the experimental behaviour look like to confirm these hypotheses? Currently, the manuscript reads more as an exploratory study, which is certainly fine if true, it should just be explicitly stated in the introduction. Note: on line 144, this is a prediction, not a hypothesis. Line 225: this idea could be sharpened. I believe the authors are speaking to the idea of having more explicit knowledge of action-target pairings changing behaviour.

      We have included our hypotheses and predictions at two points in the paper In the introduction we modified the text to:

      "We hypothesized that children's reinforcement learning abilities would improve with age, and depend on the developmental trajectory of exploration variability, learning rate (how much people adjust their reach after success), and motor noise (here defined as all sources of noise associated with movement, including sensory noise, memory noise, and motor noise). We think that these factors depend on the developmental progression of neural circuits that contribute to reinforcement learning abilities (Raznahan et al., 2014; Nelson et al., 2000; Schultz, 1998)."

      In results we modified the sentence to:

      "We predicted that discrete targets could increase exploration by encouraging children to move to a different target after failure.”

      Reviewer #2 (Public review):

      Summary:

      In this study, Hill and colleagues use a novel reinforcement-based motor learning task ("RML"), asking how aspects of RML change over the course of development from toddler years through adolescence. Multiple versions of the RML task were used in different samples, which varied on two dimensions: whether the reward probability of a given hand movement direction was deterministic or probabilistic, and whether the solution space had continuous reach targets or discrete reach targets. Using analyses of both raw behavioral data and model fits, the authors report four main results: First, developmental improvements reflected 3 clear changes, including increases in exploration, an increase in the RL learning rate, and a reduction of intrinsic motor noise. Second, changes to the task that made it discrete and/or deterministic both rescued performance in the youngest age groups, suggesting that observed deficits could be linked to continuous/probabilistic learning settings. Overall, the results shed light on how RML changes throughout human development, and the modeling characterizes the specific learning deficits seen in the youngest ages.

      Strengths:

      (1) This impressive work addresses an understudied subfield of motor control/psychology - the developmental trajectory of motor learning. It is thus timely and will interest many researchers.

      (2) The task, analysis, and modeling methods are very strong. The empirical findings are rather clear and compelling, and the analysis approaches are convincing. Thus, at the empirical level, this study has very few weaknesses.

      (3) The large sample sizes and in-lab replications further reflect the laudable rigor of the study.

      (4) The main and supplemental figures are clear and concise.

      Thank you.

      Weaknesses:

      (1) Framing.

      One weakness of the current paper is the framing, namely w/r/t what can be considered "cognitive" versus "non-cognitive" ("procedural?") here. In the Intro, for example, it is stated that there are specific features of RML tasks that deviate from cognitive tasks. This is of course true in terms of having a continuous choice space and motor noise, but spatially correlated reward functions are not a unique feature of motor learning (see e.g. Giron et al., 2023, NHB). Given the result here that simplifying the spatial memory demands of the task greatly improved learning for the youngest cohort, it is hard to say whether the task is truly getting at a motor learning process or more generic cognitive capacities for spatial learning, working memory, and hypothesis testing. This is not a logical problem with the design, as spatial reasoning and working memory are intrinsically tied to motor learning. However, I think the framing of the study could be revised to focus in on what the authors truly think is motor about the task versus more general psychological mechanisms. Indeed, it may be the case that deficits in motor learning in young children are mostly about cognitive factors, which is still an interesting result!

      Thank you for these comments on the framing of our study. We now clearly acknowledge that all motor tasks have cognitive components (new paragraph at line 65). We also explain why we think our tasks has features not present in typical cognitive tasks.

      (2) Links to other scholarship.

      If I'm not mistaken a common observation in tudies of the development of reinforcement learning is a decrease in exploration over-development (e.g., Nussenbaum and Hartley, 2019; Giron et al., 2023; Schulz et al., 2019); this contrasts with the current results which instead show an increase. It would be nice to see a more direct discussion of previous findings showing decreases in exploration over development, and why the current study deviates from that. It could also be useful for the authors to bring in concepts of different types of exploration (e.g. "directed" vs "random"), in their interpretations and potentially in their modeling.

      We recognize that our results differ from prior work. The optimal exploration pattern differs from task to task. We now discuss that exploration is not one size fits all, it's benefits vary depending upon the task. We have added the following paragraphs to the Discussion section:

      "One major finding from this study is that exploration variability increases with age. Some other studies of development have shown that exploration can decrease with age indicating that adults explore less compared to children (Schulz et al., 2019; Meder et al., 2021; Giron et al., 2023). We believe the divergence between our work and these previous findings is largely due to the experimental design of our study and the role of motor noise. In the paradigm used initially by Schulz et al. (2019) and replicated in different age groups by Meder et al. (2021) and Giron et al. (2023), participants push buttons on a two-dimensional grid to reveal continuous-valued rewards that are spatially correlated. Participants are unaware that there is a maximum reward available and therefore children may continue to explore to reduce uncertainty if they have difficulty evaluating whether they have reached a maxima. In our task by contrast, participants are given binary reward and told that there is a region in which reaches will always be rewarded. Motor noise is an additional factor which plays a key role in our reaching task but minimal if any role in the discretized grid task. As we show in simulations of our task, as motor noise goes down (as it is known to do through development) the optimal amount of exploration goes up (see Figure 7—figure Supplement 2 and Appendix 1). Therefore, the behavior of our participants is rational in terms of R230 increasing exploration as motor noise decreases.

      A key result in our study is that exploration in our task reflects sensitivity to failure. Older children make larger adjustments after failure compared to younger children to find the highly rewarded zone more quickly. Dhawale et al. (2017) discuss the different contexts in which a participant may explore versus exploit (i.e., stick at the same position). Exploration is beneficial when reward is low as this indicates that the current solution is no longer ideal, and the participant should search for a better solution. Konrad et al. (2025) have recently shown this behavior in a real-world throwing task where 6 to 12 year old children increased throwing variability after missed trials and minimized variability after successful trials. This has also been shown in a postural motor control task where participants were more variable after non-rewarded trials compared to rewarded trials (Van Mastrigt et al., 2020). In general, these studies suggest that the optimal amount of exploration is dependent on the specifics of the task."

      (3) Modeling.

      First, I may have missed something, but it is unclear to me if the model is actually accounting for the gradient of rewards (e.g., if I get a probabilistic reward moving at 45°, but then don't get one at 40°, I should be more likely to try 50° next then 35°). I couldn't tell from the current equations if this was the case, or if exploration was essentially "unsigned," nor if the multiple-trials-back regression analysis would truly capture signed behavior. If the model is sensitive to the gradient, it would be nice if this was more clear in the Methods. If not, it would be interesting to have a model that does "function approximation" of the task space, and see if that improves the fit or explains developmental changes.

      The model we use (similar to Roth et al. (2023) and Therrien et al. (2016, 2018)) does not model the gradient. Exploration is always zero-mean Gaussian. As suggested by the reviewer, we now also fit a value-based model (described starting at line 810) which we adapted from the model presented in Giron et al. (2023). We show that the exploration and noise-based model is preferred over the value-based model.

      The multiple-trials-back regression was unsigned as the intent was to look at the magnitude and not the direction of the change in movement. We have decided to remove this analysis from the manuscript as it was a source of confusion and secondary analysis that did not add substantially to the findings of these studies.

      Second, I am curious if the current modeling approach could incorporate a kind of "action hysteresis" (aka perseveration), such that regardless of previous outcomes, the same action is biased to be repeated (or, based on parameter settings, avoided).

      In some sense, the learning rate in the model in the original submission is highly related to perseveration. For example if the learning rate is 0, then there is complete perseveration as you simply repeat the same desired movement. If the rate is 1, there is no perseveration and values in between reflect different amounts of perseveration. Therefore, it is not easy to separate learning rate from perseveration. Adding perseveration as another parameter would likely make it and the learning unidentifiable. However, we now compare 31 models and those that have a non-unity learning rate are not preferred suggesting there is little perseveration.

      (4) Psychological mechanisms. There is a line of work that shows that when children and adults perform RL tasks they use a combination of working memory and trial-by-trial incremental learning processes (e.g., Master et al., 2020; Collins and Frank 2012). Thus, the observed increase in the learning rate over development could in theory reflect improvements in instrumental learning, working memory, or both. Could it be that older participants are better at remembering their recent movements in short-term memory (Hadjiosif et al., 2023; Hillman et al., 2024)?

      We agree that cognitive processes, such as working memory or visuospatial processing, play a role in our task and describe cognitive elements of our task in the introduction (new paragraph at line 65). However, the sensorimotor model we fit to the data does a good job of explaining the variation across age, which suggests that that age-dependent cognitive processes probably play a smaller role.

      Reviewer #3 (Public review):

      Summary:

      The study investigates reinforcement learning across the lifespan with a large sample of participants recruited for an online game. It finds that children gradually develop their abilities to learn reward probability, possibly hindered by their immature spatial processing and probabilistic reasoning abilities. Motor noise, reinforcement learning rate, and exploration after a failure all contribute to children's subpar performance.

      Strengths:

      (1) The paradigm is novel because it requires continuous movement to indicate people's choices, as opposed to discrete actions in previous studies.

      (2) A large sample of participants were recruited.

      (3) The model-based analysis provides further insights into the development of reinforcement learning ability.

      Thank you.

      Weaknesses:

      (1 ) The adequacy of model-based analysis is questionable, given the current presentation and some inconsistency in the results.

      Thank you for raising this concern. We have substantially revised the model from our first submission. We now compare 31 noise-based models and 1 value-based model and fit all of the tasks with the preferred model. We perform model selection using the two tasks with the largest datasets to identify the preferred model. From the preferred model, we found the parameter fits for each individual dataset and simulated the trial by trial behavior allowing comparison between all four tasks. We now show examples of individual fits as well as provide a measure of goodness of fit. The expansion of our modeling approach has resolved inconsistencies and sharpened the conclusions drawn from our model.

      (2) The task should not be labeled as reinforcement motor learning, as it is not about learning a motor skill or adapting to sensorimotor perturbations. It is a classical reinforcement learning paradigm.

      We now make it clear that our reinforcement learning task has both motor and cognitive demands, but does not fall entirely within one of these domains. We use the term motor learning because it captures the fact that participants maximize reward by making different movements, corrupted by motor noise, to unmarked locations on a continuous target zone. When we look at previous ublications, it is clear that our task is similar to those that also refer to this as reinforcement motor learning Cashaback et al. (2019) (reaching task using a robotic arm in adults), Van Mastrigt et al. (2020) (weight shifting task in adults), and Konrad et al. (2025) (real-world throwing task in children). All of these tasks involve trial-by-trial learning through reinforcement to make the movement that is most effective for a given situation. We feel it is important to link our work to these previous studies and prefer to preserve the terminology of reinforcement motor learning.

      Recommendations for the authors:

      Reviewing Editor Comments:

      Thank you for this summary. Rather than repeat the extended text from the responses to the reviewers here, we point the Editor to the appropriate reviewer responses for each issue raised.

      The reviewers and editors have rated the significance of the findings in your manuscript as "Valuable" and the strength of evidence as "Solid" (see eLife evalutation). A consultancy discussion session to integrate the public reviews and recommendations per reviewer (listed below), has resulted in key recommendations for increasing the significance and strength of evidence:

      To increase the Significance of the findings, please consider the following:

      (1) Address and reframe the paper around whether the task is truly getting at a motor learning process or more generic cognitive decision-making capacities such as spatial memory, reward processing, and hypothesis testing.

      We have revised the paper to address the comments on the framing of our work. Please see responses to the public review comments of Reviewers #2 and #3.

      (2) It would be beneficial to specify the differences between traditional reinforcement algorithms (i.e., using softmax functions to explore, and build representations of state-action-reward) and the reinforcement learning models used here (i.e., explore with movement variability, update reach aim towards the last successful action), and compare present findings to previous cognitive reinforcement learning studies in children.

      Please see response to the public review comments of Reviewer #1 in which we explain the expansion of our modeling approach to fit a value-based model as well as 31 other noise-based models. In our response to the public review comments of Reviewer #2, we comment on our expanded discussion of how our findings compare with previous cognitive reinforcement learning studies.

      To move the "Strength of Evidence" to "Convincing", please consider doing the following:

      (1 ) Address some apparently inconsistent and unrealistic values of motor noise, exploration noise, and learning rate shown for individual participants (e.g., Figure 5b; see comments reviewers 1 and take the following additional steps: plotting r squares for individual participants, discussing whether individual values of the fitted parameters are plausible and whether model parameters in each age group can extrapolate to the two clamp conditions and baselines.

      We have substantially updated our modeling approach. Now that we compare 31 noise-based models, the preferred model does not show any inconsistent or unrealistic values (see response to Reviewer #3). Additionally, we now show example individual fits and provide both relative and absolute goodness of fit (see response to Reviewer #3).

      (2) Relatedly, to further justify if model assumptions are met, it would be valuable to show that the current learning model fits the data better than alternative models presented in the literature by the authors themselves and by others (reviewer 1). This could include alternative development models that formalise the proposed explanations for age-related change: poor spatial memory, reward/outcome processing, and exploration strategies (reviewer 2).

      Please see response to public review comments of Reviewer #1 in which we explain that we have now fit a value-based model as well as 31 other noise-based models providing a comparison of previous models as well as novel models. This led to a slightly different model being preferred over the model in the original submission (updated model has a learning rate of unity). These models span many of the processes previously proposed for such tasks. We feel that 32 models span a reasonable amount of space and do not believe we have the power to include memory issues or heuristic exploration strategies in the model.

      (3) Perform the mediation analysis with all the possible variables (i.e., not informed by multiple regression) to see if the results are more consistent across studies and with the current approach (see comments reviewer 1).

      Please see response to public review comments of Reviewer #1. We chose to focus only on the model based analysis because it allowed us to distinguish between exploration variability and motor noise.

      Please see below for further specific recommendations from each reviewer.

      Reviewer #1 (Recommendations for the author):

      (1) In general, there should be more discussion and contextualization of other binary reinforcement tasks used in the motor literature. For example, work from Jeroen Smeets, Katinka van der Kooij, and Joseph Galea.

      Thank you for this comment. We have edited the Introduction to better contextualize our work within the reinforcement motor learning literature (see line 67 and line 83).

      (2) Line 32. Very minor. This sentence is fine, but perhaps could be slightly improved. “select a location along a continuous and infinite set of possible options (anywhere along the span of the bridge)"

      Thank you for this comment. We have edited the sentence to reflect this suggestion.

      (3) Line 57. To avoid some confusion in successive sentences: Perhaps, "Both children over 12 and adolescents...".

      Thank you for this comment. We have edited the sentence to reflect this suggestion.

      (4) Line 80. This is arguably not a mechanistic model, since it is likely not capturing the reward/reinforcement machinery used by the nervous system, such as updating the expected value using reward predic tion errors/dopamine. That said, this phenomenological model, and other similar models in the field, do very well to capture behaviour with a very simple set of explore and update rules.

      We use mechanistic in the standard use in modeling, as in Levenstein et al. (2023), for example. The contrast is not with neural modeling, but with normative modeling, in which one develops a model to optimize a function (or descriptive models as to what a system is trying to achieve). In mechanistic modeling one proposes a mechanism and this can be at a state-space level (as in our case) or a neural level (as suggested my the reviewer) but both are considered mechanistic, just at different levels. Quoting Levenstein "... mechanistic models, in which complex processes are summarized in schematic or conceptual structures that represent general properties of components and their interactions, are also commonly used." We now reference the Levenstein paper to clarify what we mean by mechanistic.

      (5) Figure 1. It would be useful to state that the x-axis in Figure 1 is in normalized units, depending on the device.

      Thank you for this comment. We have added a description of the x-axis units to the Fig. 1 caption.

      (6) Were there differences in behaviour for these different devices? e.g., how different was motor noise for the mouse, trackpad, and touchscreen?

      Thank you for this question. We did not find a significant effect of device on learning or precision in the baseline block. We have added these one way ANOVA results for each task in Supplementary Table 1.

      (7) Line 98. Please state that participants received reinforcement feedback during baseline.

      Thank you for this comment. We have updated the text to specify that participants receive reward feedback during the baseline block.

      (8) Line 99. Did the distance from the last baseline trial influence whether the participant learned or did not learn? For example, would it place them too far from the peak success location such that it impacted learning?

      Thank you for this question. We looked at whether the position of movement on the last baseline block trial was correlated with the first movement position in the learning block. We did not find any correlations between these positions for any of the tasks. Interestingly, we found that the majority of participants move to the center of the workspace on the first trial of the learning block for all tasks (either in the presence of the novel continuous target scene or the presentation of 7 targets all at once). We do not think that the last movement in the baseline block "primed" the participant for the location of the success zone in the learning block. We have added the following sentence to the Results section:

      "Note that the reach location for the first learning trial was not affected by (correlated with) the target position on the last baseline trial (p > 0.3 for both children and adults, separately)."

      (9) The term learning distance could be improved. Perhaps use distance from target.

      Thank you for this comment. We appreciate that learning distance defined with 0 as the best value is counter intuitive. We have changed the language to be "distance from target" as the learning metric.

      (10) Line 188. This equation is correct, but to estimate what the standard deviation by the distribution of changes in reach position is more involved. Not sure if the authors carried out this full procedure, which is described in Cashaback et al., 2019; Supplemental 2.

      There appear to be no Supplemental 2 in the referenced paper so we assume the reviewer is referring to Supplemental B which deals with a shuffling procedure to examine lag-1 correlations.

      In our tasks, we are limited to only 9 trials to analyze in each clamp phase so do not feel a shuffling analysis is warranted. In these blocks, we are not trying to 'estimate what the standard deviation by the distribution of changes in reach position' but instead are calculating the standard deviation of the reach locations and comparing the model fit (for which the reviewer says the formula is correct) with the data. We are unclear what additional steps the reviewer is suggesting. In our updated model analysis, we fit the data including the clamp phases for better parameter estimation. We use simulations to estimate s.d. in the clamp phase (as we ensure in simulations the data does not fall outside the workspace) making the previous analytic formulas an approximation that are no longer used.

      (11) Line 197-199. Having done the demo task, it is somewhat surprising that a 3-year-old could understand these instructions (whose comprehension can be very different from even a 5-year old).

      Thank you for raising this concern. We recognize that the younger participants likely have different comprehension levels compared to older participants. However, we believe that the majority of even the youngest participants were able to sufficiently understand the goal of the task to move in a way to get the video clip to play. We intentionally designed the tasks to be simple such that the only instructions the child needed to understand were that the goal was to get the video clip to play as much as possible and the video clip played based on their movement. Though the majority of younger children struggled to learn well on the probabilistic tasks, they were able to learn well on the deterministic tasks where the task instructions were virtually identical with the exception of how many places in the workspace could gain reward. On the continuous probabilistic task, we did have a small number (n = 3) of 3 to 5 year olds who exhibited more mature learning ability which gives us confidence that the younger children were able to understand the task goal.

      (12) Line 497: Can the authors please report the F-score and p-value separately for each of these one-way ANOVA (the device is of particular interest here).

      Thank you for this request. We have added ina upplementarytable (Supplementary Table 1) with the results of these ANOVAs.

      (13) Past work has discussed how motivation influences learning, which is a function of success rate (van der Kooij, K., in 't Veld, L., & Hennink, T. (2021). Motivation as a function of success frequency. Motivation and Emotion, 45, 759-768.). Can the authors please discuss how that may change throughout development?

      Thank you for this comment. While motivation most probably plays a role in learning, in particular in a game environment, this was out of the scope of the direct focus of this work and not something that our studies were designed to test. We have added the following sentence to the discussion section to address this comment:

      "We also recognize that other processes, such as memory and motivation, could affect performance on these tasks however our study was not designed to test these processes directly and future work would benefit from exploring these other components more explicitly."

      (14) Supplement 6. This analysis is somewhat incomplete because it does not consider success.

      Pekny and collegues (2015) looked at 3 trials back but considered both success and reward. However, their analysis has issues since successive time points are not i.i.d., and spurious relationships can arise. This issue is brought up by Dwahale (Dhawale, A. K., Miyamoto, Y. R., Smith, M. A., & R475 Ölveczky, B. P. (2019). Adaptive regulation of motor variability. Current Biology, 29(21), 3551-3562.). Perhaps it is best to remove this analysis from the paper.

      Thank you for this comment. We have decided to remove this secondary analysis from the paper as it was a source of confusion and did not add to the understanding and interpretation of our behavioral results.

      Reviewer #2 (Recommendations for the author):

      (1 ) the path length ratio analyses in the supplemental are interesting but are not mentioned in the main paper. I think it would be helpful to mention these as they are somewhat dramatic effects

      Thank you for this comment. Path length ratios are defined in the Methods and results are briefly summarized in the Results section with a point to the supplementary figures. We have updated the text to more explicitly report the age related differences in path length ratios.

      (2) The second to last paragraph of the intro could use a sentence motivating the use ofthe different task features (deterministic/probabilistic and discrete/continuous).

      Thank you for this comment. We have added an additional motivating sentence to the introduction.

      Reviewer #3 (Recommendations for the author):

      The paper labeled the task as one for reinforcement motor learning, which is not quite appropriate in my opinion. Motor learning typically refers to either skill learning or motor adaptation, the former for improving speed-accuracy tradeoffs in a certain (often new) motor skill task and the latter for accommodating some sensorimotor perturbations for an existing motor skill task. The gaming task here is for neither. It is more like a

      decision-making task with a slight contribution to motor execution, i.e., motor noise. I would recommend the authors label the learning as reinforcement learning instead of reinforcement motor learning.

      Thank you for this comment. As noted in the response to the public review comments, we agree that this task has components of classical reinforcement learning (i.e. responding to a binary reward) but we specifically designed it to require the learning of a movement within a novel game environment. We have added a new paragraph to the introduction where we acknowledge the interplay between cognitive and motor mechanisms while also underscoring the features in our task that we think are not present in typical cognitive tasks.

      My major concern is whether the model adequately captures subjects' behavior and whether we can conclude with confidence from model fitting. Motor noise, exploration noise, and learning rate, which fit individual learning patterns (Figure 5b), show some quite unrealistic values. For example, some subjects have nearly zero motor noise and a 100% learning rate.

      We have now compared 31 models and the preferred model is different from the one in the first submission. The parameter fits of the new model do not saturate in any way and appear reasonable to us. The updates to the model analysis have addressed the concern of previously seen unrealistic values in the prior draft.

      Currently, the paper does not report the fitting quality for individual subjects. It is good to have an exemplary subject's fit shown, too. My guess is that the r-squared would be quite low for this type of data. Still, given that the children's data is noisier, it might be good to use the adult data to show how good the fitting can be (individual fits, r squares, whether the fitted parameters make sense, whether it can extrapolate to the two clamp phases). Indeed, the reliability of model fitting affects how we should view the age effect of these model parameters.

      We now show fits to individual subjects. But since this is a Kalman smoother it fits the data perfectly by generating its best estimate of motor noise and exploration variability on each trial to fully account for the data — so in that sense R<sup>2</sup> is always 1 so that is not helpful.

      While the BIC analysis with the other model variants provides a relative goodness of fit, it is not straightforward to provide an absolute goodness of fit such as standard R<sup>2</sup> for a feedforward simulation of the model given the parameters (rather than the output of the Kalman smoother). There are two problems. First, there is no single model output. Each time the model is simulated with the fit parameters it produces a different output (due to motor noise, exploration variability and reward stochasticity). Second, the model is not meant to reproduce the actual motor noise, exploration variability and reward stochasticity of a trial. For example, the model could fit pure Gaussian motor noise across trials (for a poor learner) by accurately fitting the standard deviation of motor noise but would not be expected to actually match each data point so would have a traditional R<sup>2</sup> of O.

      To provide an overall goodness of fit we have to reduce the noise component and to do so we exam ined the traditional R<sup>2</sup> between the average of all the children's data and the average simulation of the model (from the median of 1000 simulations per participant) so as to reduce the stochastic variation. The results for the continuous probabilistic and discrete probabilistic task are R<sup>2</sup> of 0.41 and 0.72, respectively.

      Not that variability in the "success clamp" doe not change across ages (Figure 4C) and does not contribute to the learning effect (Figure 4F). However, it is regarded as reflecting motor noise (Figure SC), which then decreases over age from the model fitting (Figure 5B). How do we reconcile these contradictions? Again, this calls the model fitting into question.

      For the success clamp, we only have 9 trials to calculate variability which limits our power to detect significance with age. In contrast, the model uses all 120 trials to estimate motor noise. There is a downward trend with age in the behavioral data which we now show overlaid on the fits of the model for both probabilistic conditions (Figure 5—figure Supplement 4) and Figure 6—figure Supplement 4). These show a reasonable match and although the variance explained is 1 6 and 56% (we limit to 9 trials so as to match the fail clamp), the correlations are 0.52 and 0.78 suggesting we have reasonable relation although there may be other small sources of variability not captured in the model.

      Figure 5C: it appears one bivariate outlier contributes a lot to the overall significant correlation here for the "success clamp".

      Recalculating after removing that point in original Fig 5C was still significant and we feel the plots mentioned in the previous point add useful information to this issue. With the new model this figure has changed.

      It is still a concern that the young children did not understand the instructions. Nine 3-to-8 children (out of 48) were better explained by the noisy only model than the full model. In contrast, ten of the rest of the participants (out of 98) were better explained by the noisy-only model. It appears that there is a higher percentage of the "young" children who didn't get the instruction than the older ones.

      Thank you for this comment. We did take participant comprehension of the task into consideration during the task design. We specifically designed it so that the instructions were simple and straight forward. The child simply needs to understand the underlying goal to make the video clip play as often as possible and that they must move the penguin to certain positions to get it to play. By having a very simple task goal, we are able to test a naturalistic response to reinforcement in the absence of an explicit strategy in a task suited even for young children.

      We used the updated reinforcement learning model to assess whether an individual's performance is consistent with understanding the task. In the case of a child who does not understand the task, we expect that they simply have motor noise on their reach, and crucially, that they would not explore more after failure, nor update their reach after success. Therefore, we used a likelihood ratio test to examine whether the preferred model was significantly better at explaining each participant's data compared to the model variant which had only motor noise (Model 1). Focusing on only the youngest children (age 3-5), this analysis showed that that 43, 59, 65 and 86% of children (out of N = 21, 22, 20 and 21 ) for the continuous probabilistic, discrete probabilistic, continuous deterministic, and discrete deterministic conditions, respectively, were better fit with the preferred model, indicating non-zero exploration after failure. In the 3-5 year old group for the discrete deterministic condition, 18 out of 21 had performance better fit by the preferred model, suggesting this age group understands the basic task of moving in different directions to find a rewarding location.

      The reduced numbers fit by the preferred model for the other conditions likely reflects differences in the task conditions (continuous and/or probabilistic) rather than a lack of understanding of the goal of the task. We include this analysis as a new subsection at the end of the Results.

      Supplementary Figure 2: the first panel should belong to a 3-year-old not a 5-year-old? How are these panels organized? This is kind of confusing.

      Thank you for this comment. Figure 2—figure Supplement 1 and Figure 2—figure Supplement 2 are arranged with devices in the columns and a sample from each age bin in the rows. For example in Figure 2—figure Supplement 1, column 1, row 1 is a mouse using participant age 3 to 5 years old while column 3, row 2 is a touch screen using participant age 6 to 8 years old. We have edited the labeling on both figures to make the arrangement of the data more clear.

      Line 222: make this a complete sentence.

      This sentence has been edited to a complete sentence.

      Line 331: grammar.

      This sentence has been edited for grammar.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer 1 (Public review):

      The first part of the manuscript is not particularly novel, and it would be beneficial to clearly state which aspects of the analyses and derivations are different from previous literature. For example, the derivation that rank-1 RNNs cannot implement selection vector modulation is already present in the Extended Discussion of Pagan et al., 2022 (Equations 42-43). Similarly, it would be helpful to more clearly explain how the proposed pathway-based information flow analysis differs from the circuit diagram of latent dynamics in Dubreuil et al., 2022.

      We thank the reviewer for the insightful comments and providing us a good opportunity to better clarify the novelty of our work regarding the analyses and derivations. In general, as the reviewer pointed out, the major novelty of our work lies in explicitly linking selection mechanisms (proposed in Mante et al. 2013) with circuit-level descriptions of low-rank RNNs (developed in Dubreuil et al. 2022). This is made possible through a set of analyses and derivation integrating both linearized dynamical systems analysis (Mante et al., 2013) and the circuit diagram of latent dynamics (Dubreuil et al. 2022). Specifically, starting from rank-3 RNN models, we first derived the circuit diagram of latent dynamics (Eqs. 18 and 19) by applying the theory developed in Dubreuil et al. 2022. However, without further analysis, there is no explicit link between this latent dynamics and selection mechanism. In this manuscript, based on the line attractor assumption, we linearized the latent dynamics around the line attractor (Mante et al., 2013), which enabled us to explicitly solve the equation (from eq. 20 to eq. 27) and derive an explicit formula for the effective coupling of information flow (Fig. 5A). This formula of effective coupling strength supported an explicit pathway-based definition of selection vector modulation (Fig. 5) and selection vector (Fig. 6), the core result of this manuscript. Importantly, the same analysis can be extended to higher-order lowrank RNNs (Eqs. 47-55), suggesting the general applicability of our result. We have revised the manuscript to clearly state the novelty of our work. Please see Lines 292-294.

      As such a set of analyses and derivation integrates many results from previous literatures, it naturally shared many similarities with previous results as the reviewer pointed out. Below, we compared our work with previous ones mentioned by the reviewer:

      (1) For example, the derivation that rank-1 RNNs cannot implement selection vector modulation is already present in the Extended Discussion of Pagan et al., 2022 (Equations 42-43). 

      For this point, we totally agree with the reviewer that the derivation of rank-1 RNNs’ limitations in implementing selection vector modulation is not particularly novel. The reason why we started from rank-1 RNNs is because these RNNs are the simplest examples revealing the intriguing link between the connectivity property and the modulation mechanism and thereby serving as the ideal introduction for the subsequent in-depth discussion for general audiences. In the original manuscript, we cited the Pagan et al. 2023 note but may not make it explicit enough. As the reviewer pointed out that the derivation has been added into the latest version of Pagan et al. paper (Pagan et al. 2024), we now cite the Pagan et al. 2024 paper and make it clear that the derivation has been derived in Pagan et al. 2024. Please see Lines 186-188 in the main text.

      (2) Similarly, it would be helpful to more clearly explain how the proposed pathway-based information flow analysis differs from the circuit diagram of latent dynamics in Dubreuil et al., 2022.

      As we explained earlier, the latent dynamics in Dubreuil et al. alone did not provide an explicit link between circuit diagram and selection mechanisms. Our analysis go beyond the theory developed in Dubreuil et al. 2022 paper by integrating the linearized dynamical systems analysis (Mante et al. 2013), eventually providing a previously-unknown explicit link between circuit diagram and selection mechanisms.

      With regard to the results linking selection vector modulation and dimensionality, more work is required to understand the generality of these results, and how practical it would be to apply this type of analysis to neural recordings. For example, it is possible to build a network that uses input modulation and to greatly increase the dimensionality of the network simply by adding additional dimensions that do not directly contribute to the computation. Similarly, neural responses might have additional high-dimensional activity unrelated to the task. My understanding is that the currently proposed method would classify such networks incorrectly, and it is reasonable to imagine that the dimensionality of activity in high-order brain regions will be strongly dependent on activity that does not relate to this task.

      We thank the reviewer for this insightful comment. As what the reviewer suggested, we did more work to better understand the generality and applicability of the index proposed in the manuscript.

      Firstly, to see if the currently proposed method can work when there is significant amount of neural activity variance irrelevant to the task, we manually added irrelevant neural activity into the trained RNNs (termed as redundant RNNs, see Methods for details, Lines 1200-1215). As expected, we found that for these redundant RNNs, the correlation between the proposed index and the proportion of selection vector modulation indeed disappeared (Figure 7-figure supplement 4B). In fact, in the original version of our manuscript, we presented an extreme example of this idea in our discussion, where we designed two RNNs with theoretically identical neural activity patterns—one relying purely on input modulation and the other on selection vector modulation (Figure 7-figure supplement 3). Therefore, for this extreme example, any activity-based index alone would fail to differentiate between these two mechanisms, suggesting the challenge of distinguishing different selection mechanisms when taskirrelevant neural activity is added.

      Secondly, we asked why the proposed index works well for the trained RNNs, which is kind of surprising in the first place as the reviewer pointed out. One possibility is that for trained RNNs, the task-irrelevant neural activity is minimal. To test this possibility, we conducted in-silico lesion experiments for the trained RNNs. The main idea is that if an RNN contains a large portion of taskirrelevant variance, there will exist a subspace (termed as task-irrelevant subspace) that captures this part of variance and removing this task-irrelevant subspace will not affect the network’s behavior. Based on this idea, we developed an optimization method to identify such a task-irrelevant subspace for any given RNN (see Methods for details, Lines 1216-1244). The results show that in the originally trained RNNs, the identified task-irrelevant subspace can only explain a small portion of neural activity variance (Figure 7-figure supplement 4, panel C). As a control, when applying the same optimization method to the redundant RNNs, we found that the identified task-irrelevant subspace can explain a significantly larger portion of neural activity variance (Figure 7-figure supplement 4, panel C). Taken together, we concluded that the reason why the index works for trained RNNs is because the major variance of the neural activity of the network learned through backpropagation is task-relevant.

      Therefore, this set of analyses provided an understanding why the proposed index works for trained RNNs and failed for the redundant RNNs. We have added this part of analyses in the Discussion part. See Lines 601-610. As the reviewer pointed out that it is highly likely that there exists taskirrelevant neural activity variance in high brain regions, the proposed index may not work well in neural recordings. With this understanding, we tone down the conclusion related to experimentally testable prediction in the main text (e.g., in Abstract and Introduction). We thank the reviewer again for helping us improve the clarity of our work.

      Finally, a number of aspects of the analysis are not clear. The most important element to clarify is how the authors quantify the "proportion of selection vector modulation" in vanilla RNNs (Figures 7d and 7g). I could not find information about this in the Methods, yet this is a critical element of the study results. In Mante et al., 2013 and in Pagan et al., 2022 this was done by analyzing the RNN linearized dynamics around fixed points: is this the approach used also in this study? Also, how are the authors producing the trial-averaged analyses shown in Figures 2f and 3f? The methods used to produce this type of plot differ in Mante et al., 2013 and Pagan et al., 2022, and it is necessary for the authors to explain how this was computed in this case.

      We thank the reviewer for the valuable comments. Yes, for proportion of selection vector modulation (Figure 7D and 7G) we employed the method used in Mante et al., 2013. For the trial-averaged analyses shown in Figures 2f and 3f, we followed a procedure used in Mante et al., 2013. In the revised version, we have added the relate information. See Lines 852-853 and 872-889. We thank the reviewer again for improving the clarify of our work.

      I am also confused by a number of analyses done to verify mathematical derivations, which seem to suggest that the results are close to identical, but not exactly identical. For example, in the histogram in Figure 6b, or the histogram in Figure 7-figure supplement 3d: what is the source of the small variability leading to some of the indices being less than 1?

      In Figure 6B, the two selection vectors are considered theoretically equivalent under the meanfield assumption. However, because the RNNs we use have a finite number of neurons, finite-size effects inevitably cause slight deviations from perfect equivalence.

      To verify this, we generated rank-3 RNNs of different sizes in the experiment for Figure 6b (see the Supplementary section “Building rank-3 RNNs with both input and selection vector modulations”). Specifically, for a fixed number of neurons 𝑁, we independently sampled 𝛼, 𝛽 and 𝛾 from a Uniform(0,1) distribution and built an RNN with 𝑁 neurons based on the procedure as in Figure 5C. We then computed the selection vector for the RNN in a given context (for example, context 1) in two ways:

      (1) via linearized dynamical system analysis following Mante et al. (2013), producing the selection vector sc<sup>classical</sup>

      (2) using the theoretical derivation

      Author response image 1.

      cos angles for selection vectors computed using two methods in RNN with different size. Black bars indicate median values.

      We repeated this process 1000 times for each 𝑁 and measured the cosine angle between these two selection vectors. As shown in Author response image 1, as 𝑁 increases, the cosine angles approach 1 more consistently, indicating that the two selection vectors become nearly equivalent in larger RNNs. Conversely, smaller RNNs display more pronounced finite-size effects, which accounts for indices slightly below 1.

      Reviewer 2 (Public review):

      The introduction could have been written in a more accessible manner for any non-expert readers.

      We sincerely thank the reviewer for the constructive feedback on the introduction and have revised it accordingly.

      Reviewer #2 (Recommendations for the authors):

      The level of mastery of the low-rank framework is altogether impressive. I need however to point to a technical detail. The derivations of the information flow assume that the vectors m and vectors I are orthogonal (e.g. in Equation 14). This is not necessarily the case in trained networks, and Figure 2F suggests this is not the case in the trained rank 1 network. In that situation, the overlap between m and I leads to an additional term in the Equation going directly from the input to the output vector (see, e.g., Equation 15 in Beiran et al. Neuron 2023). In general, these kind of overlaps can contribute an additional pathway in higher rank networks too.

      We thank the reviewer for the valuable comments. The derivations presented in Equation 14 do not actually require that the vectors 𝒎 and 𝑰 are orthogonal. Rather, our definition of the task variable differs slightly from the one in Beiran et al. (2023). Consider a rank-1 RNN with a single input channel:

      Author response image 2.

      Difference of the definition of task variable with previous work. (A) Our definition of task variable. (B) Definition of task variable in Beiran et al. 2023.

      As long as 𝒎 and 𝑰 are linearly independent, the state 𝒙(𝑡) can be uniquely written as a linear combination of the two vectors (Author response image 2):

      where and are the task variables associated with 𝒎 and 𝑰, respectively. Substituting this expression into the dynamical equations yields:

      Hence, there is no additional term directly linking the input to the output vector in our formulation. By contrast, in Beiran et al. (2023), the input vector 𝑰 is decomposed into components parallel (𝐼//) and perpendicular (𝑰-) to 𝒎, and the task variables are defined as (Figure 4-figure supplement 3B):

      This leads to dynamics of the form:

      thus creating an additional direct term from the input to the output vector under their definition.

      The designed rank 3 network relies on a multi-population structure. This is explained clearly in the methods, but it could be stressed more in the main text to dispel the notion that higherrank networks may not need a multi-population structure to perform this task (cf Dubreuil et al 2022).

      Thank you for the valuable comments. In the revised version, we emphasize this point by adding the following sentence: “our rank-3 network relies on a multi-population structure, consistent with the notion that higher-rank networks still require a multi-population structure to perform flexible computations (Dubreuil et al. 2022)”. See Lines 238-240.

      (3) An important result in Pagan et al and Mante et al is that the line attractor direction is invariant across contexts. I believe this is explicitly enforced in the models studied here, but this could be made more clear. It would be interesting to discuss the importance of this constraint.

      We thank the reviewer for the valuable comments. In our hand-crafted RNN examples (Figures 3– 6), we enforce the choice axis to be identical across the two contexts (Figure R4B). Even in the rank-1 example (Figure 2), where we analyze a trained RNN, the choice axis still shows a substantial overlap between the two contexts (Figure R4A). However, in the trained vanilla RNNs shown in Figure 7, when the regularization term is relatively small, the overlap in the choice axis between contexts is smaller (Figure R4C)—i.e., the line attractor direction shifts between different contexts.

      Author response image 3.

      Cosine angle between the choice axes in two contexts for different RNNs. (A) Rank-1 RNNs in Figure 2. (B) Rank-3 RNNs in Figure 3-6. (C) Vanilla RNNs in Figure 7.

      Our theoretical framework can also accommodate situations where the direction of the choice axis changes. For instance, consider the rank-3 RNN in Figure 6, where the choice axis is defined as with 𝐺 being a diagonal matrix whose elements represent the slopes of each neuron’s activation function. Since these slopes can change across contexts, itself can vary across contexts. Likewise, the input representation direction may be written as , allowing both the choice axis and the input axis to adapt to the context. The selection vector is given by:

      Here, we no longer assume that is context-invariant; rather, we only assume its norm remains the same across contexts. Under this weaker assumption, we still have

      Substituting these into the equations yields the following expressions for input modulation and selection vector modulation:

      Figure 6B: it was not clear to me what exactly is plotted here.

      We thank the reviewer for pointing out the missing explanation. In Figure 6B, we show the distribution of the cosine angles between two ways of computing the selection vector for randomly generated rank-3 RNNs. Specifically, We generate 1000 RNNs according to the procedure in Figure 5C, with each RNN defined by parameters 𝛼 , 𝛽 and 𝛾 independently sampled from a Uniform(0,1) distribution. For each RNN, we computed the selection vector for the RNN in a given context (e.g., context 1 or 2) in two ways:

      (1)  via linearized dynamical system analysis following Mante et al. (2013), producing the selection vector sv<supclassical</sup> (classical in Figure 6B),

      (2)  using the theoretical derivation (“our’s” in Figure 6B)

      We repeated this process 1000 times and measured the cosine angle between these two selection vectors and plot the resulting distribution for context 1 (gray) and context 2 (blue) in Figure 6B. The figure shows that the computed selection vectors via the two methods are almost equal, as evidenced by the cosine angles clustering very close to 1.

      We have revised it accordingly. See Lines 1135-1143.

      In Figure 7, how was the effective dimension of vanilla RNNs controlled or varied? The metric used (effective dimension) is relatively non-standard, it would be useful to give some intuition to the reader about it.

      We thank the reviewer for these valuable comments.

      Controlling the effective dimension

      When train vanilla RNNs, we included a regularization term in the loss function of the form

      where 𝑤536 is a regularization coefficient. By adjusting 𝑤536, we can influence the distribution of singular values of connectivity of 𝐽. When w<sub>reg</sub> is larger, the learned 𝐽 tends to have fewer large singular values, hence with lower effectivity dimension; when 𝑤536 is small, more singular values remain large, increasing the matrix’s effective dimension.

      Definition and intuition: effective dimension

      Consider a connectivity matrix 𝐽 with singular values . The matrix’s rank is the number of nonzero singular values. However, rank alone can overlook differences in how quickly those singular values decay. To capture this, we define the effective dimension as:

      Each term lies between 0 and 1, so the effective dimension satisfies:

      When all nonzero singular values are equal, edim(𝐽) equals the matrix rank. But if some singular values are much smaller than others, effective dimension will be closer to 1. For example:

      -  𝐽<sub>1</sub> has nonzero singular values (1, 0.1, 0.01). Its effective dimension is 1.0101, indicating that most of the variance is captured by the largest singular value.

      -  𝐽sub>0</sub> has nonzero singular values (1, 0.8, 0.7). Its effective dimension is 2.13, which reflects that multiple singular values contribute significantly.

      Hence, while both >𝐽<sub>1</sub> and 𝐽sub>0</sub> are rank-3 matrices, their effective dimensions highlight the difference in how each matrix distributes its variance.

      We have added the intuition underlying this concept in Methods (see Lines 1135-1143). We thank the reviewer for improving the clarity of our work. 

      Eqs 19&21: n^T_r should be n^T_dv?

      Thank you for point out this mistake. We have fixed it in the revised version.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews: 

      Reviewer #1 (Public review): 

      Summary: 

      This article investigates the phenotype of macrophages with a pathogenic role in arthritis, particularly focusing on arthritis induced by immune checkpoint inhibitor (ICI) therapy. 

      Building on prior data from monocyte-macrophage coculture with fibroblasts, the authors hypothesized a unique role for the combined actions of prostaglandin PGE2 and TNF. The authors studied this combined state using an in vitro model with macrophages derived from monocytes of healthy donors. They complemented this with single-cell transcriptomic and epigenetic data from patients with ICI-RA, specifically, macrophages sorted out of synovial fluid and tissue samples. The study addressed critical questions regarding the regulation of PGE2 and TNF: Are their actions co-regulated or antagonistic? How do they interact with IFN-γ in shaping macrophage responses? 

      This study is the first to specifically investigate a macrophage subset responsive to the PGE2 and TNF combination in the context of ICI-RA, describes a new and easily reproducible in vitro model, and studies the role of IFNgamma regulation of this particular Mф subset. 

      Strengths: 

      Methodological quality: The authors employed a robust combination of approaches, including validation of bulk RNA-seq findings through complementary methods. The methods description is excellent and allows for reproducible research. Importantly, the authors compared their in vitro model with ex vivo single-cell data, demonstrating that their model accurately reflects the molecular mechanisms driving the pathogenicity of this macrophage subset. 

      Weaknesses: 

      Introduction: The introduction lacks a paragraph providing an overview of ICI-induced arthritis pathogenesis and a comparison with other types of arthritis. Including this would help contextualize the study for a broader audience.

      Thank you for this suggestion, we have added a paragraph on ICI-arthritis to intro (pg. 4, middle paragraph).  

      Results Section: At the beginning of the results section, the experimental setup should be described in greater detail to make an easier transition into the results for the reader, rather than relying just on references to Figure 1 captions.

      We have clarified the experimental setup (pg. 5).  

      There is insufficient comparison between single-cell RNA-seq data from ICI-induced arthritis and previously published single-cell RA datasets. Such a comparison may include DEGs and GSEA, pathway analysis comparison for similar subsets of cells. Ideally, an integration with previous datasets with RA-tissue-derived primary monocytes would allow for a direct comparison of subsets and their transcriptomic features.

      We thank the Reviewer for this suggestion, which has increased the impact of our data and analysis. A computationally rigorous representation mapping approach showed that ICI-arthritis myeloid subsets predominantly mapped onto 4 previously defined RA subsets including IL-1β+ cells. This result was corroborated using a complementary data integration approach. Analysis of (TNF + PGE)-induced gene sets (TP signatures) in ICI-arthritis myeloid cells projected onto the RA subsets using the AUCell package showed elevated TP gene expression in similar ICI-arthritis and RA monocytic cell subsets. We also found mutually exclusive expression of TP and IFN signatures in distinct RA and ICI-arthritis myeloid cell subsets, which supports that the opposing cross-regulation between IFN-γ and PGE2 pathways that we identified in vitro also functions similarly in vivo. This analysis is shown in the new Fig. 3, described on pg. 7, and discussed on pp. 13-14.

      While it's understandable that arthritis samples are limited in numbers and myeloid cell numbers, it would still be interesting to see the results of PGE2+TNF in vitro stimulation on the primary RA or ICI-RA macrophages. It would be valuable to see RNA-Seq signatures of patient cell reactivation in comparison to primary stimulation of healthy donor-derived monocytes.

      We agree that this would be interesting but given limited samples and distribution of samples amongst many studies and investigators this is beyond the scope of the current study.  

      Discussion: Prior single-cell studies of RA and RA macrophage subpopulations from 2019, 2020, 2023 publications deserve more discussion. A thorough comparison with these datasets would place the study in a broader scientific context. 

      Creating an integrated RA myeloid cell atlas that combines ICI-RA data into the RA landscape would be ideal to add value to the field. 

      As one of the next research goals, TNF blockade data in RA and ICI-RA patients would be interesting to add to such an integrated atlas. Combining responders and non-responders to TNF blockade would help to understand patient stratification with the myeloid pathogenic phenotypes. It would be great to read the authors' opinion on this in the Discussion section. 

      Please see our response to point 3 above. This point is addressed in Fig. 3, pg. 7, and pp. 13-14, which includes a discussion of responders and nonresponders and patient stratification.  

      Conclusion: The authors demonstrated that while PGE2 maintains the inflammatory profile of macrophages, it also induces a distinct phenotype in simultaneous PGE2 and TNF treatment. The study of this specific subset in single-cell data from ICI-RA patients sheds light on the pathogenic mechanisms underlying this condition, however, how it compares with conventional RA is not clear from the manuscript. 

      Given the substantial incidence of ICI-induced autoimmune arthritis, understanding the unique macrophage subsets involved for future targeting them therapeutically is an important challenge. The findings are significant for immunologists, cancer researchers, and specialists in autoimmune diseases, making the study relevant to a broad scientific audience. 

      Reviewer #2 (Public review): 

      Summary/Significance of the findings: 

      The authors have done a great job by extensively carrying out transcriptomic and epigenomic analyses in the primary human/mouse monocytes/macrophages to investigate TNF-PGE2 (TP) crosstalk and their regulation by IFN-γ in the Rheumatoid arthritis (RA) synovial macrophages. They proposed that TP induces inflammatory genes via a novel regulatory axis whereby IFN-γ and PGE2 oppose each other to determine the balance between two distinct TNF-induced inflammatory gene expression programs relevant to RA and ICI-arthritis. 

      Strengths: 

      The authors have done a great job on RT-qPCR analysis of gene expression in primary human monocytes stimulated with TNF and showing the selective agonists of PGE2 receptors EP2 and EP4 22 that signal predominantly via cAMP. They have beautifully shown IFN-γ opposes the effects of PGE2 on TNF-induced gene expression. They found that TP signature genes are activated by cooperation of PGE2-induced AP-1, CEBP, and NR4A with TNF-induced NF-κB activity. On the other hand, they found that IFN-γ suppressed induction of AP-1, CEBP, and NR4A activity to ablate induction of IL-1, Notch, and neutrophil chemokine genes but promoted expression of distinct inflammatory genes such as TNF and T cell chemokines like CXCL10 indicating that TP induces inflammatory genes via IFN-γ in the RA and ICI-arthritis. 

      Weaknesses: 

      (1) The authors carried out most of the assays in the monocytes/macrophages. How do APCcells like Dendritic cells behave with respect to this TP treatment similar dosing? 

      We agree that this is an interesting topic especially as TNF + PGE2 is one of the standard methods of maturing in vitro generated human DCs and promoting antigen-presenting function. As DC maturation is quite different from monocyte activation this would represent a new study and is beyond the scope of the current manuscript. We have instead added a paragraph to the discussion (pg. 12) and cited the literature on DC maturation by TNF + PGE2 including one of our older papers (PMID: 18678606; 2008)  

      (2) The authors studied 3h and 24h post-treatment transcriptomic and epigenomic. What happens to TP induce inflammatory genes post-treatment 12h, 36h, 48h, 72h. It is critical to see the upregulated/downregulated genes get normalised or stay the same throughout the innate immune response.

      We now clarify that subsets of inducible genes showed distinct kinetics of induction with transient expression at 3 hr versus sustained expression over the 24 hr stimulation period as shown in Supplementary Fig. 1 (pg. 5).

      (3) The authors showed IL1-axis in response to the TP-treatment. Do other cytokine axes get modulated? If yes, then how do they cooperate to reduce/induce inflammatory responses along this proposed axis?

      This is an interesting question, which we approached using a combination of pathway analysis and targeted inspection of pathways important pathogenesis of RA, which is the inflammatory condition most relevant for this study. In addition to genes in the IL-1-NF-κB core inflammatory pathway, pathway analysis of genes induced by TP co-stimulation showed enrichment of genes related to leukocyte chemotaxis, in particular neutrophil migration. Accordingly, TP costimulation increased expression of CSF3, which plays a key role in mobilizing neutrophils from the bone marrow, and major neutrophil chemokines CXCL1, CXCL2, CXCL3 and CXCL5 that recruit neutrophils to sites of inflammation including in inflammatory arthritis. Analysis of the late response to TNF similarly showed enrichment of genes important in chemotaxis, and suppression of genes in the cholesterol biosynthetic pathway, which we and others have previously linked to IFN responses. Targeted inspection of genes in additional pathways implicated in RA pathogenesis showed increased expression of genes in the Notch pathway. We believe that these pathways work together with the IL-1 pathway to increase immune cell recruitment and activation in inflammatory responses; these results are described on pp. 5-6 and are incorporated into Figures 1, 2 and Supplementary Fig. 2. 

      Overall, the data looks good and acceptable but I need to confirm the above-mentioned criticisms. 

      Recommendations for the authors: 

      Reviewer #1 (Recommendations for the authors):   

      The discussion section of the manuscript claims: "In this study, we utilized transcriptomics to demonstrate a 'TNF + PGE2' (TP) signature in RA and ICI-arthritis IL-1β+ synovial macrophages." This statement is misleading, as no new transcriptomic data from RA synovial samples were generated in this study. To support such a claim, the authors would need to compare primary monocytes or macrophages from RA patients using bulk RNA-seq or singlecell RNA-seq. Based on the current data, the comparison is limited to bulk RNA-seq findings from the authors' in vitro model and prior monocyte-fibroblast coculture studies. 

      We have modified the abstract and discussion (pg. 10) to reflect that we have compared an in vitro generated TP signature with gene expression in previously identified RA macrophage subsets.

    1. Author response:

      [The following is the authors’ response to the original reviews.]

      We extend our sincere thanks to the editor, referees for eLife, and other commentators who have written evaluations of this manuscript, either in whole or in part. Sources of these comments were highly varied, including within the bioRxiv preprint server, social media (including many comments received on X/Twitter and some YouTube presentations and interviews), comments made by colleagues to journalists, and also some reviews of the work published in other academic journals. Some of these are formal and referenced with citations. Others were informal but nonetheless expressed perspectives that helped enable us to revise the manuscript with the inclusion of broader perspectives than the formal review process. It is beyond the scope of this summary to list every one of these, which have often been brought to the attention of different coauthors, but we begin by acknowledging the very wide array of peer and public commentary that have contributed to this work. The reaction speaks to a broad interest in open discussion and review of preprints. 

      As we compiled this summary of changes to the manuscript, we recognized that many colleagues made comments about the process of preprint dissemination and evaluation rather than the data or analyses in the manuscript. Addressing such comments is outside the scope of this revised manuscript, but we do feel that a broader discussion of these comments would be valuable in another venue. Many commentators have expressed confusion about the eLife system of evaluation of preprints, which differs from the editorial acceptance or rejection practiced in most academic journals. As authors in many different nations, in varied fields, and in varied career stages, we ourselves are still working to understand how the academic publication landscape is changing, and how best to prepare work for new models of evaluation and dissemination. 

      The manuscript and coauthor list reflect an interdisciplinary collaboration. Analyses presented in the manuscript come from a wide range of scientific disciplines. These range from skeletal inventory, morphology, and description, spatial taphonomy, analysis of bone fracture patterns and bone surface modifications, sedimentology, geochemistry, and traditional survey and mapping. The manuscript additionally draws upon a large number of previous studies of the Rising Star cave system and the Dinaledi Subsystem, which have shaped our current work. No analysis within any one area of research stands alone within this body of work: all are interpreted in conjunction with the outcomes of other analyses and data from other areas of research. Any single analysis in isolation might be consistent with many different hypotheses for the formation of sediments and disposition of the skeletal remains. But testing a hypothesis requires considering all data in combination and not leaving out data that do not fit the hypothesis. We highlight this general principle at the outset because a number of the comments from referees and outside specialists have presented alternative hypotheses that may arguably be consistent with one kind of analysis that we have presented, while seeming to overlook other analyses, data, or previous work that exclude these alternatives. In our revision, we have expanded all sections describing results to consider not only the results of each analysis, but how the combination of data from different kinds of analysis relate to hypotheses for the deposition and subsequent history of the Homo naledi remains. We address some specific examples and how we have responded to these in our summary of changes below. 

      General organization:

      The referee and editor comments are mostly general and not line-by-line questions, and we have compiled them and treated them as a group in this summary of changes, except where specifically noted. 

      The editorial comments on the previous version included the suggestion that the manuscript should be reorganized to test “natural” (i.e. noncultural) hypotheses for the situations that we examine. The editorial comment suggested this as a “null hypothesis” testing approach. Some outside comments also viewed noncultural deposition as a null hypothesis to be rejected. We do not concur that noncultural processes should be construed as a null hypothesis, as we discuss further below. However, because of the clear editorial opinion we elected to revise the manuscript to make more explicit how the data and analyses test noncultural depositional hypotheses first, followed by testing of cultural hypotheses. This reorganization means that the revised manuscript now examines each hypothesis separately in turn. 

      Taking this approach resulted in a substantial reorganization of the “Results” section of the manuscript. The “Results” section now begins with summaries of analyses and data conducted on material from each excavation area. After the presentation of data and analyses from each area, we then present a separate section for each of several hypotheses for the disposition and sedimentary context of the remains. These hypotheses include deposition of bodies upon a talus (as hypothesized in some previous work), slow sedimentary burial on a cave floor or within a natural depression, rapid burial by gravity-driven slumping, and burial of naturally mummified remains. We then include sections to test the hypothesis of primary cultural burial and secondary cultural burial. This approach adds substantial length to the Results. While some elements may be repeated across sections, we do consider the new version to be easier to take piece by piece for a reader trying to understand how each hypothesis relates to the evidence. 

      The Results section includes analyses on several different excavation areas within the Dinaledi Subsystem. Each of these presents somewhat different patterns of data. We conceived of this manuscript combining these distinct areas because each of them provides information about the formation history of the Homo naledi-associated sediments and the deposition of the Homo naledi remains. Together they speak more strongly than separately. In the previous version of the manuscript, two areas of excavation were considered in detail (Dinaledi Feature 1 and the Hill Antechamber Feature), with a third area (the Puzzle Box area) included only in the Discussion and with reference to prior work. We now describe the new work undertaken after the 2013-2014 excavations in more detail. This includes an overview of areas in the Hill Antechamber and Dinaledi Chamber that have not yielded substantial H. naledi remains and that thereby help contextualize the spatial concentration of H. naledi skeletal material. The most substantial change in the data presented is a much expanded reanalysis of the Puzzle Box area. This reanalysis provides greater clarity on how previously published descriptions relate to the new evidence. The reanalysis also provides the data to integrate the detailed information on bone identification fragmentation, and spatial taphonomy from this area with the new excavation results from the other areas. 

      In addition to Results, the reorganization also affected the manuscript’s Introduction section. Where the previous version led directly from a brief review of Pleistocene burial into the description of the results, this revised manuscript now includes a review of previous studies of the Rising Star cave system. This review directly addresses referee comments that express some hesitation to accept previous results concerning the structure and formation of sediments, the accessibility of the Dinaledi Subsystem, the geochronological setting of the H. naledi remains, and the relation of the Dinaledi Subsystem to nearby cave areas. Some parts of this overview are further expanded in the Supplementary Information to enable readers to dive more deeply into the previous literature on the site formation and geological configuration of the Rising Star cave system without needing to digest the entirety of the cited sources. 

      The Discussion section of the revised manuscript is differentiated from Results and focuses on several areas where the evidence presented in this study may benefit from greater context. One new section addresses hypothesis testing and parsimony for Pleistocene burial evidence, which we address at greater length in this summary below. The majority of the Discussion concerns the criteria for recognizing evidence for burial as applied in other studies. In this research we employ a minimal definition but other researchers have applied varied criteria. We consider whether these other criteria have relevance in light of our observations and whether they are essential to the recognition of burial evidence more broadly. 

      Vocabulary:

      We introduce the term “cultural burial” in this revised manuscript to refer to the burial of dead bodies as a mortuary practice. “Burial” as an unmodified term may refer to the passive covering of remains by sedimentary processes. Use of the term “intentional burial” would raise the question of interpreting intent, which we do not presume based on the evidence presented in this research. The relevant question in this case is whether the process of burial reflects repeated behavior by a group. As we received input from various colleagues it became clear that burial itself is a highly loaded term. In particular there is a common assumption within the literature and among professionals that burial must by definition be symbolic. We do not take any position on that question in this manuscript, and it is our hope that the term “cultural burial” may focus the conversation around the extent that the behavioral evidence is repeated and patterned. 

      Sedimentology and geochemistry of Dinaledi Feature 1:

      Reviewer 4 provided detailed comments on the sedimentological and geochemical context that we report in the manuscript. One outside review (Foecke et al. 2024) included some of the points raised by reviewer 4, and additionally addressed the reporting of geochemical and sedimentological data in previous work that we cite. 

      To address these comments we have revised the sedimentary context and micromorphology of sediments associated with Dinaledi Feature 1. In the new text we demonstrate the lack of microstratigraphy (supported by grain size analysis) in the unlithified mud clast breccia (UMCB), while such a microstratigraphy is observed in the laminated orange-red mudstones (LORM) that contribute clasts to the UMCB. Thus, we emphasize the presence and importance of a laterally continuous layer of LORM nature occurring at a level that appears to be the maximum depth of fossil occurrence. This layer is severely broken under extensive accumulation of fossils such as Feature 1 and only evidenced by abundant LORM clasts within and around the fossils. 

      We have completely reworked the geochemical context associated with Feature 1 following the comments of reviewer 4. We described the variations and trends observed in the major oxides separate from trace and rare-earth elements. We used Harker variations plots to assess relationships between these element groups with CaO and Zn, followed by principal component analysis of all elements analyzed. The new geochemical analysis clearly shows that Feature 1 is associated with localized trace element signatures that exist in the sediments only in association with the fossil bones, which suggests lack of postdepositional mobilization of the fossils and sediments. We additionally have included a fuller description of XRF methods. 

      To clarify the relation of all results to the features described in this study, we removed the geochemical and sedimentological samples from other sites within the Dinaledi Subsystem. These localities within the fissure network represent only surface collection of sediment, as no excavation results are available from those sites to allow for comparison in the context of assessing evidence of burial. These were initially included for comparison, but have now been removed to avoid confusion.  

      Micromorphology of sediments:

      Some referees (1, 3, and 4) and other commentators (including Martinón-Torres et al. 2024) have suggested that the previous manuscript was deficient due to an insufficient inclusion of micromorphological analysis of sediments. Because these commentators have emphasized this kind of evidence as particularly important, we review here what we have included and how our revision has addressed this comment. Previous work in the Dinaledi Chamber (Dirks et al., 2015; 2017) included thin section illustrations and analysis of sediment facies, including sediments in direct association with H. naledi remains within the Puzzle Box area. The previous work by Wiersma and coworkers (2020) used micromorphological analysis as one of several approaches to test the formation history of Unit 3 sediments in the Dinaledi Subsystem, leading to the interpretation of autobrecciation of earlier Unit 1 sediment. In the previous version of this manuscript we provided citations to this earlier work. The previous manuscript also provided new thin section illustrations of Unit 3 sediment near Dinaledi Feature 1 to place the disrupted layer of orange sediment (now designated the laminated orange silty mudstone unit) into context. 

      In the new revised manuscript we have added to this information in three ways. First, as noted above in response to reviewer 4, we have revised and added to our discussion of micromorphology within and adjacent to the Dinaledi Feature 1. Second, we have included more discussion in the Supplementary Information of previous descriptions of sediment facies and associated thin section analysis, with illustrations from prior work (CC-BY licensed) brought into this paper as supplementary figures, so that readers can examine these without following the citations. Third, we have included Figure 10 in the manuscript which includes six panels with microtomographic sections from the Hill Antechamber Feature. This figure illustrates the consistency of sub-unit 3b sediment in direct contact with H. naledi skeletal material, including anatomically associated skeletal elements, with previous analyses that demonstrate the angular outlines and chaotic orientations of LORM clasts. It also shows density contrasts of sediment in immediate contact with some skeletal elements, the loose texture of this sediment with air-filled voids, and apparent invertebrate burrowing activity. To our knowledge this is the first application of microtomography to sediment structure in association with a Pleistocene burial feature. 

      To forestall possible comments that the revised manuscript does not sufficiently employ micromorphological observations, or that any one particular approach to micromorphology is the standard, we present here some context from related studies of evidence from other research groups working at varied sites in Africa, Europe, and Asia. Hodgkins et al. (2021) noted: “Only a handful of micromorphological studies have been conducted on human burials and even fewer have been conducted on suspected burials from Paleolithic or hunter-gatherer contexts.” In that study, one supplementary figure with four photomicrographs of thin sections of sediments was presented. Interpretation of the evidence for a burial pit by Hodgkins et al. (2021) noted the more open microstructure of sediment but otherwise did not rely upon the thin section data in characterizing the sediments associated with grave fill. Martinón-Torres et al. (2021) included one Extended Data figure illustrating thin sections of sediments and bone, with two panels showing sediments (the remainder showing bone histology). The micromorphological analysis presented in the supplementary information of that paper was restricted to description of two microfacies associated with the proposed “pit” in that study. That study did carry out microCT scanning of the partially-prepared skeletal remains but did not report any sediment analysis from the microtomographic results. Maloney et al. (2022) reported no micromorphological or thin section analysis. Pomeroy et al. (2020a) included one illustration of a thin section; this study may be regarded as a preliminary account rather than a full description of the work undertaken. Goldberg et al. (2017) analyzed the geoarchaeology of the Roc de Marsal deposits in which possible burial-associated sediments had been fully excavated in the 1960s, providing new morphological assessments of sediment facies; the supplementary information to this work included five scans (not microscans) of sediment thin sections and no microphotographs. Fewlass et al. (2023) presented no thin section or micromorphological illustrations or methods. In summary of this research, we note that in one case micromorphological study provided observations that contributed to the evidence for a pit, in other cases micromorphological data did not test this hypothesis, and many researchers do not apply micromorphological techniques in their particular contexts. 

      Sediment micromorphology is a growing area of research and may have much to provide to the understanding of ancient burial evidence as its standards continue to develop (Pomeroy et al. 2020b). In particular microtomographic analysis of sediments, as we have initiated in this study, may open new horizons that are not possible with more destructive thin-section preparation. In this manuscript, the thin section data reveals valuable evidence about the disruption of sediment structure by features within the Dinaledi Chamber, and microtomographic analysis further documents that the Hill Antechamber Feature reflects similar processes, in addition to possible post-burial diagenesis and invertebrate activity. Following up in detail on these processes will require further analysis outside the scope of this manuscript. 

      Access into the Dinaledi Subsystem:

      Reviewer 1 emphasizes the difficulty of access into the Dinaledi Subsystem as a reason why the burial hypothesis is not parsimonious. Similar comments have been made by several outside commentators who question whether past accessibility into the Dinaledi Subsystem may at one time have been substantially different from the situation documented in previous work. Several pieces of evidence are relevant to these questions and we have included some discussion of them in the Introduction, and additionally include a section in the Supplementary Information (“Entrances to the cave system”) to provide additional context for these questions. Homo naledi remains are found not only within the Dinaledi Subsystem but also in other parts of the cave system including the Lesedi Chamber, which is similarly difficult for non-expert cavers to access. The body plan, mass, and specific morphology of H. naledi suggest that this species would be vastly more suited to moving and climbing within narrow underground passages than living people. On this basis it is not unparsimonious to suggest that the evidence resulted from H. naledi activity within these spaces. We note that the accessibility of the subsystem is not strictly relevant to the hypothesis of cultural burial, although the location of the remains does inform the overall context which may reflect a selection of a location perceived as special in some way. 

      Stuffing bodies down the entry to the subsystem:

      Reviewer 3 suggests that one explanation for the emplacement of articulated remains at the top of the sloping floor of the Hill Antechamber is that bodies were “stuffed” into the chute that comprises the entry point of the subsystem and passively buried by additional accumulation of remains. This was one hypothesis presented in earlier work (Dirks et al. 2015) and considered there as a minimal explanation because it did not entail the entry of H. naledi individuals into the subsystem. The further exploration (Elliott et al. 2021) and ongoing survey work, as well as this manuscript, all have resulted in data that rejects this hypothesis. The revised manuscript includes a section in the results “Deposition upon a talus with passive burial” that examines this hypothesis in light of the data. 

      Recognition of pits:

      Referee 3 and 4 and several additional commentators have emphasized that the recognition of pit features is necessary to the hypothesis of burial, and questioned whether the data presented in the manuscript were sufficient to demonstrate that pits were present. We have revised the manuscript in several ways to clarify how all the different kinds of evidence from the subsystem test the hypothesis that pits were present. This includes the presentation of a minimal definition of burial to include a pit dug by hominins, criteria for recognizing that a pit was present, and an evaluation of the evidence in each case to make clear how the evidence relates to the presence of a pit and subsequent infill. As referee 3 notes, it can be challenging to recognize a pit when sediment is relatively homogeneous. This point was emphasized in the review by Pomeroy and coworkers (2020b), who reflected on the difficulty seeing evidence for shallow pits constructed by hominins, and we have cited this in the main text. As a result, the evidence for pits has been a recurrent topic of debate for most Pleistocene burial sites. However in addition to the sedimentological and contextual evidence in the cases we describe, the current version also reflects upon other possible mechanisms for the accumulation of bones or bodies. The data show that the sedimentary fill associated with the H. naledi remains in the cases we examine could not have passively accumulated slowly and is not indicative of mass movement by slumping or other high-energy flow. To further put these results into context, we added a section to the Discussion that briefly reviews prior work on distinguishing pits in Pleistocene burial contexts, including the substantial number of sites with accepted burial evidence for which no evidence of a pit is present. 

      Extent of articulation and anatomical association:

      We have added significantly greater detail to the descriptions of articulated remains and orientation of remains in order to describe more specifically the configuration of the skeletal material. We also provide 14 figures in main text (13 of them new) to illustrate the configuration of skeletal remains in our data. For the Puzzle Box area, this now includes substantial evidence on the individuation of skeletal fragments, which enables us to illustrate the spatial configuration of remains associated with the DH7 partial skeleton, as well as the spatial position of fragments refitted as part of the DH1, DH2, DH3, and DH4 crania. For Dinaledi Feature 1 and the Hill Antechamber Feature we now provide figures that key skeletal parts as identified, including material that is unexcavated where possible, and a skeletal part representation figure for elements excavated from Dinaledi Feature 1. 

      Archaeothanatology:

      Reviewer 2 suggests that a greater focus on the archaeothanatology literature would be helpful to the analysis, with specific reference to the sequence of joint disarticulation, the collapse of sediment and remains into voids created by decomposition, and associated fragmentation of the remains. In the revised manuscript we have provided additional analysis of the Hill Antechamber Feature with this approach in mind. This includes greater detail and illustration of our current hypothesis for individuation of elements. We now discuss a hypothesis of body disposition, describe the persistent joints and articulation of elements, and examine likely decomposition scenarios associated with these remains. Additionally, we expand our description and illustration of the orientation of remains and degree of anatomical association and articulation within Dinaledi Feature 1. For this feature and for the Hill Antechamber Feature we have revised the text to describe how fracturing and crushing patterns are consistent with downward pressure from overlying sediment and material. In these features, postdepositional fracturing occurred subsequent to the decomposition of soft tissue and partial loss of organic integrity of the bone. We also indicate that the loss by postdepositional processes of most long bone epiphyses, vertebral bodies, and other portions of the skeleton less rich in cortical bone, poses a challenge for testing the anatomical associations of the remaining elements. This is a primary reason why we have taken a conservative approach to identification of elements and possible associations. 

      A further aspect of the site revealed by our analysis is the selective reworking of sediments within the Puzzle Box area subsequent to the primary deposition of some bodies. The skeletal evidence from this area includes body parts with elements in anatomical association or articulation, juxtaposed closely with bone fragments at varied pitch and orientation. This complexity of events evidenced within this area is a challenge for approaches that have been developed primarily based on comparative data from single-burial situations. In these discussions we deepen our use of references as suggested by the referee.   

      Burial positions:

      Reviewer 2 further suggests that illustrations of hypothesized burial positions would be valuable. We recognize that a hypothesized burial position may be an appealing illustration, and that some recent studies have created such illustrations in the context of their scientific articles. However such illustrations generally include a great deal of speculation and artist imagination, and tend to have an emotive character. We have added more discussion to the manuscript of possible primary disposition in the case of the Hill Antechamber Feature as discussed above. We have not created new illustrations of hypothesized burial positions for this revision. 

      Carnivore involvement:

      Referee 1 suggests that the manuscript should provide further consideration of whether carnivore activity may have introduced bones or bodies into the cave system. The reorganized Introduction now includes a review of previous work, and an expanded discussion within the Supplementary Information (“Hypotheses tested in previous work”). This includes a review of literature on the topic of carnivore accumulation and the evidence from the Dinaledi and Lesedi Chamber that rejects this hypothesis. 

      Water transport and mud:

      The eLife referees broadly accepted previous work showing that water inundation or mass flow of water-saturated sediment did not occur within the history of Unit 2 and 3 sediments, including those associated with H. naledi remains. However several outside commentators did refer specifically to water flow or mud flow as a mechanism for slumping of deposits and possible sedimentary covering of the remains. To address these comments we have added a section to the

      Supplementary Information (“Description of the sedimentary deposits of the Dinaledi Subsystem”) that reviews previous work on the sedimentary units and formation processes documented in this area. We also include a subsection specifically discussing the term “mud” as used in the description of the sedimentology within the system, as this term has clearly been confusing for nonspecialists who have read and commented on the work. We appreciate the referees’ attention to the previous work and its terminology.  

      Redescription of areas of the cave system:

      Reviewer 1 suggests that a detailed reanalysis of all portions of the cave system in and around the Dinaledi Subsystem is warranted to reject the hypothesis that bodies entered the space passively and were scattered from the floor by natural (i.e. noncultural) processes. The referee suggests that National Geographic could help us with these efforts. To address this comment we have made several changes to the manuscript. As noted above, we have added material in Supplementary Information to review the geochronology of the Dinaledi Subsystem and nearby Dragon’s Back Chamber, together with a discussion of the connections between these spaces. 

      Most directly in response to this comment we provide additional documentation of the possibility of movement of bodies or body parts by gravity within the subsystem itself. This includes detailed floor maps based on photogrammetry and LIDAR measurement, where these are physically possible, presented in Figures 2 and 3. In some parts of the subsystem the necessary equipment cannot be used due to the extremely confined spaces, and for these areas our maps are based on traditional survey methods. In addition to plan maps we have included a figure showing the elevation of the subsystem floor in a cross-section that includes key excavation areas, showing their relative elevation. All figures that illustrate excavation areas are now keyed to their location with reference to a subsystem plan. These data have been provided in previous publications but the visualization in the revised manuscript should make the relationship of areas clear for readers. The Introduction now includes text that discusses the configuration of the Hill Antechamber, Dinaledi Chamber, and nearby areas, and also discusses the instances in which gravity-driven movement may be possible, at the same time reviewing that gravity-driven movement from the entry point of the subsystem to most of the localities with hominin skeletal remains is not possible. 

      Within the Results, we have added a section on the relationship of features to their surroundings in order to assist readers in understanding the context of these bone-bearing areas and the evidence this context brings to the hypothesis in question. We have also included within this new section a discussion of the discrete nature of these features, a question that has been raised by outside commentators. 

      Passive sedimentation upon a cave floor or within a natural depression:

      Reviewer 3 suggests that the situation in the Dinaledi Subsystem may be similar to a European cave where a cave bear skeleton might remain articulated on a cave floor (or we can add, within a hollow for hibernation), later to be covered in sediment. The reviewer suggests that articulation is therefore no evidence of burial, and suggests that further documentation of disarticulation processes is essential to demonstrating the processes that buried the remains. We concur that articulation by itself is not sufficient evidence of cultural burial. To address this comment we have included a section in the Results that tests the hypothesis that bodies were exposed upon the cave floor or within a natural depression. To a considerable degree, additional data about disarticulation processes subsequent to deposition are provided in our reanalysis of the Puzzle Box area, including evidence for selective reworking of material after burial. 

      Postdepositional movement and floor drains:

      Reviewer 3 notes that previous work has suggested that subsurface floor drains may have caused some postdepositional movement of skeletal remains. The hypothesis of postdepositional slumping or downslope movement has also been discussed by some external commentators (including Martinón-Torres et al. 2024). We have addressed this question in several places within the revised manuscript. As we now review, previous discussion of floor drains attempted to explain the subvertical orientation of many skeletal elements excavated from the Puzzle Box area. The arrangement of these bones reflects reworking as described in our previous work, and without considering the possibility of reworking by hominins, one mechanism that conceivably might cause reworking was downward movement of sediments into subsurface drains. Further exploration and mapping, combined with additional excavation into the sediments beneath the Puzzle Box area provided more information relevant to this hypothesis. In particular this evidence shows that subsurface drains cannot explain the arrangement of skeletal material observed within the Puzzle Box area. As now discussed in the text, the reworking is selective and initiated from above rather than below. This is best explained by hominin activity subsequent to burial. 

      In a new section of the Results we discuss slumping as a hypothesis for the deposition of the remains. This includes discussion of downslope movement within the Hill Antechamber and the idea that floor drains may have been a mechanism for sediment reworking in and around the Puzzle Box area and Dinaledi Feature 1. As described in this section the evidence does not support these hypotheses. 

      Hypothesis testing and parsimony:

      Referees 1 and 3 and the editorial guidance all suggested that a more appropriate presentation would adopt a null hypothesis and test it. The specific suggestion that the null hypothesis should be a natural sedimentary process of deposition was provided not only by these reviewers but also by some outside commentators. To address this comment, we have edited the manuscript in two ways. The first is the addition of a section to the Discussion that specifically discusses hypothesis testing and parsimony as related to Pleistocene evidence of cultural burial. This includes a brief synopsis of recent disciplinary conversations and citation of work by other groups of authors, none of whom adopted this “null hypothesis” approach in their published work. 

      As we now describe in the manuscript, previous work on the Dinaledi evidence never assumed any role for H. naledi in the burial of remains. Reading the reviewer reports caused us to realize that this previous work had followed exactly the “null hypothesis” approach that some suggested we follow. By following this null hypothesis approach, we neglected a valuable avenue of investigation. In retrospect, we see how this approach impeded us from understanding the pattern of evidence within the Puzzle Box area. Thus in the revised manuscript we have mentioned this history within the Discussion and also presented more of the background to our previous work in the Introduction. Hopefully by including this discussion of these issues, the manuscript will broaden conversation about the relation of parsimony to these issues. 

      Language and presentation style:

      Reviewer 4 criticizes our presentation, suggesting that the text “gives the impression that a hypothesis was formulated before data were collected.” Other outside commentators have mentioned this notion also, including Martinón-Torres et al. (2024) who suggest that the study began from a preferred hypothesis and gathered data to support it. The accurate communication of results and hypotheses in a scientific article is a broader issue than this one study. Preferences about presentation style vary across fields of study as well as across languages. We do not regret using plain language where possible. In any study that combines data and methods from different scientific disciplines, the use of plain language is particularly important to avoid misunderstandings where terms may mean different things in different fields. 

      The essential question raised by these comments is whether it is appropriate to present the results of a study in terms of the hypothesis that is best supported. As noted above, we read carefully many recent studies of Pleistocene burial evidence. We note that in each of these studies that concluded that burial is the best hypothesis, the authors framed their results in the same way as our previous manuscript: an introduction that briefly reviews background evidence for treatment of the dead, a presentation of results focused on how each analysis supports the hypothesis of burial for the case, and then in some (but not all) cases discussion of why some alternative hypotheses could be rejected. We do not infer from this that these other studies started from a presupposition and collected data only to confirm it. Rather, this is a simple matter of presentation style. 

      The alternative to this approach is to present an exhaustive list of possible hypotheses and to describe how the data relate to each of them, at the end selecting the best. This is the approach that we have followed in the revised manuscript, as described above under the direction of the reviewer and editorial guidance. This approach has the advantage of bringing together evidence in different combinations to show how each data point rejects some hypotheses while supporting others. It has the disadvantage of length and repetition. 

      Possible artifact:

      We have chosen to keep the description of the possible artifact associated with the Hill Antechamber Feature in the Supplementary Information. We do this while acknowledging that this is against the opinion of reviewer 4, who felt the description should be removed unless the object in question is fully excavated and physically analyzed. The previous version of the manuscript did not rely upon the stone as positive evidence of grave goods or symbolic content, and it noted that the data do not test whether the possible artifact was placed or was intentionally modified. However this did not satisfy reviewer 4, and some outside commentators likewise asserted that the object must be a “geofact” and that it should be removed. 

      We have three arguments against this line of thinking. First, we do not omit data from our reporting. Whether Homo naledi shaped the rock or not, used it as a tool or not, whether the rock was placed with the body or not, it is unquestionably there. Omitting this one object from the report would be simply dishonest. Second, the data on this rock are at 16 micron resolution. While physical inspection of its surface may eventually reveal trace evidence and will enable better characterization of the raw material, no mode of surface scanning will produce better evidence about the object’s shape. Third, the position of this possible artifact within the feature provides significant information about the deposition of the skeletal material and associated sediments. The pitch, orientation, and position of the stone is not consistent with slow deposition but are consistent with the hypothesis that the surrounding sediment was rapidly emplaced at the same time as the articulated elements less than 2 cm away. 

      In the current version, we have redoubled our efforts to provide information about the position and shape of this stone while not presupposing the intentionality of its shape or placement. We add here that the attitude expressed by referee 4 and other commentators, if followed at other sites, would certainly lead to the loss or underreporting of evidence, which we are trying to avoid.  

      Consistency versus variability of behavior:

      As described in the revised manuscript, different features within the Dinaledi Subsystem exhibit some shared characteristics. At the same time, they vary in positioning, representation of individuals and extent of commingling. Other localities within the subsystem and broader cave system present different evidence. Some commentators have questioned whether the patterning is consistent with a single common explanation, or whether multiple explanations are necessary. To address this line of questioning, we have added several elements to the manuscript. We created a new section on secondary cultural burial, discussing whether any of the situations may reflect this practice. In the Discussion, we briefly review the ways in which the different features support the involvement of H. naledi without interpreting anything about the intentionality or meaning of the behavior. We further added a section to the Discussion to consider whether variation among the features reflects variation in mortuary practices by H. naledi. One aspect of this section briefly cites variation in the location and treatment of skeletal remains at other sites with evidence of burial. 

      Grave goods:

      Some commentators have argued that grave goods are a necessary criterion for recognizing evidence of ancient burial. We added a section to the Discussion to review evidence of grave goods at other Pleistocene sites where burial is accepted. 

      References:

      • Dirks, P. H., Berger, L. R., Roberts, E. M., Kramers, J. D., Hawks, J., Randolph-Quinney, P. S., Elliott, M., Musiba, C. M., Churchill, S. E., de Ruiter, D. J., Schmid, P., Backwell, L. R., Belyanin, G. A., Boshoff, P., Hunter, K. L., Feuerriegel, E. M., Gurtov, A., Harrison, J. du G., Hunter, R., … Tucker, S. (2015). Geological and taphonomic context for the new hominin species Homo naledi from the Dinaledi Chamber, South Africa. eLife, 4, e09561. https://doi.org/10.7554/eLife.09561

      • Dirks, P. H., Roberts, E. M., Hilbert-Wolf, H., Kramers, J. D., Hawks, J., Dosseto, A., Duval, M., Elliott, M., Evans, M., Grün, R., Hellstrom, J., Herries, A. I., Joannes-Boyau, R., Makhubela, T. V., Placzek, C. J., Robbins, J., Spandler, C., Wiersma, J., Woodhead, J., & Berger, L. R. (2017). The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa. eLife, 6, e24231. https://doi.org/10.7554/eLife.24231

      • Elliott, M., Makhubela, T., Brophy, J., Churchill, S., Peixotto, B., FEUERRIEGEL, E., Morris, H., Van Rooyen, D., Ramalepa, M., Tsikoane, M., Kruger, A., Spandler, C., Kramers, J., Roberts, E., Dirks, P., Hawks, J., & Berger, L. R. (2021). Expanded Explorations of the Dinaledi Subsystem,Rising Star Cave System, South Africa. PaleoAnthropology, 2021(1), 15–22. https://doi.org/10.48738/2021.iss1.68

      • Fewlass, H., Zavala, E. I., Fagault, Y., Tuna, T., Bard, E., Hublin, J.-J., Hajdinjak, M., & Wilczyński, J. (2023). Chronological and genetic analysis of an Upper Palaeolithic female infant burial from Borsuka Cave, Poland. iScience, 26(12). https://doi.org/10.1016/j.isci.2023.108283

      • Foecke, Kimberly K., Queffelec, Alain, & Pickering, Robyn. (n.d.). No Sedimentological Evidence for Deliberate Burial by Homo naledi – A Case Study Highlighting the Need for Best Practices in Geochemical Studies Within Archaeology and Paleoanthropology. PaleoAnthropology, 2024. https://doi.org/10.48738/202x.issx.xxx

      • Goldberg, P., Aldeias, V., Dibble, H., McPherron, S., Sandgathe, D., & Turq, A. (2017). Testing the Roc de Marsal Neandertal “Burial” with Geoarchaeology. Archaeological and Anthropological Sciences, 9(6), 1005–1015. https://doi.org/10.1007/s12520-013-0163-2

      • Maloney, T. R., Dilkes-Hall, I. E., Vlok, M., Oktaviana, A. A., Setiawan, P., Priyatno, A. A. D., Ririmasse, M., Geria, I. M., Effendy, M. A. R., Istiawan, B., Atmoko, F. T., Adhityatama, S., Moffat, I., Joannes-Boyau, R., Brumm, A., & Aubert, M. (2022). Surgical amputation of a limb 31,000 years ago in Borneo. Nature, 609(7927), 547–551. https://doi.org/10.1038/s41586-022-05160-8

      • Martinón-Torres, M., d’Errico, F., Santos, E., Álvaro Gallo, A., Amano, N., Archer, W., Armitage, S. J., Arsuaga, J. L., Bermúdez de Castro, J. M., Blinkhorn, J., Crowther, A., Douka, K., Dubernet, S., Faulkner, P., Fernández-Colón, P., Kourampas, N., González García, J., Larreina, D., Le Bourdonnec, F.-X., … Petraglia, M. D. (2021). Earliest known human burial in Africa. Nature, 593(7857), Article 7857. https://doi.org/10.1038/s41586021-03457-8

      • Martinón-Torres, M., Garate, D., Herries, A. I. R., & Petraglia, M. D. (2023). No scientific evidence that Homo naledi buried their dead and produced rock art. Journal of Human Evolution, 103464. https://doi.org/10.1016/j.jhevol.2023.103464

      • Pomeroy, E., Bennett, P., Hunt, C. O., Reynolds, T., Farr, L., Frouin, M., Holman, J., Lane, R., French, C., & Barker, G. (2020a). New Neanderthal remains associated with the ‘flower burial’ at Shanidar Cave. Antiquity, 94(373), 11–26. https://doi.org/10.15184/aqy.2019.207

      • Pomeroy, E., Hunt, C. O., Reynolds, T., Abdulmutalb, D., Asouti, E., Bennett, P., Bosch, M., Burke, A., Farr, L., Foley, R., French, C., Frumkin, A., Goldberg, P., Hill, E., Kabukcu, C., Lahr, M. M., Lane, R., Marean, C., Maureille, B., … Barker, G. (2020b). Issues of theory and method in the analysis of Paleolithic mortuary behavior: A view from Shanidar Cave. Evolutionary Anthropology: Issues, News, and Reviews, 29(5), 263–279. https://doi.org/10.1002/evan.21854

      • Robbins, J. L., Dirks, P. H. G. M., Roberts, E. M., Kramers, J. D., Makhubela, T. V., HilbertWolf, H. L., Elliott, M., Wiersma, J. P., Placzek, C. J., Evans, M., & Berger, L. R. (2021). Providing context to the Homo naledi fossils: Constraints from flowstones on the age of sediment deposits in Rising Star Cave, South Africa. Chemical Geology, 567, 120108. https://doi.org/10.1016/j.chemgeo.2021.120108

      • Wiersma, J. P., Roberts, E. M., & Dirks, P. H. G. M. (2020). Formation of mud clast breccias and the process of sedimentary autobrecciation in the hominin-bearing (Homo naledi) Rising Star Cave system, South Africa. Sedimentology, 67(2), 897–919. https://doi.org/10.1111/sed.12666

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This work tried to map the synaptic connectivity between the inputs and outputs of the song premotor nucleus, HVC in zebra finches to understand how sensory (auditory) to motor circuits interact to coordinate song production and learning. The authors optimized the optogenetic technique via AAV to manipulate auditory inputs from a specific auditory area one-by-one and recorded synaptic activity from a neuron with whole-cell recording from slice preparation with identification of the projection area by retrograde neuronal tracing. This thorough and detailed analysis provides compelling evidence of synaptic connections between 4 major auditory inputs (3 forebrain and 1 thalamic region) within three projection neurons in the HVC; all areas give monosynaptic excitatory inputs and polysynaptic inhibitory inputs, but proportions of projection to each projection neuron varied. They also find specific reciprocal connections between mMAN and Av. Taken together the authors provide the map of the synaptic connection between intercortical sensory to motor areas which is suggested to be involved in zebra finch song production and learning.

      Strengths:

      The authors optimized optogenetic tools with eGtACR1 by using AAV which allow them to manipulate synaptic inputs in a projection-specific manner in zebra finches. They also identify HVC cell types based on projection area. With their technical advance and thorough experiments, they provided detailed map synaptic connections.

      Weaknesses:

      As it is the study in brain slice, the functional implication of synaptic connectivity is limited. Especially as all the experiments were done in the adult preparation, there could be a gap in discussing the functions of developmental song learning.

      We thank the reviewer for their appreciation of our work. Although we agree that there can be limitations to brain slice preparations, the approaches used here for synaptic connectivity mapping are well-designed to identify long-range synaptic connectivity patterns. Optogenetic stimulation of axon terminals in brain slices does not require intact axons and works well when axons are cut, allowing identification of all inputs expressing optogenetic channels from aXerent regions. Terminal stimulation in slices yields stable post-synaptic responses for hours without rundown, assuring that polysynaptic and monosynaptic connections can be reliably identified in our brain slices.  Additionally, conducting similar types of experiments in vivo can run into important limitations. First, the extent of TTX and 4-AP diXusion, which is necessary for identification of long-range monosynaptic connections, can be diXicult to verify in vivo - potentially confounding identification of monosynaptic connectivity.  Second, conducting whole-cell patch-clamp experiments in vivo, particularly in deeper brain regions, is technically challenging, and would limit the number of cells that can be patched and increase the number of animals needed. 

      We agree that there may well be important diXerences between adult connectivity and connectivity patterns in the juvenile brain. Indeed, learning and experience during development almost certainly shape connectivity patterns and these patterns of connectivity may change incrementally and/or dynamically during development. Ultimately, adult connectivity patterns are the result of changes in the brain that accrue over development. Given that this is the first study mapping long-range connectivity of HVC input-output pathways, we reasoned that the adult connectivity would provide a critical reference allowing future studies to map diXerent stages of juvenile connectivity and the changes in connectivity driven by milestones like forming a tutor song memory, sensorimotor learning, and song crystallization.

      In this revision we worked to better highlight the points raised above and thank the reviewer for their comments.

      Reviewer #2 (Public review):

      Summary:

      The manuscript describes synaptic connectivity in the Songbird cortex's four main classes of sensory neuron aXerents onto three known classes of projection neurons of the pre-motor cortical region HVC. HVC is a region associated with the generation of learned bird songs. Investigators here use all male zebra finches to examine the functional anatomy of this region using patch clamp methods combined with optogenetic activation of select neuronal groups.

      Strengths:

      The quality of the recordings is extremely high and the quantity of data is on a very significant scale, this will certainly aid the field.

      Weaknesses:

      The authors could make the figures a little easier to navigate. Most of the figures use actual anatomical images but it would be nice to have this linked with a zebra finch atlas in more of a cartoon format that accompanied each fluro image. Additionally, for the most part, figures showing the labeling lack scale bar values (in um). These should be added not just shown in the legends.

      The authors could make it clear in the abstract that this is all male zebra finches - perhaps this is obvious given the bird song focus, but it should be stated. The number of recordings from each neuron class and the overall number of birds employed should be clearly stated in the methods (this is in the figures, but it should say n=birds or cells as appropriate).

      The authors should consider sharing the actual electrophysiology records as data.

      We thank the reviewer for their assessment of our research and suggestions. We have implemented many of these suggestions and provide details in our response to their specific Recommendations. Additionally, we are organizing our data and will make it publicly available with the version of record.

      Reviewer #3 (Public review):

      Nucleus HVC is critical both for song production as well as learning and arguably, sitting at the top of the song control system, is the most critical node in this circuit receiving a multitude of inputs and sending precisely timed commands that determine the temporal structure of song. The complexity of this structure and its underlying organization seem to become more apparent with each experimental manipulation, and yet our understanding of the underlying circuit organization remains relatively poorly understood. In this study, Trusel and Roberts use classic whole-cell patch clamp techniques in brain slices coupled with optogenetic stimulation of select inputs to provide a careful characterization and quantification of synaptic inputs into HVC. By identifying individual projection neurons using retrograde tracer injections combined with pharmacological manipulations, they classify monosynaptic inputs onto each of the three main classes of glutamatergic projection neurons in HVC (RA-, Area X- and Av-projecting neurons). This study is remarkable in the amount of information that it generates, and the tremendous labor involved for each experiment, from the expression of opsins in each of the target inputs (Uva, NIf, mMAN, and Av), the retrograde labelling of each type of projection neuron, and ultimately the optical stimulation of infected axons while recording from identified projection neurons. Taken together, this study makes an important contribution to increasing our identification, and ultimately understanding, of the basic synaptic elements that make up the circuit organization of HVC, and how external inputs, which we know to be critical for song production and learning, contribute to the intrinsic computations within this critic circuit.

      This study is impressive in its scope, rigorous in its implementation, and thoughtful regarding its limitations. The manuscript is well-written, and I appreciate the clarity with which the authors use our latest understanding of the evolutionary origins of this circuit to place these studies within a larger context and their relevance to the study of vocal control, including human speech. My comments are minor and primarily about legibility, clarification of certain manipulations, and organization of some of the summary figures.

      We thank the reviewer for their thoughtful assessment of our research.

      Recommendations for the authors:

      The following recommendations were considered by all reviewers to be important to incorporate for improving this paper:

      (1) Clarify the site of viral injection and the possibility of labeling other structures a) Show images of viral injection sites.

      We provide a representative image of viral expression for each pathway studied in this manuscript. Please see panel A in Figures 2-3 and 5-6 showing our viral expression in Uva, NIf, mMAN, and Av respectively.  

      b) Include in discussion caveats that the virus may spread beyond the boundaries of structures (e.g. especially injections into NIF could spread into Field L).

      For each HVC aXerent nucleus we have now included a sentence describing the possible spread of viral infection in surrounding structures in the Results. We also now expanded the image from the Av section to include NIf, to showcase lack of viral expression in NIf (see Fig. 6A).

      (2) Clarify the logic and precise methods of the TTX and 4-AP experiments

      a) Please see the detailed issue raised by Reviewer 3, Major Point 1 below.

      The TTX and 4AP application is the gold-standard of opsin-assisted synaptic circuit interrogation, pioneered by the Svoboda lab in 2009 (Petreanu, Mao et al. 2009) and widely used to assess monosynaptic connectivity in multiple brain circuits, as summarized in a recent review(Linders, Supiot et al. 2022). We now better describe the logic of this approach in the second paragraph of the Results section and cite the first description of this method from the Svoboda lab and a recent review weighing this method with other optogenetic methods for tracing synaptic connections in the brain.

      (3) Include caveats in discussion

      a) Note that there may be other inputs to HVC that were not examined in this study (e.g. CMM, Field L)

      In our original manuscript we did state “Although a complete description of HVC circuitry will require the examination of other potential inputs (i.e. RA<sub>HVC</sub> PNs, A11 glutamatergic neurons(Roberts, Klein et al. 2008, Ben-Tov, Duarte et al. 2023)) and a characterization of interneuron synaptic connectivity, here we provide a map of the synaptic connections between the 4 best described aPerents to HVC and its 3 populations of projection neurons” in the last paragraph of the Discussion. We have now edited this sentence to include the projection from NCM to HVC and cited Louder et al., 2024.

      We have extensively mapped input pathways to HVC, and consistent with Vates (Vates, Broome et al. 1996) we have not found evidence that Field L projects to HVC. Rather that it projects to the shelf region outside of HVC. Consistent with this, we do not see retrogradely labeled neurons in Field L following tracer injections confined to HVC (see Fig. 3G). Additionally, we find that CM projections to HVC arise from the nucleus Avalanche (Roberts, Hisey et al. 2017) which we specifically examine in this study. We do not dispute that there may be other pathways projecting to HVC that will need to be examined in the future, including known projections from neuromodulatory regions and RA, from developmentally restricted pathway(s) like NCM (Louder, Kuroda et al. 2024), and from yet unidentified pathways.

      b) Also note that birds in this study were adults and that some inputs to HVC likely to be important for learning may recede during development (e.g. Louder et al, 2024).

      In the second to last paragraph of the Discussion we now state: While our opsin-assisted circuit mapping provides us with a new level of insight into HVC synaptic circuitry, there are limitations to this research that should be considered. All circuit mapping in this study was carried out in brain slices from adult male zebra finches. Future studies will be needed to examine how this adult connectivity pattern relates to patterns of connectivity in juveniles during sensory or sensorimotor phases of vocal learning and connectivity patterns in female birds.   

      (4) Consider cosmetic changes to figures as suggested by Reviewers 2-3 below.

      We thank the reviewers for their suggestions and have implemented the changes as best we can.

      (5) Address all minor issues raised below.

      Reviewer #1 (Recommendations for the authors):

      I see this study is well designed to answer the author's specific question, mapping synaptic auditorymotor connections within HVC. Their experiments with advanced techniques of projection-specific optogenetic manipulation of synaptic inputs and retrograde identification of projection areas revealed input-output combination selective synaptic mapping.

      As I found this study advanced our knowledge with the compelling dataset, I have only some minor comments here.

      (1) One technical concern is we don't see how much the virus infection was focused on the target area and if we can ignore the eXect of synaptic connectivity from surrounding areas. As the amount of virus they injected is large (1.5ul) and target areas are small, we assume the virus might spread to the surrounding area, such as field L which also projects to HVC when targeting Nif. While I think the majority of the projections were from their target areas, it would be better to mention (also the images with larger view areas) the possibilities of projections of surrounding areas.

      We agree with the reviewer about the concern about specificity of viral expression. For this reason, we included sample images of the viral expression in each target area (panel A in Fig. 2,3,5,6). We have now also included a sentence at the beginning of each subsection of our Result to describe how we have ensured interpretability of the results. Uva and mMAN’s surrounding areas are not known to project to HVC. Possible cross-infection is an issue for Av and NIf, and we checked each bird’s injection site to ensure that eGtACR1+ cells were not visible in the unintended HVC-projecting areas.

      As mentioned in our response the public comment, consistent with Vates (Vates, Broome et al. 1996) we do not see evidence that Field L projects directly to HVC (see Fig. 3G).

      (2) Another concern about the technical issue is the damage to axonal projections. While I understand the authors stimulated axonal terminals axonal projections were assumed to be cut and their ability to release neurotransmitters would be reduced especially after long-term survival or repeated stimulation. Mentioning whether projection pathways were within their 230um-thick slice (probably depends on input sites) or not and the eXect of axonal cut would be helpful.

      We agree that slice electrophysiology has limitations. However, we disagree with the claim of reduced reliability or stability of the evoked response. We and others find that electrical and optogenetic repeated terminal stimulation in slices can yield stable post-synaptic responses for tens of minutes and even hours (Bliss and Gardner-Medwin 1973, Bliss and Lomo 1973, Liu, Kurotani et al. 2004, Pastalkova, Serrano et al. 2006, Xu, Yu et al. 2009, Trusel, Cavaccini et al. 2015, Trusel, Nuno-Perez et al. 2019). Indeed, long-term synaptic plasticity experiments in most preparations and across brain areas rely on such stability of the presynaptic machinery for synaptic release, despite axons being severed from their parent soma. Our assumption is the vast majority, if not all, connections between axon terminals and their cell body in the aXerent regions have been cut in our preparations. Nonetheless, the diversity of outcomes we report (currents returning after TTX+4AP or not, depending on the specific combination of input and HVCPN class) is consistent with the robustness of the synaptic interrogation method. 

      (3) While I understand this study focused on 4 major input areas and the authors provide good pictures of synaptic HVC connections from those areas, HVC has been reported to receive auditory inputs from other areas as well (CMM, FieldL, etc.). It is worth mentioning that there are other auditory inputs and would be interesting to discuss coordination with the inputs from other areas.

      We have extensively mapped input pathways to HVC, and consistent with Vates (Vates, Broome et al. 1996) we have not found evidence that Field L projects to HVC. Rather that it projects to the shelf region outside of HVC. Consistent with this, we do not see retrogradely labeled neurons in Field L following tracer injections confined to HVC (see Fig. 3G). Additionally, we find that CM projections to HVC arise from the nucleus Avalanche (Roberts, Hisey et al. 2017) which we specifically examine in this study. We do not dispute that there may be other pathways projecting to HVC that will need to be examined in the future, including known projections from neuromodulatory regions and RA, from developmentally restricted pathway(s) like NCM (Louder, Kuroda et al. 2024), and from yet unidentified pathways.

      (4) The HVC local neuronal connections have been reported to be modified and a recent study revealed the transient auditory inputs into HVC during song learning period. The author discusses the functions of HVC synaptic connections on song learning (also title says synaptic connection for song learning), however, the experiments were done in adults and dp not discuss the possibility of diXerent synaptic connection mapping in juveniles in the song learning period. Mentioning the neuronal activities and connectivity changes during song learning is important. Also, it would be helpful for the readers to discuss the potential diXerences between juveniles/adults if they want to discuss the functions of song learning.

      We now mention in the Discussion that this is an important caveat of our research and that future studies will be needed to examine how these adult connectivity patterns relate to connectivity patterns in juveniles during sensory or sensorimotor phases of vocal learning and connectivity patterns in female birds. Nonetheless, the title and abstract cite song learning because it is important for the broader public to understand that at least some of these aXerent brain regions carry an essential role in song learning (Foster and Bottjer 2001, Roberts, Gobes et al. 2012, Roberts, Hisey et al. 2017, Zhao, Garcia-Oscos et al. 2019, Koparkar, Warren et al. 2024).

      Reviewer #2 (Recommendations for the authors):

      The work is very detailed and will be an important resource to those working in the field. The recordings are of a high quality and lots of information is included such as measures of response kinetics amplitude and pharmacological confirmation of excitatory and inhibitory synaptic responses. In general, I feel the quality is extremely high and the quantity of data is on a very significant exhaustive scale that will certainly aid the field. I have come at this conclusion as a non zebra finch person but I feel the connection information shown will be of benefit given its high quality.

      Figure 7 is a nice way of showing the overall organization. Optional suggestion, consider highlighting anything in Figure 7 that results in a new understanding of the song system as compared to previous work on anatomy and function.

      We thank the reviewer for the kind comments about our research. We have highlighted our newly found connection between mMAN and Av and all the connections onto the HVC PNs in Panel B are newly identified in this study.

      Reviewer #3 (Recommendations for the authors):

      Major points

      (1) Clarification regarding methods for determining monosynaptic events:

      One of the manipulations that I struggled the most with was those describing the use of TTX + 4AP to isolate monosynaptic events. Initially, not being as familiar with the use of optically based photostimulation of axons to release transmitter locally, I was initially confused by statements such as "we found that oEPSC returned after application of TTX+4AP". This might be clear to someone performing these manipulations, but a bit more clarification would be helpful. Should I assume that an existing monosynaptic EPSC would be masked by co-occurring polysynaptic IPSCs which disappear following application of TTX + 4AP, thereby unmasking the monosynaptic EPSC, thereby causing the EPSC to "return"? A word that I am not sure works. Continuing my confusion with these experiments, I am unsure how this cocktail of drugs is added, if it is even added as a cocktail, which is what I initially assumed. The methods and the results are not so clear if they are added in sequence and why and if traces are recorded after the addition of both drugs or if they are recorded for TTX and then again for TTX + 4AP. Finally, looking at the traces in the experimental figures (e.g. Figures 2F, 3F, 5F, and 6F), it is diXicult to see what is being shown, at least for me. First, the authors need to describe better in the results why they stimulate twice in short succession and why they seem to use the response to the second pulse (unless I am mistaken) to measure the monosynaptic event. Second, I was confused by the traces (which are very small) in the presence of TTX. I would have expected to see a response if there was a monosynaptic EPSC but I only seem to see a flat line.  

      The confusion that I list above might be due in part to my ignorance, but it is important in these types of papers not to assume too much expertise if you want readers with a less sophisticated understanding of synaptic physiology to understand the data. In other words, a little bit more clarity and hand-holding would be welcome.

      We understand the reviewer’s confusion about the methodology.  In Voltage clamp, the amplifier injects current through the electrode maintaining the membrane voltage to -70mV, where the equilibrium potential for Cl- is near equilibrium, and therefore the only synaptic current evoked by light stimulation is due to cation influx, mainly through AMPA receptors (see Fig. 1).  Therefore, cooccurring polysynaptic IPSCs wouldn’t be visible. We examine those holding the membrane voltage at +10mV, see Fig. 1. TTX application suppresses V-dependent Na+ channels and therefore stops all neurotransmission. We show the traces upon TTX to show that currents we were recording prior to TTX application were of synaptic origin, and not due to accidental expression of opsin in the patched cell. Also, this ensures that any current visible after 4AP application is due to monosynaptic transmission and not to a failure of TTX application.

      After recording and light stimulation with TTX, we then add 4AP, which is a blocker of presynaptic K+ channels. This prevents the repolarization of the terminals that would occur in response to opsinmediated local depolarization. 4AP application, therefore, allows local opsin-driven depolarizations to reach the threshold for Ca2+-dependent vesicle docking and release. This procedure selectively reveals or unmasks the monosynaptic currents because any non-monosynaptically connected neuron would still need V-dependent Na+ channels to eXectively produce indirect neurotransmission onto the patched cell. The TTX and 4AP application is the gold-standard of opsinassisted synaptic circuit interrogation, pioneered by the Svoboda lab in 2009 and widely used to assess monosynaptic connectivity in multiple brain circuits, as summarized in a recent review (Linders et al., 2022). We now include 2 more sentences near the beginning of the Results to clarify this process and directly point to the Linders review for researchers wanting a deeper explanation of this technique. 

      The double stimulation is unrelated to our testing of monosynaptic connections. We originally conducted the experiments by delivering 2 pulses of light separated by 50ms, a common way to examine the pair-pulse ratio (PPR) – a physiological measure which is used to probe synapses for short-term plasticity and release probability. However, through discussions with colleagues we realized that the slow decay time of eGtACR1 may complicate interpretation of the response to the second light pulse. Thus, we elected to not report these results and indicated this in the Methods section:  “We calculated the paired-pulse ratio (PPR) as the amplitude of the second peak divided by the amplitude of the first peak elicited by the twin stimuli, however due to slow kinetics of eGtACR1 the results would be diPicult to interpret, and therefore we are not currently reporting them.” 

      (2) Suggestions for improving summary figures:

      Summary Figure 1a: The circuit diagram (schematic to the right of 1a) is OK but I initially found it a bit diXicult to interpret. For example, it is not clear why pink RA projecting neurons don't reach as far to the right as X or Av projecting neurons, suggesting that they are not really projection neurons. Also, the big question marks in the intermediate zone are not entirely intuitive. It seems there might be a better way of representing this. It might also be worth stating in the figure legend that the interconnectivity patterns shown in the figure between PNs in HVC are based on specific prior studies.

      We thank the reviewer for the constructive criticism. We have modified the figure to extend the RA projection line and mentioned in the figure legend that connectivity between PNs is based on prior studies.

      Summary Figure 1a: I am not sure I love this figure. There are a few minor issues. First, there are too many browns [Nif/AV and mMAN] which makes it more challenging to clearly disambiguate the diXerent projections. Second, it is unclear why this figure does not represent projections from RA to HVC. My biggest concern with this figure is that it oversimplifies some of the findings. From the figure, one gets the impression that Uva only projects to RA-PNs and that Av only projects to X-PNs even though the authors show connections to other PNs. With the small sample size in this current study for each projection and each PN type, one really cannot rule out that these "minority" projections are not important. I, therefore, suggest that the authors qualitatively represent the strength/probability of connections by weighting with thickness of aXerent connections.

      We assume the reviewer is commenting on our summary figure panel 7B. We agree with the referee that this is a simplified representation of our findings. We had indeed indicated in the legend that this was just a “Schematic of the HVC aXerent connectivity map resulting from the present work” and that “For conceptualization purposes, aXerent connectivity to HVC-PNs is shown only when the rate of monosynaptic connectivity reaches 50% of neurons examined”. We have added a title to highlight that this is but a simplification. We have now adjusted the colors to make the figure easier to follow. Based on the reviewers critique we searched for a better method for summarizing the complex connectivity patterns described in this research. We settled on a Sankey diagram of connectivity. This is now Figure 7C. In this diagram, we are able to show the proportion of connections from each input pathway onto each class of neuron and if these connections are poly or monosynaptic. We find this to a straightforward way of displaying all of the connectivity patterns identified in our figure 2-3 and 4-5 look forward to understanding if the reviewers find this a useful way of illustrating our findings.

      Minor points:

      (1) Line 50 - typo - song circuits.

      Thank you for catching this.

      (2) Line 106 - 111 - The findings suggest that 100% of Uva projections onto HVCRA neurons are monosynaptic. However, because the authors only tested 6 neurons their statements that their findings are so diXerent from other studies, should be somewhat tempered since these other studies (e.g. Moll et al.) looked at 251 neurons in HVC and sampling bias could still somewhat explain the diXerence.

      We observed oEPSCs in 43 of 51 (84.3%) HVC-RA neurons recorded (mean rise time = 2.4 ms) and monosynaptic connections onto 100% of the HVC-RA neurons tested (n = 6). Moll et al. combined electrical stimulation of Uva with two-photon calcium imaging (GCaMP6s) of putative HVC-RA neurons (n = 251 neurons). We should note that these are putative HVC-RA neurons because they were not visually identified using retrograde tracing or using some other molecular handle. They report that only ~16% of HVC-RA neurons showed reliable calcium responses following Uva stimulation. Although the experiments by Moll et al are technically impressive, calcium imaging is an insensitive technique for measuring post-synaptic responses, particularly subthreshold responses, when compared to whole-cell patch-clamp recordings. This approach cannot identify monosynaptic connections and is likely limited to only be sensitive suprathreshold activity that likely relies on recruitment of other polysynaptic inputs onto the neurons in HVC. Furthermore, as indicated in the Discussion, our opsin-mediated synaptic interrogation recruits any eGtACR1+ Uva terminal in the slice and therefore will have great likelihood of revealing any existing connections. 

      A limitation of whole-cell patch-clamp recordings is that it is a laborious low throughput technique. Future experiments using better imaging approaches, like voltage imaging, may be able to weigh in on diXerences between what we report here using whole-cell patch-clamp recordings from visually identified HVC-RA neurons combined with optogenetic manipulations of Uva terminals and the calcium imaging results reported by Moll. Nonetheless, whole-cell patch-clamp recordings combined with optogenetic manipulations is likely to remain the most sensitive method for identifying synaptic connectivity.

      (3) Figure 2G - the significance of white circles is not clear.

      The figure legend indicates that those highlight and mark the position of “retrogradely labeled HVCprojecting neurons in Uva (cyan, white circles)” to facilitate identification of colocalization with the in-situ markers.

      (4) Line 135 - Cardin et al. (J. Neurophys. 2004) is the first to show that song production does not require Nif.

      We thank the reviewer pointing this out and we have cited this important study. 

      (5) Line 183 - This is a confusing sentence because I initially thought that mMAN-mMANHVC PNs was a category!

      We switched the dash with a colon.

      (6) Figure 4d could use some arrows to identify what is shown. It is assumed that the box represents mMAN. Should it be assumed that Av is not in the plane of this section? If not, this should be stated in the legend. It is also unclear where the anterograde projections are. Is this the dork highway that goes from the box to the dorsal surface? If yes this should be indicated but it should also be made clear why the projections go both in the dorsal as well as the ventral directions.

      The inset, as indicated by the lines around it, is a magnification of the terminal fields in Av. We added an explanation of the inset.

      (7) Discussion. In the introduction, the authors mention projections from RA to HVC but never end up studying them in the current manuscript which seems like a missed opportunity and perhaps even a weakness of the study. In the discussion, it would certainly be good for the authors to at least discuss the possible significance of these projections and perhaps why they decided not to study them.

      We thank the reviewer for the comment. Unfortunately, we couldn’t reliably evoke interpretable currents from RA, and we elected to publish the current version of the paper with these 4 major inputs. Nonetheless, we have indicated in the Introduction and in the Discussion that more inputs (e.g. RA, A11, NCM) remain to be evaluated. 

      (8) Line 622 - Is this reference incomplete?

      We thank the reviewer. We have corrected the reference.

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    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Wang et al., recorded concurrent EEG-fMRI in 107 participants during nocturnal NREM sleep to investigate brain activity and connectivity related to slow oscillations (SO), sleep spindles, and in particular their co-occurrence. The authors found SO-spindle coupling to be correlated with increased thalamic and hippocampal activity, and with increased functional connectivity from the hippocampus to the thalamus and from the thalamus to the neocortex, especially the medial prefrontal cortex (mPFC). They concluded the brain-wide activation pattern to resemble episodic memory processing, but to be dissociated from task-related processing and suggest that the thalamus plays a crucial role in coordinating the hippocampal-cortical dialogue during sleep.

      The paper offers an impressively large and highly valuable dataset that provides the opportunity for gaining important new insights into the network substrate involved in SOs, spindles, and their coupling. However, the paper does unfortunately not exploit the full potential of this dataset with the analyses currently provided, and the interpretation of the results is often not backed up by the results presented. I have the following specific comments.

      Thank you for your thoughtful and constructive feedback. We greatly appreciate your recognition of the strengths of our dataset and findings Below, we address your specific comments and provide responses to each point you raised to ensure our methods and results are as transparent and comprehensible as possible. We hope these revisions address your comments and further strengthen our manuscript. Thank you again for the constructive feedback.

      (1) The introduction is lacking sufficient review of the already existing literature on EEG-fMRI during sleep and the BOLD-correlates of slow oscillations and spindles in particular (Laufs et al., 2007; Schabus et al., 2007; Horovitz et al., 2008; Laufs, 2008; Czisch et al., 2009; Picchioni et al., 2010; Spoormaker et al., 2010; Caporro et al., 2011; Bergmann et al., 2012; Hale et al., 2016; Fogel et al., 2017; Moehlman et al., 2018; Ilhan-Bayrakci et al., 2022). The few studies mentioned are not discussed in terms of the methods used or insights gained.

      We acknowledge the need for a more comprehensive review of prior EEG-fMRI studies investigating BOLD correlates of slow oscillations and spindles. However, these articles are not all related to sleep SO or spindle. Articles (Hale et al., 2016; Horovitz et al., 2008; Laufs, 2008; Laufs, Walker, & Lund, 2007; Spoormaker et al., 2010) mainly focus on methodology for EEG-fMRI, sleep stages, or brain networks, which are not the focus of our study. Thank you again for your attention to the comprehensiveness of our literature review, and we will expand the introduction to include a more detailed discussion of the existing literature, ensuring that the contributions of previous EEG-fMRI sleep studies are adequately acknowledged.  

      Introduction, Page 4 Lines 62-76

      “Investigating these sleep-related neural processes in humans is challenging because it requires tracking transient sleep rhythms while simultaneously assessing their widespread brain activation. Recent advances in simultaneous EEG-fMRI techniques provide a unique opportunity to explore these processes. EEG allows for precise event-based detection of neural signal, while fMRI provides insight into the broader spatial patterns of brain activation and functional connectivity (Horovitz et al., 2008; Huang et al., 2024; Laufs, 2008; Laufs, Walker, & Lund, 2007; Schabus et al., 2007; Spoormaker et al., 2010). Previous EEG-fMRI studies on sleep have focused on classifying sleep stages or examining the neural correlates of specific waves (Bergmann et al., 2012; Caporro et al., 2012; Czisch et al., 2009; Fogel et al., 2017; Hale et al., 2016; Ilhan-Bayrakcı et al., 2022; Moehlman et al., 2019; Picchioni et al., 2011). These studies have generally reported that slow oscillations are associated with widespread cortical and subcortical BOLD changes, whereas spindles elicit activation in the thalamus, as well as in several cortical and paralimbic regions. Although these findings provide valuable insights into the BOLD correlates of sleep rhythms, they often do not employ sophisticated temporal modeling (Huang et al., 2024), to capture the dynamic interactions between different oscillatory events, e.g., the coupling between SOs and spindles.”

      (2) The paper falls short in discussing the specific insights gained into the neurobiological substrate of the investigated slow oscillations, spindles, and their interactions. The validity of the inverse inference approach ("Open ended cognitive state decoding"), assuming certain cognitive functions to be related to these oscillations because of the brain regions/networks activated in temporal association with these events, is debatable at best. It is also unclear why eventually only episodic memory processing-like brain-wide activation is discussed further, despite the activity of 16 of 50 feature terms from the NeuroSynth v3 dataset were significant (episodic memory, declarative memory, working memory, task representation, language, learning, faces, visuospatial processing, category recognition, cognitive control, reading, cued attention, inhibition, and action).

      Thank you for pointing this out, particularly regarding the use of inverse inference approaches such as “open-ended cognitive state decoding.” Given the concerns about the indirectness of this approach, we decided to remove its related content and results from Figure 3 in the main text and include it in Supplementary Figure 7. We will refocus the main text on direct neurobiological insights gained from our EEG-fMRI analyses, particularly emphasizing the hippocampal-thalamocortical network dynamics underlying SO-spindle coupling, and we will acknowledge the exploratory nature of these findings and highlight their limitations.

      Discussion, Page 17-18 Lines 323-332

      “To explore functional relevance, we employed an open-ended cognitive state decoding approach using meta-analytic data (NeuroSynth: Yarkoni et al. (2011)). Although this method usefully generates hypotheses about potential cognitive processes, particularly in the absence of a pre- and post-sleep memory task, it is inherently indirect. Many cognitive terms showed significant associations (16 of 50), such as “episodic memory,” “declarative memory,” and “working memory.” We focused on episodic/declarative memory given the known link with hippocampal reactivation (Diekelmann & Born, 2010; Staresina et al., 2015; Staresina et al., 2023). Nonetheless, these inferences regarding memory reactivation should be interpreted cautiously without direct behavioral measures. Future research incorporating explicit tasks before and after sleep would more rigorously validate these potential functional claims.”

      (3) Hippocampal activation during SO-spindles is stated as a main hypothesis of the paper - for good reasons - however, other regions (e.g., several cortical as well as thalamic) would be equally expected given the known origin of both oscillations and the existing sleep-EEG-fMRI literature. However, this focus on the hippocampus contrasts with the focus on investigating the key role of the thalamus instead in the Results section.

      We appreciate your insight regarding the relative emphasis on hippocampal and thalamic activation in our study. We recognize that the manuscript may currently present an inconsistency between our initial hypothesis and the main focus of the results. To address this concern, we will ensure that our Introduction and Discussion section explicitly discusses both regions, highlighting the complementary roles of the hippocampus (memory processing and reactivation) and the thalamus (spindle generation and cortico-hippocampal coordination) in SO-spindle dynamics.

      Introduction, Page 5 Lines 87-103

      “To address this gap, our study investigates brain-wide activation and functional connectivity patterns associated with SO-spindle coupling, and employs a cognitive state decoding approach (Margulies et al., 2016; Yarkoni et al., 2011)—albeit indirectly—to infer potential cognitive functions. In the current study, we used simultaneous EEG-fMRI recordings during nocturnal naps (detailed sleep staging results are provided in the Methods and Table S1) in 107 participants. Although directly detecting hippocampal ripples using scalp EEG or fMRI is challenging, we expected that hippocampal activation in fMRI would coincide with SO-spindle coupling detected by EEG, given that SOs, spindles, and ripples frequently co-occur during NREM sleep. We also anticipated a critical role of the thalamus, particularly thalamic spindles, in coordinating hippocampal-cortical communication.

      We found significant coupling between SOs and spindles during NREM sleep (N2/3), with spindle peaks occurring slightly before the SO peak. This coupling was associated with increased activation in both the thalamus and hippocampus, with functional connectivity patterns suggesting thalamic coordination of hippocampal-cortical communication. These findings highlight the key role of the thalamus in coordinating hippocampal-cortical interactions during human sleep and provide new insights into the neural mechanisms underlying sleep-dependent brain communication. A deeper understanding of these mechanisms may contribute to future neuromodulation approaches aimed at enhancing sleep-dependent cognitive function and treating sleep-related disorders.”

      Discussion, Page 16-17 Lines 292-307

      “When modeling the timing of these sleep rhythms in the fMRI, we observed hippocampal activation selectively during SO-spindle events. This suggests the possibility of triple coupling (SOs–spindles–ripples), even though our scalp EEG was not sufficiently sensitive to detect hippocampal ripples—key markers of memory replay (Buzsáki, 2015). Recent iEEG evidence indicates that ripples often co-occur with both spindles (Ngo, Fell, & Staresina, 2020) and SOs (Staresina et al., 2015; Staresina et al., 2023). Therefore, the hippocampal involvement during SO-spindle events in our study may reflect memory replay from the hippocampus, propagated via thalamic spindles to distributed cortical regions.

      The thalamus, known to generate spindles (Halassa et al., 2011), plays a key role in producing and coordinating sleep rhythms (Coulon, Budde, & Pape, 2012; Crunelli et al., 2018), while the hippocampus is found essential for memory consolidation (Buzsáki, 2015; Diba & Buzsá ki, 2007; Singh, Norman, & Schapiro, 2022). The increased hippocampal and thalamic activity, along with strengthened connectivity between these regions and the mPFC during SO-spindle events, underscores a hippocampal-thalamic-neocortical information flow. This aligns with recent findings suggesting the thalamus orchestrates neocortical oscillations during sleep (Schreiner et al., 2022). The thalamus and hippocampus thus appear central to memory consolidation during sleep, guiding information transfer to the neocortex, e.g., mPFC.”

      (4) The study included an impressive number of 107 subjects. It is surprising though that only 31 subjects had to be excluded under these difficult recording conditions, especially since no adaptation night was performed. Since only subjects were excluded who slept less than 10 min (or had excessive head movements) there are likely several datasets included with comparably short durations and only a small number of SOs and spindles and even less combined SO-spindle events. A comprehensive table should be provided (supplement) including for each subject (included and excluded) the duration of included NREM sleep, number of SOs, spindles, and SO+spindle events. Also, some descriptive statistics (mean/SD/range) would be helpful.

      We appreciate your recognition of our sample size and the challenges associated with simultaneous EEG-fMRI sleep recordings. We acknowledge the importance of transparently reporting individual subject data, particularly regarding sleep duration and the number of detected SOs, spindles, and SO-spindle events. To address this, we will provide comprehensive tables in the supplementary materials, contains descriptive information about sleep-related characteristics (Table S1), as well as detailed information about sleep waves at each sleep stage for all 107 subjects(Table S2-S4), listing for each subject:(1)Different sleep stage duration; (2)Number of detected SOs; (3)Number of detected spindles; (4)Number of detected SO-spindle coupling events; (5)Density of detected SOs; (6)Density of detected spindles; (7)Density of detected SO-spindle coupling events.

      However, most of the excluded participants were unable to fall asleep or had too short a sleep duration, so they basically had no NREM sleep period, so it was impossible to count the NREM sleep duration, SO, spindle, and coupling numbers.

      Supplementary Materials, Page 42-54, Table S1-S4

      (5) Was the 20-channel head coil dedicated for EEG-fMRI measurements? How were the electrode cables guided through/out of the head coil? Usually, the 64-channel head coil is used for EEG-fMRI measurements in a Siemens PRISMA 3T scanner, which has a cable duct at the back that allows to guide the cables straight out of the head coil (to minimize MR-related artifacts). The choice for the 20-channel head coil should be motivated. Photos of the recording setup would also be helpful.

      Thank you for your comment regarding our choice of the 20-channel head coil for EEG-fMRI measurements. We acknowledge that the 64-channel head coil is commonly used in Siemens PRISMA 3T scanners; however, the 20-channel coil was selected due to specific practical and technical considerations in our study. In particular, the 20-channel head coil was compatible with our EEG system and ensured sufficient signal-to-noise ratio (SNR) for both EEG and fMRI acquisition. The EEG electrode cables were guided through the lateral and posterior openings of the head coil, secured with foam padding to reduce motion and minimize MR-related artifacts. Moreover, given the extended nature of nocturnal sleep recordings, the 20-channel coil allowed us to maintain participant comfort while still achieving high-quality simultaneous EEG-fMRI data.

      We have made this clearer in the revised manuscript. 

      Methods, Page 20 Lines 385-392

      “All MRI data were acquired using a 20-channel head coil on a research-dedicated 3-Tesla Siemens Magnetom Prisma MRI scanner. Earplugs and cushions were provided for noise protection and head motion restriction. We chose the 20-channel head coil because it was compatible with our EEG system and ensured sufficient signal-to-noise ratio (SNR) for both EEG and fMRI acquisition. The EEG electrode cables were guided through the lateral and posterior openings of the head coil, secured with foam padding to reduce motion and minimize MR-related artifacts. Moreover, given the extended nature of nocturnal sleep recordings, the 20-channel coil helped maintain participant comfort while still achieving high-quality simultaneous EEG-fMRI data.”

      (6) Was the EEG sampling synchronized to the MR scanner (gradient system) clock (the 10 MHz signal; not referring to the volume TTL triggers here)? This is a requirement for stable gradient artifact shape over time and thus accurate gradient noise removal.

      Thank you for raising this important point. We confirm that the EEG sampling was synchronized to the MR scanner’s 10 MHz gradient system clock, ensuring a stable gradient artifact shape over time and enabling accurate artifact removal. This synchronization was achieved using the standard clock synchronization interface of the EEG amplifier, minimizing timing jitter and drift. As a result, the gradient artifact waveform remained stable across volumes, allowing for more effective artifact correction during preprocessing. We appreciate your attention to this critical aspect of EEG-fMRI data acquisition.

      We have made this clearer in the revised manuscript. 

      Methods, Page 19-20 Lines 371-383

      “EEG was recorded simultaneously with fMRI data using an MR-compatible EEG amplifier system (BrainAmps MR-Plus, Brain Products, Germany), along with a specialized electrode cap. The recording was done using 64 channels in the international 10/20 system, with the reference channel positioned at FCz. In order to adhere to polysomnography (PSG) recording standards, six electrodes were removed from the EEG cap: one for electrocardiogram (ECG) recording, two for electrooculogram (EOG) recording, and three for electromyogram (EMG) recording. EEG data was recorded at a sample rate of 5000 Hz, the resistance of the reference and ground channels was kept below 10 kΩ, and the resistance of the other channels was kept below 20 kΩ. To synchronize the EEG and fMRI recordings, the BrainVision recording software (BrainProducts, Germany) was utilized to capture triggers from the MRI scanner. The EEG sampling was synchronized to the MR scanner’s 10 MHz gradient system clock, ensuring a stable gradient artifact shape over time and enabling accurate artifact removal. This was achieved via the standard clock synchronization interface of the EEG amplifier, minimizing timing jitter and drift.”

      (7) The TR is quite long and the voxel size is quite large in comparison to state-of-the-art EPI sequences. What was the rationale behind choosing a sequence with relatively low temporal and spatial resolution?

      We acknowledge that our chosen TR and voxel size are relatively long and large compared to state-of-the-art EPI sequences. This decision was made to optimize the signal-to-noise ratio (SNR) and reduce susceptibility-related distortions, which are particularly critical in EEG-fMRI sleep studies where head motion and physiological noise can be substantial. A longer TR allowed us to sample whole-brain activity with sufficient coverage, while a larger voxel size helped enhance BOLD sensitivity and minimize partial volume effects in deep brain structures such as the thalamus and hippocampus, which are key regions of interest in our study. We appreciate your concern and hope this clarification provides sufficient rationale for our sequence parameters.

      We have made this clearer in the revised manuscript. 

      Methods, Page 20-21 Lines 398-408

      “Then, the “sleep” session began after the participants were instructed to try and fall asleep. For the functional scans, whole-brain images were acquired using k-space and steady-state T2*-weighted gradient echo-planar imaging (EPI) sequence that is sensitive to the BOLD contrast. This measures local magnetic changes caused by changes in blood oxygenation that accompany neural activity (sequence specification: 33 slices in interleaved ascending order, TR = 2000 ms, TE = 30 ms, voxel size = 3.5 × 3.5 × 4.2 mm3, FA = 90°, matrix = 64 × 64, gap = 0.7 mm). A relatively long TR and larger voxel size were chosen to optimize SNR and reduce susceptibility-related distortions, which are critical in EEG-fMRI sleep studies where head motion and physiological noise can be substantial. The longer TR allowed whole-brain coverage with sufficient temporal resolution, while the larger voxel size helped enhance BOLD sensitivity and minimize partial volume effects in deep brain structures (e.g., the thalamus and hippocampus), which are key regions of interest in this study.”

      (8) The anatomically defined ROIs are quite large. It should be elaborated on how this might reduce sensitivity to sleep rhythm-specific activity within sub-regions, especially for the thalamus, which has distinct nuclei involved in sleep functions.

      We appreciate your insight regarding the use of anatomically defined ROIs and their potential limitations in detecting sleep rhythm-specific activity within sub-regions, particularly in the thalamus. Given the distinct functional roles of thalamic nuclei in sleep processes, we acknowledge that using a single, large thalamic ROI may reduce sensitivity to localized activity patterns. To address this, we will discuss this limitation in the revised manuscript, acknowledging that our approach prioritizes whole-structure effects but may not fully capture nucleus-specific contributions.

      Discussion, Page 18 Lines 333-341

      “Despite providing new insights, our study has several limitations. First, our scalp EEG did not directly capture hippocampal ripples, preventing us from conclusively demonstrating triple coupling. Second, the combination of EEG-fMRI and the lack of a memory task limit our ability to parse fine-grained BOLD responses at the DOWN- vs. UP-states of SOs and link observed activations to behavioral outcomes. Third, the use of large anatomical ROIs may mask subregional contributions of specific thalamic nuclei or hippocampal subfields. Finally, without a memory task, we cannot establish a direct behavioral link between sleep-rhythm-locked activation and memory consolidation. Future studies combining techniques such as ultra-high-field fMRI or iEEG with cognitive tasks may refine our understanding of subregional network dynamics and functional significance during sleep.”

      (9) The study reports SO & spindle amplitudes & densities, as well as SO+spindle coupling, to be larger during N2/3 sleep compared to N1 and REM sleep, which is trivial but can be seen as a sanity check of the data. However, the amount of SOs and spindles reported for N1 and REM sleep is concerning, as per definition there should be hardly any (if SOs or spindles occur in N1 it becomes by definition N2, and the interval between spindles has to be considerably large in REM to still be scored as such). Thus, on the one hand, the report of these comparisons takes too much space in the main manuscript as it is trivial, but on the other hand, it raises concerns about the validity of the scoring.

      We appreciate your concern regarding the reported presence of SOs and spindles in N1 and REM sleep and the potential implications. Our detection method for detecting SO, spindle, and coupling were originally designed only for N2&N3 sleep data based on the characteristics of the data itself, and this method is widely recognized and used in the sleep research (Hahn et al., 2020; Helfrich et al., 2019; Helfrich et al., 2018; Ngo, Fell, & Staresina, 2020; Schreiner et al., 2022; Schreiner et al., 2021; Staresina et al., 2015; Staresina et al., 2023). While, because the detection methods for SO and spindle are based on percentiles, this method will always detect a certain number of events when used for other stages (N1 and REM) sleep data, but the differences between these events and those detected in stage N23 remain unclear. We will acknowledge the reasons for these results in the Methods section and emphasize that they are used only for sanity checks.

      Methods, Page 25 Lines 515-524

      “We note that the above methods for detecting SOs, spindles, and their couplings were originally developed for N2 and N3 sleep data, based on the specific characteristics of these stages. These methods are widely recognized in sleep research (Hahn et al., 2020; Helfrich et al., 2019; Helfrich et al., 2018; Ngo, Fell, & Staresina, 2020; Schreiner et al., 2022; Schreiner et al., 2021; Staresina et al., 2015; Staresina et al., 2023). However, because this percentile-based detection approach will inherently identify a certain number of events if applied to other stages (e.g., N1 and REM), the nature of these events in those stages remains unclear compared to N2/N3. We nevertheless identified and reported the detailed descriptive statistics of these sleep rhythms in all sleep stages, under the same operational definitions, both for completeness and as a sanity check. Within the same subject, there should be more SOs, spindles, and their couplings in N2/N3 than in N1 or REM (see also Figure S2-S4, Table S1-S4).”

      (10) Why was electrode F3 used to quantify the occurrence of SOs and spindles? Why not a midline frontal electrode like Fz (or a number of frontal electrodes for SOs) and Cz (or a number of centroparietal electrodes) for spindles to be closer to their maximum topography?

      We appreciate your suggestion regarding electrode selection for SO and spindle quantification. Our choice of F3 was primarily based on previous studies (Massimini et al., 2004; Molle et al., 2011), where bilateral frontal electrodes are commonly used for detecting SOs and spindles. Additionally, we considered the impact of MRI-related noise and, after a comprehensive evaluation, determined that F3 provided an optimal balance between signal quality and artifact minimization. We also acknowledge that alternative electrode choices, such as Fz for SOs and Cz for spindles, could provide additional insights into their topographical distributions.

      (11) Functional connectivity (hippocampus -> thalamus -> cortex (mPFC)) is reported to be increased during SO-spindle coupling and interpreted as evidence for coordination of hippocampo-neocortical communication likely by thalamic spindles. However, functional connectivity was only analysed during coupled SO+spindle events, not during isolated SOs or isolated spindles. Without the direct comparison of the connectivity patterns between these three events, it remains unclear whether this is specific for coupled SO+spindle events or rather associated with one or both of the other isolated events. The PPIs need to be conducted for those isolated events as well and compared statistically to the coupled events.

      We appreciate your critical perspective on our functional connectivity analysis and the interpretation of hippocampus-thalamus-cortex (mPFC) interactions during SO-spindle coupling. We acknowledge that, in the current analysis, functional connectivity was only examined during coupled SO-spindle events, without direct comparison to isolated SOs or isolated spindles. To address this concern, we have conducted PPI analyses for all three ROIs(Hippocampus, Thalamus, mPFC) and all three event types (SO-spindle couplings, isolated SOs, and isolated spindles). Our results indicate that neither isolated SOs nor isolated Spindles yielded significant connectivity changes in all three ROIs, as all failed to survive multiple comparison corrections. This suggests that the observed connectivity increase is specific to SO-spindle coupling, rather than being independently driven by either SOs or spindles alone.

      Results, Page 14 Lines 248-255

      “Crucially, the interaction between FC and SO-spindle coupling revealed that only the functional connectivity of hippocampus -> thalamus (ROI analysis, t(106) = 1.86, p = 0.0328) and thalamus -> mPFC (ROI analysis, t(106) = 1.98, p = 0.0251) significantly increased during SO-spindle coupling, with no significant changes in all other pathways (Fig. 4e). We also conducted PPI analyses for the other two events (SOs and spindles), and neither yielded significant connectivity changes in the three ROIs, as all failed to survive whole-brain FWE correction at the cluster level (p < 0.05). Together, these findings suggest that the thalamus, likely via spindles, coordinates hippocampal-cortical communication selectively during SO-spindle coupling, but not isolated SOs or spindle events alone.”

      (12) The limited temporal resolution of fMRI does indeed not allow for easily distinguishing between fMRI activation patterns related to SO-up- vs. SO-down-states. For this, one could try to extract the amplitudes of SO-up- and SO-down-states separately for each SO event and model them as two separate parametric modulators (with the risk of collinearity as they are likely correlated).

      We appreciate your insightful comment regarding the challenge of distinguishing fMRI activation patterns related to SO-up vs. SO-down states due to the limited temporal resolution of fMRI. While our current analysis does not differentiate between these two phases, we acknowledge that separately modeling SO-up and SO-down states using parametric modulators could provide a more refined understanding of their distinct neural correlates. However, as you notes, this approach carries the risk of collinearity, and there is indeed a high correlation between the two amplitudes across all subjects in our results (r=0.98). Future studies could explore more on leveraging high-temporal-resolution techniques. While implementing this in the current study is beyond our scope, we will acknowledge this limitation in the Discussion section.

      Discussion, Page 17 Lines 308-322

      “An intriguing aspect of our findings is the reduced DMN activity during SOs when modeled at the SO trough (DOWN-state). This reduced DMN activity may reflect large-scale neural inhibition characteristic of the SO trough. The DMN is typically active during internally oriented cognition (e.g., self-referential processing or mind-wandering) and is suppressed during external stimuli processing (Yeshurun, Nguyen, & Hasson, 2021). It is unlikely, however, that this suppression of DMN during SO events is related to a shift from internal cognition to external responses given it is during deep sleep time. Instead, it could be driven by the inherent rhythmic pattern of SOs, which makes it difficult to separate UP- from DOWN-states (the two temporal regressors were highly correlated, and similar brain activation during SOs events was obtained if modelled at the SO peak instead, Fig. S5). Since the amplitude at the SO trough is consistently larger than that at the SO peak, the neural activation we detected may primarily capture the large-scale inhibition from DOWN-state. Interestingly, no such DMN reduction was found during SO-spindle coupling, implying that coupling may involve distinct neural dynamics that partially re-engage DMN-related processes, possibly reflecting memory-related reactivation. Future research using high-temporal-resolution techniques like iEEG could clarify these possibilities.”

      Discussion, Page 18 Lines 333-341

      “Despite providing new insights, our study has several limitations. First, our scalp EEG did not directly capture hippocampal ripples, preventing us from conclusively demonstrating triple coupling. Second, the combination of EEG-fMRI and the lack of a memory task limit our ability to parse fine-grained BOLD responses at the DOWN- vs. UP-states of SOs and link observed activations to behavioral outcomes. Third, the use of large anatomical ROIs may mask subregional contributions of specific thalamic nuclei or hippocampal subfields. Finally, without a memory task, we cannot establish a direct behavioral link between sleep-rhythm-locked activation and memory consolidation. Future studies combining techniques such as ultra-high-field fMRI or iEEG with cognitive tasks may refine our understanding of subregional network dynamics and functional significance during sleep.”

      (13) L327: "It is likely that our findings of diminished DMN activity reflect brain activity during the SO DOWN-state, as this state consistently shows higher amplitude compared to the UP-state within subjects, which is why we modelled the SO trough as its onset in the fMRI analysis." This conclusion is not justified as the fact that SO down-states are larger in amplitude does not mean their impact on the BOLD response is larger.

      We appreciate your concern regarding our interpretation of diminished DMN activity reflecting the SO down-state. We acknowledge that the current expression is somewhat misleading, and our interpretation of it is: it could be driven by the inherent rhythmic pattern of SOs, which makes it difficult to separate UP- from DOWN-states (the two temporal regressors were highly correlated, and similar brain activation during SOs events was obtained if modelled at the SO peak instead). Since the amplitude at the SO trough is consistently larger than that at the SO peak, the neural activation we detected may primarily capture the large-scale inhibition from DOWN-state. And we will make this clear in the Discussion section.

      Discussion, Page 17 Lines 308-322

      “An intriguing aspect of our findings is the reduced DMN activity during SOs when modeled at the SO trough (DOWN-state). This reduced DMN activity may reflect large-scale neural inhibition characteristic of the SO trough. The DMN is typically active during internally oriented cognition (e.g., self-referential processing or mind-wandering) and is suppressed during external stimuli processing (Yeshurun, Nguyen, & Hasson, 2021). It is unlikely, however, that this suppression of DMN during SO events is related to a shift from internal cognition to external responses given it is during deep sleep time. Instead, it could be driven by the inherent rhythmic pattern of SOs, which makes it difficult to separate UP- from DOWN-states (the two temporal regressors were highly correlated, and similar brain activation during SOs events was obtained if modelled at the SO peak instead, Fig. S5). Since the amplitude at the SO trough is consistently larger than that at the SO peak, the neural activation we detected may primarily capture the large-scale inhibition from DOWN-state. Interestingly, no such DMN reduction was found during SO-spindle coupling, implying that coupling may involve distinct neural dynamics that partially re-engage DMN-related processes, possibly reflecting memory-related reactivation. Future research using high-temporal-resolution techniques like iEEG could clarify these possibilities.”

      (14) Line 77: "In the current study, while directly capturing hippocampal ripples with scalp EEG or fMRI is difficult, we expect to observe hippocampal activation in fMRI whenever SOs-spindles coupling is detected by EEG, if SOs- spindles-ripples triple coupling occurs during human NREM sleep". Not all SO-spindle events are associated with ripples (Staresina et al., 2015), but hippocampal activation may also be expected based on the occurrence of spindles alone (Bergmann et al., 2012).

      We appreciate your clarification regarding the relationship between SO-spindle coupling and hippocampal ripples. We acknowledge that not all SO-spindle events are necessarily accompanied by ripples (Staresina et al., 2015). However, based on previous research, we found that hippocampal ripples are significantly more likely to occur during SO-spindle coupling events. This suggests that while ripple occurrence is not guaranteed, SO-spindle coupling creates a favorable network state for ripple generation and potential hippocampal activation. To ensure accuracy, we will revise the manuscript to delete this misleading sentence in the Introduction section and acknowledge in the Discussion that our results cannot conclusively directly observe the triple coupling of SO, spindle, and hippocampal ripples.

      Discussion, Page 18 Lines 333-341

      “Despite providing new insights, our study has several limitations. First, our scalp EEG did not directly capture hippocampal ripples, preventing us from conclusively demonstrating triple coupling. Second, the combination of EEG-fMRI and the lack of a memory task limit our ability to parse fine-grained BOLD responses at the DOWN- vs. UP-states of SOs and link observed activations to behavioral outcomes. Third, the use of large anatomical ROIs may mask subregional contributions of specific thalamic nuclei or hippocampal subfields. Finally, without a memory task, we cannot establish a direct behavioral link between sleep-rhythm-locked activation and memory consolidation. Future studies combining techniques such as ultra-high-field fMRI or iEEG with cognitive tasks may refine our understanding of subregional network dynamics and functional significance during sleep.”

      Reviewer #2 (Public review):

      In this study, Wang and colleagues aimed to explore brain-wide activation patterns associated with NREM sleep oscillations, including slow oscillations (SOs), spindles, and SO-spindle coupling events. Their findings reveal that SO-spindle events corresponded with increased activation in both the thalamus and hippocampus. Additionally, they observed that SO-spindle coupling was linked to heightened functional connectivity from the hippocampus to the thalamus, and from the thalamus to the medial prefrontal cortex-three key regions involved in memory consolidation and episodic memory processes.

      This study's findings are timely and highly relevant to the field. The authors' extensive data collection, involving 107 participants sleeping in an fMRI while undergoing simultaneous EEG recording, deserves special recognition. If shared, this unique dataset could lead to further valuable insights. While the conclusions of the data seem overall well supported by the data, some aspects with regard to the detection of sleep oscillations need clarification.

      The authors report that coupled SO-spindle events were most frequent during NREM sleep (2.46 [plus minus] 0.06 events/min), but they also observed a surprisingly high occurrence of these events during N1 and REM sleep (2.23 [plus minus] 0.09 and 2.32 [plus minus] 0.09 events/min, respectively), where SO-spindle coupling would not typically be expected. Combined with the relatively modest SO amplitudes reported (~25 µV, whereas >75 µV would be expected when using mastoids as reference electrodes), this raises the possibility that the parameters used for event detection may not have been conservative enough - or that sleep staging was inaccurately performed. This issue could present a significant challenge, as the fMRI findings are largely dependent on the reliability of these detected events.

      Thank you very much for your thorough and encouraging review. We appreciate your recognition of the significance and relevance of our study and dataset, particularly in highlighting how simultaneous EEG-fMRI recordings can provide complementary insights into the temporal dynamics of neural oscillations and their associated spatial activation patterns during sleep. In the sections that follow, we address each of your comments in detail. We have revised the text and conducted additional analyses wherever possible to strengthen our argument, clarify our methodological choices. We believe these revisions improve the clarity and rigor of our work, and we thank you for helping us refine it.

      We appreciate your insightful comments regarding the detection of sleep oscillations. Our methods for detecting SOs, spindles, and their couplings were originally developed for N2 and N3 sleep data, based on the specific characteristics of these stages. These methods are widely recognized in sleep research (Hahn et al., 2020; Helfrich et al., 2019; Helfrich et al., 2018; Ngo, Fell, & Staresina, 2020; Schreiner et al., 2022; Schreiner et al., 2021; Staresina et al., 2015; Staresina et al., 2023). However, because this percentile-based detection approach will inherently identify a certain number of events if applied to other stages (e.g., N1 and REM), the nature of these events in those stages remains unclear compared to N2/N3. We nevertheless identified and reported the detailed descriptive statistics of these sleep rhythms in all sleep stages, under the same operational definitions, both for completeness and as a sanity check. Within the same subject, there should be more SOs, spindles, and their couplings in N2/N3 than in N1 or REM. We will acknowledge the reasons for these results in the Methods section and emphasize that they are used only for sanity checks.

      Regarding the reported SO amplitudes (~25 µV), during preprocessing, we applied the Signal Space Projection (SSP) method to more effectively remove MRI gradient artifacts and cardiac pulse noise. While this approach enhances data quality, it also reduces overall signal power, leading to systematically lower reported amplitudes. Despite this, our SO detection in NREM sleep (especially N2/N3) remain physiologically meaningful and are consistent with previous fMRI studies using similar artifact removal techniques. We appreciate your careful evaluation and valuable suggestions.

      In addition, we will provide comprehensive tables in the supplementary materials, contains descriptive information about sleep-related characteristics (Table S1), as well as detailed information about sleep waves at each sleep stage for all 107 subjects(Table S2-S4), listing for each subject:(1)Different sleep stage duration; (2)Number of detected SOs; (3)Number of detected spindles; (4)Number of detected SO-spindle coupling events; (2)Density of detected SOs; (3)Density of detected spindles; (4)Density of detected SO-spindle coupling events.

      Methods, Page 25 Lines 515-524

      “We note that the above methods for detecting SOs, spindles, and their couplings were originally developed for N2 and N3 sleep data, based on the specific characteristics of these stages. These methods are widely recognized in sleep research (Hahn et al., 2020; Helfrich et al., 2019; Helfrich et al., 2018; Ngo, Fell, & Staresina, 2020; Schreiner et al., 2022; Schreiner et al., 2021; Staresina et al., 2015; Staresina et al., 2023). However, because this percentile-based detection approach will inherently identify a certain number of events if applied to other stages (e.g., N1 and REM), the nature of these events in those stages remains unclear compared to N2/N3. We nevertheless identified and reported the detailed descriptive statistics of these sleep rhythms in all sleep stages, under the same operational definitions, both for completeness and as a sanity check. Within the same subject, there should be more SOs, spindles, and their couplings in N2/N3 than in N1 or REM (see also Figure S2-S4, Table S1-S4).”

      Supplementary Materials, Page 42-54, Table S1-S4

      Reviewer #3 (Public review):

      Summary:

      Wang et al., examined the brain activity patterns during sleep, especially when locked to those canonical sleep rhythms such as SO, spindle, and their coupling. Analyzing data from a large sample, the authors found significant coupling between spindles and SOs, particularly during the upstate of the SO. Moreover, the authors examined the patterns of whole-brain activity locked to these sleep rhythms. To understand the functional significance of these brain activities, the authors further conducted open-ended cognitive state decoding and found a variety of cognitive processing may be involved during SO-spindle coupling and during other sleep events. The authors next investigated the functional connectivity analyses and found enhanced connectivity between the hippocampus, the thalamus, and the medial PFC. These results reinforced the theoretical model of sleep-dependent memory consolidation, such that SO-spindle coupling is conducive to systems-level memory reactivation and consolidation.

      Strengths:

      There are obvious strengths in this work, including the large sample size, state-of-the-art neuroimaging and neural oscillation analyses, and the richness of results.

      Weaknesses:

      Despite these strengths and the insights gained, there are weaknesses in the design, the analyses, and inferences.

      Thank you for your detailed and thoughtful review of our manuscript. We are delighted that you recognize our advanced analysis methods and rich results of neuroimaging and neural oscillations as well as the large sample size data. In the following sections, we provide detailed responses to each of your comments. And we have revised the text and conducted additional analyses to strengthen our arguments and clarify our methodological choices. We believe these revisions enhance the clarity and rigor of our work, and we sincerely appreciate your thoughtful feedback in helping us refine the manuscript.

      (1) A repeating statement in the manuscript is that brain activity could indicate memory reactivation and thus consolidation. This is indeed a highly relevant question that could be informed by the current data/results. However, an inherent weakness of the design is that there is no memory task before and after sleep. Thus, it is difficult (if not impossible) to make a strong argument linking SO/spindle/coupling-locked brain activity with memory reactivation or consolidation.

      We appreciate your suggestion regarding the lack of a pre- and post-sleep memory task in our study design. We acknowledge that, in the absence of behavioral measures, it is hard to directly link SO-spindle coupling to memory consolidation in an outcome-driven manner. Our interpretation is instead based on the well-established role of these oscillations in memory processes, as demonstrated in previous studies. We sincerely appreciate this feedback and will adjust our Discussion accordingly to reflect a more precise interpretation of our findings.

      Discussion, Page 18 Lines 333-341

      “Despite providing new insights, our study has several limitations. First, our scalp EEG did not directly capture hippocampal ripples, preventing us from conclusively demonstrating triple coupling. Second, the combination of EEG-fMRI and the lack of a memory task limit our ability to parse fine-grained BOLD responses at the DOWN- vs. UP-states of SOs and link observed activations to behavioral outcomes. Third, the use of large anatomical ROIs may mask subregional contributions of specific thalamic nuclei or hippocampal subfields. Finally, without a memory task, we cannot establish a direct behavioral link between sleep-rhythm-locked activation and memory consolidation. Future studies combining techniques such as ultra-high-field fMRI or iEEG with cognitive tasks may refine our understanding of subregional network dynamics and functional significance during sleep.”

      (2) Relatedly, to understand the functional implications of the sleep rhythm-locked brain activity, the authors employed the "open-ended cognitive state decoding" method. While this method is interesting, it is rather indirect given that there were no behavioral indices in the manuscript. Thus, discussions based on these analyses are speculative at best. Please either tone down the language or find additional evidence to support these claims.

      Moreover, the results from this method are difficult to understand. Figure 3e showed that for all three types of sleep events (SO, spindle, SO-spindle), the same mental states (e.g., working memory, episodic memory, declarative memory) showed opposite directions of activation (left and right panels showed negative and positive activation, respectively). How to interpret these conflicting results? This ambiguity is also reflected by the term used: declarative memory and episodic memories are both indexed in the results. Yet these two processes can be largely overlapped. So which specific memory processes do these brain activity patterns reflect? The Discussion shall discuss these results and the limitations of this method.

      We appreciate your critical assessment of the open-ended cognitive state decoding method and its interpretational challenges. Given the concerns about the indirectness of this approach, we decided to remove its related content and results from Figure 3 in the main text and include it in Supplementary Figure 7. 

      Due to the complexity of memory-related processes, we acknowledge that distinguishing between episodic and declarative memory based solely on this approach is not straightforward. We will revise the Supplementary Materials to explicitly discuss these limitations and clarify that our findings do not isolate specific cognitive processes but rather suggest general associations with memory-related networks.

      Discussion, Page 17-18 Lines 323-332

      “To explore functional relevance, we employed an open-ended cognitive state decoding approach using meta-analytic data (NeuroSynth: Yarkoni et al. (2011)). Although this method usefully generates hypotheses about potential cognitive processes, particularly in the absence of a pre- and post-sleep memory task, it is inherently indirect. Many cognitive terms showed significant associations (16 of 50), such as “episodic memory,” “declarative memory,” and “working memory.” We focused on episodic/declarative memory given the known link with hippocampal reactivation (Diekelmann & Born, 2010; Staresina et al., 2015; Staresina et al., 2023). Nonetheless, these inferences regarding memory reactivation should be interpreted cautiously without direct behavioral measures. Future research incorporating explicit tasks before and after sleep would more rigorously validate these potenial functional claims.”

      (3) The coupling strength is somehow inconsistent with prior results (Hahn et al., 2020, eLife, Helfrich et al., 2018, Neuron). Specifically, Helfrich et al. showed that among young adults, the spindle is coupled to the peak of the SO. Here, the authors reported that the spindles were coupled to down-to-up transitions of SO and before the SO peak. It is possible that participants' age may influence the coupling (see Helfrich et al., 2018). Please discuss the findings in the context of previous research on SO-spindle coupling.

      We appreciate your concern regarding the temporal characteristics of SO-spindle coupling. We acknowledge that the SO-spindle coupling phase results in our study are not identical to those reported by Hahn et al. (2020); Helfrich et al. (2018). However, these differences may arise due to slight variations in event detection parameters, which can influence the precise phase estimation of coupling. Notably, Hahn et al. (2020) also reported slight discrepancies in their group-level coupling phase results, highlighting that methodological differences can contribute to variability across studies. Furthermore, our findings are consistent with those of Schreiner et al. (2021), further supporting the robustness of our observations.  

      That said, we acknowledge that our original description of SO-spindle coupling as occurring at the "transition from the lower state to the upper state" was not entirely precise. The -π/2 phase represents the true transition point, while our observed coupling phase is actually closer to the SO peak rather than strictly at the transition. We will revise this statement in the manuscript to ensure clarity and accuracy in describing the coupling phase.  

      Discussion, Page 16 Lines 283-291

      “Our data provide insights into the neurobiological underpinnings of these sleep rhythms. SOs, originating mainly in neocortical areas such as the mPFC, alternate between DOWN- and UP-states. The thalamus generates sleep spindles, which in turn couple with SOs. Our finding that spindle peaks consistently occurred slightly before the UP-state peak of SOs (in 83 out of 107 participants), concurs with prior studies, including Schreiner et al. (2021). Yet it differs from some results suggesting spindles might peak right at the SO UP-state (Hahn et al., 2020; Helfrich et al., 2018). Such discrepancies could arise from differences in detection algorithms, participant age (Helfrich et al., 2018), or subtle variations in cortical-thalamic timing. Nonetheless, these results underscore the importance of coordinated SO-spindle interplay in supporting sleep-dependent processes.”

      (4) The discussion is rather superficial with only two pages, without delving into many important arguments regarding the possible functional significance of these results. For example, the author wrote, "This internal processing contrasts with the brain patterns associated with external tasks, such as working memory." Without any references to working memory, and without delineating why WM is considered as an external task even working memory operations can be internal. Similarly, for the interesting results on SO and reduced DMN activity, the authors wrote "The DMN is typically active during wakeful rest and is associated with self-referential processes like mind-wandering, daydreaming, and task representation (Yeshurun, Nguyen, & Hasson, 2021). Its reduced activity during SOs may signal a shift towards endogenous processes such as memory consolidation." This argument is flawed. DMN is active during self-referential processing and mind-wandering, i.e., when the brain shifts from external stimuli processing to internal mental processing. During sleep, endogenous memory reactivation and consolidation are also part of the internal mental processing given the lack of external environmental stimulation. So why during SO or during memory consolidation, the DMN activity would be reduced? Were there differences in DMN activity between SO and SO-spindle coupling events?

      We appreciate your concerns regarding the brevity of the discussion and the need for clearer theoretical arguments. We will expand this section to provide more in-depth interpretations of our findings in the context of prior literature. Regarding working memory (WM), we acknowledge that our phrasing was ambiguous. We will modify this statement in the Discussion section.

      For the SO-related reduction in DMN activity, we recognize the need for a more precise explanation. This reduced DMN activity may reflect large-scale neural inhibition characteristic of the SO trough. The DMN is typically active during internally oriented cognition (e.g., self-referential processing or mind-wandering) and is suppressed during external stimuli processing (Yeshurun, Nguyen, & Hasson, 2021). It is unlikely, however, that this suppression of DMN during SO events is related to a shift from internal cognition to external responses given it is during deep sleep time. Instead, it could be driven by the inherent rhythmic pattern of SOs, which makes it difficult to separate UP- from DOWN-states (the two temporal regressors were highly correlated, and similar brain activation during SOs events was obtained if modelled at the SO peak instead). Since the amplitude at the SO trough is consistently larger than that at the SO peak, the neural activation we detected may primarily capture the large-scale inhibition from DOWN-state.

      To address your final question, we have conducted the additional post hoc comparison of DMN activity between isolated SOs and SO-spindle coupling events. Our results indicate that

      DMN activation during SOs was significantly lower than during SO-spindle coupling (t(106) = -4.17, p < 1e-4). This suggests that SO-spindle coupling may involve distinct neural dynamics that partially re-engage DMN-related processes, possibly reflecting memory-related reactivation. We appreciate your constructive feedback and will integrate these expanded analyses and discussions into our revised manuscript.

      Results, Page 11 Lines 199-208

      “Spindles were correlated with positive activation in the thalamus (ROI analysis, t(106) = 15.39, p < 1e-4), the anterior cingulate cortex (ACC), and the putamen, alongside deactivation in the DMN (Fig. 3c). Notably, SO-spindle coupling was linked to significant activation in both the thalamus (ROI analysis, t(106) \= 3.38, p = 0.0005) and the hippocampus (ROI analysis, t(106) \= 2.50, p = 0.0070, Fig. 3d). However, no decrease in DMN activity was found during SO-spindle coupling, and DMN activity during SO was significantly lower than during coupling (ROI analysis, t(106) \= -4.17, p < 1e-4). For more detailed activation patterns, see Table S5-S7. We also varied the threshold used to detect SO events to assess its effect on hippocampal activation during SO-spindle coupling and observed that hippocampal activation remained significant when the percentile thresholds for SO detection ranged between 71% and 80% (see Fig. S6).”

      Discussion, Page 17-18 Lines 308-332

      “An intriguing aspect of our findings is the reduced DMN activity during SOs when modeled at the SO trough (DOWN-state). This reduced DMN activity may reflect large-scale neural inhibition characteristic of the SO trough. The DMN is typically active during internally oriented cognition (e.g., self-referential processing or mind-wandering) and is suppressed during external stimuli processing (Yeshurun, Nguyen, & Hasson, 2021). It is unlikely, however, that this suppression of DMN during SO events is related to a shift from internal cognition to external responses given it is during deep sleep time. Instead, it could be driven by the inherent rhythmic pattern of SOs, which makes it difficult to separate UP- from DOWN-states (the two temporal regressors were highly correlated, and similar brain activation during SOs events was obtained if modelled at the SO peak instead, Fig. S5). Since the amplitude at the SO trough is consistently larger than that at the SO peak, the neural activation we detected may primarily capture the large-scale inhibition from DOWN-state. Interestingly, no such DMN reduction was found during SO-spindle coupling, implying that coupling may involve distinct neural dynamics that partially re-engage DMN-related processes, possibly reflecting memory-related reactivation. Future research using high-temporal-resolution techniques like iEEG could clarify these possibilities.

      To explore functional relevance, we employed an open-ended cognitive state decoding approach using meta-analytic data (NeuroSynth: Yarkoni et al. (2011)). Although this method usefully generates hypotheses about potential cognitive processes, particularly in the absence of a pre- and post-sleep memory task, it is inherently indirect. Many cognitive terms showed significant associations (16 of 50), such as “episodic memory,” “declarative memory,” and “working memory.” We focused on episodic/declarative memory given the known link with hippocampal reactivation (Diekelmann & Born, 2010; Staresina et al., 2015; Staresina et al., 2023). Nonetheless, these inferences regarding memory reactivation should be interpreted cautiously without direct behavioral measures. Future research incorporating explicit tasks before and after sleep would more rigorously validate these potential functional claims.”

      Recommendations for the authors:

      Reviewing Editor Comment:

      The reviewers think that you are working on a relevant and important topic. They are praising the large sample size used in the study. The reviewers are not all in line regarding the overall significance of the findings, but they all agree the paper would strongly benefit from some extra work, as all reviewers raise various critical points that need serious consideration.

      We appreciate your recognition of the relevance and importance of our study, as well as your acknowledgment of the large sample size as a strength of our work. We understand that there are differing perspectives regarding the overall significance of our findings, and we value the constructive critiques provided. We are committed to addressing the key concerns raised by all reviewers, including refining our analyses, clarifying our interpretations, and incorporating additional discussions to strengthen the manuscript. Below, we address your specific recommendations and provide responses to each point you raised to ensure our methods and results are as transparent and comprehensible as possible. We believe that these revisions will significantly enhance the rigor and impact of our study, and we sincerely appreciate your thoughtful feedback in helping us improve our work.

      Reviewer #1 (Recommendations for the authors):

      (1) The phrase "overnight sleep" suggests an entire night, while these were rather "nocturnal naps". Please rephrase.

      Response: Thank you for pointing this out. We have revised the phrasing in our manuscript to "nocturnal naps" instead of "overnight sleep" to more accurately reflect the duration of the sleep recordings.

      (2) Sleep staging results (macroscopic sleep architecture) should be provided in more detail (at least min and % of the different sleep stages, sleep onset latency, total sleep duration, total recording duration), at least mean/SD/range.

      Thank you for this suggestion. We will provide comprehensive tables in the supplementary materials, contains descriptive information about sleep-related characteristics. This information will help provide a clearer overview of the macroscopic sleep architecture in our dataset.

      Reviewer #2 (Recommendations for the authors):

      In order to allow for a better estimation of the reliability of the detected sleep events, please:

      (1) Provide densities and absolute numbers of all detected SOs and spindles (N1, NREM, and REM sleep).

      Thank you for pointing this out. We will provide comprehensive tables in the supplementary materials, contains detailed information about sleep waves at each sleep stage for all 107 subjects (Table S2-S4), listing for each subject:1) Different sleep stage duration; 2) Number of detected SOs; 3) Number of detected spindles; 4) Number of detected SO-spindle coupling events; 5) Density of detected SOs; 6) Density of detected spindles; 7) Density of detected SO-spindle coupling events.

      Supplementary Materials, Page 43-54, Table S2-S4

      (2) Show ERPs for all detected SOs and spindles (per sleep stage).

      Thank you for the suggestion. We will provide ERPs for all detected SOs and spindles, separated by sleep stage (N1, N2&N3, and REM) in supplementary Fig. S2-S4. These ERP waveforms will help illustrate the characteristic temporal profiles of SOs and spindles across different sleep stages.

      Methods, Page 25, Line 525-532

      “Event-related potentials (ERP) analysis. After completing the detection of each sleep rhythm event, we performed ERP analyses for SOs, spindles, and coupling events in different sleep stages. Specifically, for SO events, we took the trough of the DOWN-state of each SO as the zero-time point, then extracted data in a [-2 s to 2 s] window from the broadband (0.1–30 Hz) EEG and used [-2 s to -0.5 s] for baseline correction; the results were then averaged across 107 subjects (see Fig. S2a). For spindle events, we used the peak of each spindle as the zero-time point and applied the same data extraction window and baseline correction before averaging across 107 subjects (see Fig. S2b). Finally, for SO-spindle coupling events, we followed the same procedure used for SO events (see Fig. 2a, Figs. S3–S4).”

      (3) Provide detailed info concerning sleep characteristics (time spent in each sleep stage etc.).

      Thank you for this suggestion. Same as the response above, we will provide comprehensive tables in the supplementary materials, contains descriptive information about sleep-related characteristics.

      Supplementary Materials, Page 42, Table S1 (same as above)

      (4) What would happen if more stringent parameters were used for event detection? Would the authors still observe a significant number of SO spindles during N1 and REM? Would this affect the fMRI-related results?

      Thank you for this suggestion. Our methods for detecting SOs, spindles, and their couplings were originally developed for N2 and N3 sleep data, based on the specific characteristics of these stages. These methods are widely recognized in sleep research (Hahn et al., 2020; Helfrich et al., 2019; Helfrich et al., 2018; Ngo, Fell, & Staresina, 2020; Schreiner et al., 2022; Schreiner et al., 2021; Staresina et al., 2015; Staresina et al., 2023). However, because this percentile-based detection approach will inherently identify a certain number of events if applied to other stages (e.g., N1 and REM), the nature of these events in those stages remains unclear compared to N2/N3. We nevertheless identified and reported the detailed descriptive statistics of these sleep rhythms in all sleep stages, under the same operational definitions, both for completeness and as a sanity check. Within the same subject, there should be more SOs, spindles, and their couplings in N2/N3 than in N1 or REM (see also Figure S2-S4, Table S1-S4).

      Furthermore, in order to explore the impact of this on our fMRI results, we conducted an additional sensitivity analysis by applying different detection parameters for SOs. Specifically, we adjusted amplitude percentile thresholds for SO detection (the parameter that has the greatest impact on the results). We used the hippocampal activation value during N2&N3 stage SO-spindle coupling as an anchor value and found that when the parameters gradually became stricter, the results were similar to or even better than the current results. However, when we continued to increase the threshold, the results began to gradually decrease until the threshold was increased to 80%, and the results were no longer significant. This indicates that our results are robust within a specific range of parameters, but as the threshold increases, the number of trials decreases, ultimately weakening the statistical power of the fMRI analysis.

      Thank you again for your suggestions on sleep rhythm event detection. We will add the results in Supplementary and revise our manuscript accordingly.

      Results, Page 11, Line 199-208

      “Spindles were correlated with positive activation in the thalamus (ROI analysis, t(106) = 15.39, p < 1e-4), the anterior cingulate cortex (ACC), and the putamen, alongside deactivation in the DMN (Fig. 3c). Notably, SO-spindle coupling was linked to significant activation in both the thalamus (ROI analysis, t(106) \= 3.38, p = 0.0005) and the hippocampus (ROI analysis, t(106) \= 2.50, p = 0.0070, Fig. 3d). However, no decrease in DMN activity was found during SO-spindle coupling, and DMN activity during SO was significantly lower than during coupling (ROI analysis, t(106) \= -4.17, p < 1e-4). For more detailed activation patterns, see Table S5-S7. We also varied the threshold used to detect SO events to assess its effect on hippocampal activation during SO-spindle coupling and observed that hippocampal activation remained significant when the percentile thresholds for SO detection ranged between 71% and 80% (see Fig. S6).”

      Finally, we sincerely thank all again for your thoughtful and constructive feedback. Your insights have been invaluable in refining our analyses, strengthening our interpretations, and improving the clarity and rigor of our manuscript. We appreciate the time and effort you have dedicated to reviewing our work, and we are grateful for the opportunity to enhance our study based on your recommendations.  

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    1. Author response:

      The following is the authors’ response to the original reviews

      Main revision made to the manuscript

      The main revision made to the manuscript is to reconcile our findings with the line attractor model. The revision is based on Reviewer 1’s comment on reinterpreting our results as a superposition of an attractor model with fast timescale dynamics. We expanded our analysis regime to the start of a trial and characterized the overall within-trial dynamics to reinterpret our findings.

      We first acknolwedge that our results are not in contradiction with evidence integration on a line attractor. As pointed out by the reviewers, our finding that the integration of reward outcome explains the reversal probability activity x_rev (Figure 3) is compatible with the line attractor model. However, the reward integration equation is an algebraic relation and does not characterize the dynamics of reversal probability activity. So a closer analysis on the neural dynamics is needed to assess the feasibility of line attractor.

      In the revised manuscript, we show that x_rev exhibits two different activity modes (Figure 4). First, x_rev has substantial non-stationary dynamics during a trial, and this non-stationary activity is incompatible with the line attractor model, as claimed in the original manuscript. Second, we present new results showing that x_rev is stationary (i.e., constant in time) and stable (i.e., contracting) at the start of a trial. These two properties of x_rev support that it is a point attractor at the start of a trial and is compatible with the line attractor model. 

      We further analyze how the two activity modes are linked (Figure 4, Support vector regression). We show that the non-stationary activity is predictable from the stationary activity if the underlying dynamics can be inferred. In other words, the non-stationary activity during a trial is generated by an underlying dynamics with the initial condition provided by the stationary state at the start of trial.

      These results suggest an extension of the line attractor model where an attractor state at the start of a trial provides an initial condition from which non-stationary activity is generated during a trial by an underlying dynamics associated with task-related behavior (Figure 4, Augmented model). 

      The separability of non-stationary trajectories (Figure 5 and 6) is a property of the non-stationary dynamics that allows separable points in the initial stationary state to remain separable during a trial, thus making it possible to represent distinct probabilistic values in non-stationary activity.

      This revised interpretation of our results (1) retains our original claim that the non-stationary dynamics during a trial is incompatible with the line attractor model and (2) introduces attractor state at the start of a trial which is compatible with the line attractor model. Our anlaysis shows that the two activity modes are linked by an underlying dynamics, and the attractor state serves as initial state to launch the non-stationary activity.

      Responses to the Public Reviews:

      Reviewer # 1:

      (1) To provide better explanation of the reversal learning task and network training method, we added detailed description of RNN and monkey task structure (Result Section 1), included a schematic of target outputs (Figure1B), explained the rationale behind using inhibitory network model (Method Section 1) and explained the supervised RNN training scheme (Result Section 1). This information can also be found in the Methods.

      (2) Our understanding is that the augmented model discussed in the previous page is aligned with the model suggested by Reviewer 1: “a curved line attractor, with faster timescale dynamics superimposed on this structure”. It is likely that the “fast” non-stationary activity observed during the trial is driven by task-related behavior, thus is transient. For instance, we do not observe such non-stationary activity in the inter-trial-interval when the task-related behavior is absent. For this reason, the non-stationary trajectories were not considered to be part of the attractor. Instead, they are transient activity generated by the underlying neural dynamics associated with task-related behavior. We believe such characterization of faster timescale dynamics is consistent with Reviewer 1’s view and wanted to clarify that there are two different activity modes.

      (3) We appreciate the reviewers (Reviewer 1 and Reviewer 2) comment that TDR may be limited in isolating the neural subspace of interest. Our study presents what could be learned from TDR but is by no means the only way to interpret the neural data. It would be of future work to apply other methods for isolating task-related neural activities.

      We would appreciate it if the reviewers could share thoughts on what other alternative methods could better isolate the reversal probability activity.

      Reviewer # 2:

      (1) (i) We respectfully disagree with Reviewer 2’s comment that “no action is required to be performed by neurons in the RNN”. In our network setup, the output of RNN learns to choose a sign (+ or -), as Reviewer 2 pointed out, to make a choice. This is how the RNN takes an action. It is unclear to us what Reviewer 2 has intended by “action” and how reaching a target value (not just taking a sign) would make a significant difference in how the network performs the task. 

      (ii)  From Reviewer 2’s comment that “no intervening behavior is thus performed by neurons”, we noticed that the term “intervening behavior” has caused confusion. It refers to task-related behavior, such as making choices or receiving reward, that the subject must perform across trials before reversing its preferred choice. These are the behaviors that intervene the reversal of preferred choice. To clarify its meaning, in the revised manuscript, we changed the term to “task-related behavior” and put them in context. For example, in the Introduction we state that “However, during a trial, task-related behavior, such as making decisions or receiving feedback, produced …”

      (iii) As pointed out by Reviewer 2, the lack of fixation period in the RNN could make differences in the neural dynamics of RNN and PFC, especially at the start of a trial. We demonstrate this issue in Result Section 4 where we analyze the stationary activity at the start of a trial. We find that fixating the choice output to zero before making a choice promotes stationary activity and makes the RNN activity more similar to the PFC activity.

      Reviewer #3:

      (1) (i) In the previous study (Figure 1 in [Bartolo and Averbeck ‘20]), it was shown that neural activity can predict the behavioral reversal trial. This is the reason we examined the neural activity in the trials centered at the behavioral reversal trial. We explained in Result Section 2 that we followed this line of analysis in our study.

      (ii) We would like to emphasize that the main point of Figures 4 and 5 is to show the separability of neural trajectories: the entire trajectory shifts without overlapping. It is not obvious that high-dimensional neural population activity from two trials should remain separated when their activities are compressed into a one-dimensional subspace. The onedimensional activities can easily collide since their activities are compressed into a lowdimensional space. We revised the manuscript to bring out these points. We added an opening paragraph that discusses separability of trajectories and revised the main text to bring out the findings on separability. 

      (iii) We agree with Reviewer 3 that it would be interesting to look at what happens in other subspace of neural activity that are not related to reversal probability and characterize how different neural subspace interact with each. However, the focus of this paper was the reversal probability activity, and we’d consider these questions out of the scope of current paper. We point out that, using the same dataset, neural activity related to other experimental variables were analyzed in other papers [Bartolo and Averbeck ’20; Tang, Bartolo and Averbeck ‘21] 

      (2) (i) In the revised manuscript, we added explanation on the rational behind choosing inhibitory network as a simplified model for the balanced state. In brief, strong inhibitory recurrent connections with strong excitatory external input operates in the balanced state, as in the standard excitatory-inhibitory network. We included references that studied this inhibitory network. We also explained the technical reason (GPU memory) for choosing the inhibitory model.

      (ii) We thank the reviewer for pointing out that the original manuscript did not mention how the feedback and cue were initialized. They were random vectors sample from Gaussian distribution. We added this information in the revised manuscript. In our opinion, it is common to use random external inputs for training RNNs, as it is a priori unclear how to choose them. In fact, it is possible to analyze the effects of random feedback on one-dimensional x_rev dynamics by projecting the random feedback vector to the reversal probability vector. This is shown in Figure 4F.

      (iii) We agree that it would be more natural to train the RNN to solve the task without using the Bayesian model. We point out this issue in the Discussion in the revised manuscript.

      Recommendations for the authors:

      Reviewer #1:

      (1) My understanding of network training was that a Bayesian ideal observer signaled target output based on previous reward outcomes. However, the authors never mention that networks are trained by supervised learning in the main text until the last paragraph of the discussion. There is no mention that there was an offset in the target based on the behavior of the monkeys in the main text. These are really important things to consider in the context of the network solution after training. I couldn't actually find any figure that presents the target output for the network. Did I miss something key here?

      In Result Section 1, we added a paragraph that describes in detail how the RNN is trained. We explained that the network is first simulated and then the choice outputs and reward outcomes are fed into the Bayesian model to infer the scheduled reversal trial. A few trials are added to the inferred reversal trial to obtain the behavioral reversal trial, as found in a previous study [Bartolo and Averbeck ‘20]. Then the network weights are updated by backpropagation-through-time via supervised learning. 

      In the original manuscript, the target output for the network was described in Methods Section 2.5, Step 4. To make this information readily accessible, we added a schematic in Figure 1B that shows the scheduled, inferred and behavioral reversal trials. It also shows how the target choice ouputs are defined. They switch abruptly at the behavioral reversal trial.

      (2) The role of block structure in the task is an important consideration. What are the statistics of block switches? The authors say on average the reversals are every 36 trials, but also say there are random block switches. The reviewer's notes suggest that both the networks and monkeys may be learning about the typical duration of blocks, which could influence their expectations of reversals. This aspect of the task design should be explained more thoroughly and considered in the context of Figure 1E and 5 results.

      We provided more detailed description of the reversal learning task in Result Section 1. We clarified that (1) a task is completed by executing a block of fixed number of trials and (2) reversal of reward schedule occurrs at a random trial around the mid-trial in a block. The differences in the number of trials in a block that the RNNs (36) and the monkeys (80) perform are also explained. We also pointed out the differences in how the reversal trial is randomly sampled.

      However, it is unclear what Reviewer 1 meant by random block switches. Our reversal learning task is completed when a block of fixed number of trials is executed. Reversal of reward schedule occurs only once on a randomly selected trial in the block, and the reversed reward schedule is maintained until the end of a block. It is different from other versions of reveral learning where the reward schedule switches multiple times across trials. We clarified this point in Result Section 1.

      (3) The relationship between the supervised learning approach used in the RNNs and reinforcement learning was confused in the discussion. "Although RNNs in our study were trained via supervised learning, animals learn a reversal-learning task from reward feedback, making it into a reinforcement learning (RL) problem." This is fundamentally not true. In the case of this work, the outcome of the previous trial updates the target output, rather than the trial and error type learning as is typical in reinforcement learning. Networks are not learning by reinforcement learning and this statement is confusing.

      We agree with Reviewer 1’s comment that the statement in the original manuscript is confusing. Our intention was to point out that our study used supervised learning, and this is different from animals learn by reinforcement learning in rea life. We revised the sentence in Discussion as follows:

      “The RNNs in our study were trained via supervised learning. However, in real life, animals learn a reversal learning task via reinforcement learning (RL), i.e., learn the task from reward outcomes.”

      (4) The distinction between line attractors and the dynamic trajectories described by the authors deserves further investigation. A significant concern arises from the authors' use of targeted dimensionality reduction (TDR), a form of regression, to identify the axis determining reversal probability. While this approach can reveal interesting patterns in the data, it may not necessarily isolate the dimension along which the RNN computes reversal probability. This limitation could lead to misinterpretation of the underlying neural dynamics.

      a) This manuscript cites work described in "Prefrontal cortex as a meta-reinforcement learning system," which examined a similar task. In that study, the authors identified a v-shaped curve in the principal component space of network states, representing the probability of choosing left or right.

      Importantly, this curve is topologically equivalent to a line and likely represents a line attractor. However, regressing against reversal probability in such a case would show that a single principal component (PC2) directly correlates with reversal probability.

      b) The dynamics observed in the current study bear a striking resemblance to this structure, with the addition of intervening loops in the network state corresponding to within-trial state evolution. Crucially, these observations do not preclude the existence of a line attractor. Instead, they may reflect the network's need to produce fast timescale dynamics within each trial, superimposed on the slower dynamics of the line attractor.

      c) This alternative interpretation suggests that reward signals could function as inputs that shift the network state along the line attractor, with information being maintained across trials. The fast "intervening behaviors" observed by the authors could represent faster timescale dynamics occurring on top of the underlying line attractor dynamics, without erasing the accumulated evidence for reversals.

      d) Given these considerations, the authors' conclusion that their results are better described by separable dynamic trajectories rather than fixed points on a line attractor may be premature. The observed dynamics could potentially be reconciled with a more nuanced understanding of line attractor models, where the attractor itself may be curved and coexist with faster timescale dynamics.

      We appreciate the insightful comments on (1) the similarity of the work by Wang et al ’18 with our findings and (2) an alternative interpretation that augments the line attractor with fast timescale dynamics. 

      (1) We added a discussion of the work by Wang et al ’18 in Result Section 2 to point out the similarity of their findings in the principal component space with ours in the x_rev and x_choice space. We commented that such network dynamics could emerge when learning to perform the reversal learning the task, regardless of the training schemes. 

      We also mention that the RL approach in Wang et al ’18 does not consider within-trial dynamics, therefore lacks the non-stationary activity observed during the trial in the PFC of monkeys and our trained RNNs.

      (2) We revised our original manuscript substantially to reconcile the line attractor model with the nonstationary activity observed during a trial. 

      Here are the highlights of the revised interpretation of the PFC and the RNN network activity

      - The dynamics of x_rev consists of two activity modes, i.e., stationary activity at the start of a trial and non-stationary activity during the trial. Schematic of the augmented model that reconciles two activity modes is shown in Figure 4A. Analysis of the time derivative (dx_reverse / dt) and contractivity of the stationary state are shown in Figure 4B,C to demonstrate two activity modes.

      - We discuss in Result Section 4 main text that the stationary activity is consistent with the line attractor model, but the non-stationary activity deviates from the model. 

      - The two activity modes are linked dynamically. There is an underlying dynamics that can map the stationary state to the non-stationary trajectory. This is shown by predicting the nonstationary trajectory with the stationary state using a support vector regression model. The prediction results are shown in Figure 4D,E,F.

      - We discuss in Result Section 4 an extension of the standard line attractor model: points on the line attractor can serve as initial states that launch non-stationary activity associated with taskrelated behavior.

      - The separability of neural trajectories presented in Result Section 5 is framed as a property of the non-stationary dynamics associated with task-related behavior.

      To strengthen their claims, the authors should:

      (1) Provide a more detailed description of their RNN training paradigm and task structure, including clear illustrations of target outputs.

      (2) Discuss how their findings relate to and potentially extend previous work on similar tasks, particularly addressing the similarities and differences with the v-shaped state organization observed in reinforcement learning contexts. (https://www.nature.com/articles/s41593-018-0147-8 Figure1).

      (3) Explore whether their results could be consistent with a curved line attractor model, rather than treating line attractors and dynamic trajectories as mutually exclusive alternatives.

      Our response to these three comments is described above.

      Addressing these points would significantly enhance the impact of the study and provide a more nuanced understanding of how reversal probabilities are represented in neural circuits.

      In conclusion, while this study provides interesting insights into the neural representation of reversal probability, there are several areas where the methodology and interpretations could be refined.

      Additional Minor Concerns:

      (1) Network Training and Reversal Timing: The authors mention that the network was trained to switch after a reversal to match animal behavior, stating "Maximum a Posterior (MAP) of the reversal probability converges a few trials past the MAP estimate." More explanation of how this training strategy relates to actual animal behavior would enhance the reader's understanding of the meaning of the model's similarity to animal behavior in Figure 1.

      In Method Section 2.5, we described how our observation that the running estimate of MAP converges a few trials after the actual MAP is analogous to the animal’s reversal behavior.

      “This observation can be interpreted as follows. If a subject performing the reversal learning task employs the ideal observer model to detect the trial at which reward schedule is reversed, the subject can infer the reversal of reward schedule a few trials past the actual reversal and then switch its preferred choice. This delay in behavioral reversal, relative to the reversal of reward schedule, is analogous to the monkeys switching their preferred choice a few trials after the reversal of reward schedule.”

      In Step 4, we also mentioned that the target choice outputs are defined based on our observation in Step 3.

      “We used the observation from Step 3 to define target choice outputs that switch abruptly a few trials after the reversal of reward schedule, denoted as $t^*$ in the following. An example of target outputs are shown in Fig.\,\ref{fig_behavior}B.”

      (2) How is the network simulated in step 1 of training? Is it just randomly initialized? What defines this network structure?

      The initial state at the start of a block was random. We think the initial state is less relevant as the external inputs (i.e., cue and feedback) are strong and drive the network dynamics. We mentioned these setup and observation in Step 1 of training.

      “Step 1. Simulate the network starting from a random initial state, apply the external inputs, i.e., cue and feedback inputs, at each trial and store the network choices and reward outcomes at all the trials in a block. The network dynamics is driven by the external inputs applied periodically over the trials.”

      (3) Clarification on Learning Approach: More description of the approach in the main text would be beneficial. The statement "Here, we trained RNNs that learned from a Bayesian inference model to mimic the behavioral strategies of monkeys performing the reversal learning task [2, 4]" is somewhat confusing, as the model isn't directly fit to monkey data. A more detailed explanation of how the Bayesian inference model relates to monkey behavior and how it's used in RNN training would improve clarity.

      We described the learning approach in more detail, but also tried to be concise without going into technical details.

      We revised the sentence in Introduction as follows:

      “We sought to train RNNs to mimic the behavioral strategies of monkeys performing the reversal learning task. Previous studies \cite{costa2015reversal, bartolo2020prefrontal} have shown that a Bayesian inference model can capture a key aspect of the monkey's behavioral strategy, i.e., adhere to the preferred choice until the reversal of reward is detected and then switch abruptly. We trained the RNNs to replicate this behavioral strategy by training them on target behaviors generated from the Bayesian model.”

      We also added a paragraph in Result Section 1 that explains in detail how the training approach works.

      (4) In Figure 1B, it would be helpful to show the target output.

      We added a figure in Fig1B that shows a schematic of how the target output is generated.

      (5) An important point to consider is that a line attractor can be curved while still being topologically equivalent to a line. This nuance makes Figure 4A somewhat difficult to interpret. It might be helpful to discuss how the observed dynamics relate to potentially curved line attractors, which could provide a more nuanced understanding of the neural representations.

      As discussed above, we interpret the “curved” activity during the trial as non-stationary activity. We do not think this non-stationary activity would be characterized as attractor. Attractor is (1) a minimal set of states that is (2) invariant under the dynamics and (3) attracting when perturbed into its neighborhood [Strogatz, Nonlinear dynamics and chaos]. If we consider the autonomous system without the behavior-related external input as the base system, then the non-stationary states could satisfy (2) and (3) but not (1), so they are not part of the attractor. If we include the behavior-related external input to the autonomous dynamics, then it may be possible that the non-stationary trajectories are part of the attractor. We adopted the former interpretation as the behavior-related inputs are external and transient.

      (6) The results of the perturbation experiments seem to follow necessarily from the way x_rev was defined. It would be valuable to clarify if there's more to these results than what appears to be a direct consequence of the definition, or if there are subtleties in the experimental design or analysis that aren't immediately apparent.

      The neural activity x_rev is correlated to the reversal probability, but it is unclear if the activity in this neural subspace is causally linked to behavioral variables, such as choice output. We added this explanation at the beginning of Results Section 7 to clarify the reason for performing the perturbation experiments.

      “The neural activity $x_{rev}$ is obtained by identifying a neural subspace correlated to reversal probability. However, it remains to be shown if activity within this neural subspace is causally linked to behavioral variables, such as choice output.”

      Reviewer #2:

      Below is a list of things I have found difficult to understand, and been puzzled/concerned about while reading the manuscript:

      (1) It would be nice to say a bit more about the dataset that has been used for PFC analysis, e.g. number of neurons used and in what conditions is Figure 2A obtained (one has to go to supplementary to get the reference).

      We added information about the PFC dataset in the opening paragraph of Result Section 2 to provide an overview of what type of neural data we’ve analyzed. It includes information about the number of recorded neurons, recording method and spike binning process.

      (2) It would be nice to give more detail about the monkey task and better explain its trial structure.

      In Result Section 1 we added a description of the overall task structure (and its difference with other versions of revesal learning task), the RNN / monkey trial structure and differences in RNN and monkey tasks.

      (3) In the introduction it is mentioned that during the hold period, the probability of reversal is represented. Where does this statement come from?

      The fact that neural activity during a hold period, i.e., fixation period before presenting the target images, encodes the probability of reversal was demonstrated in a previous study (Bartolo and Averbeck ’20). 

      We realize that our intention was to state that, during the hold period, the reversal probability activity is stationary as in the line attractor model, instead of focusing on that the probability of reversal is represented during this period. We revised the sentence to convey this message. In addition, we revised the entire paragraph to reinterpret our findings: there are two activity modes where the stationary activity is consistent with the line attractor model but the non-stationary activity deviates from it.

      (4) "Around the behavioral reversal trial, reversal probabilities were represented by a family of rankordered trajectories that shifted monotonically". This sentence is confusing and hard to understand.

      Thank you for point this out. We rewrote the paragraph to reflect our revised interpretation. This sentence was removed, as it can be considered as part of the result on separable trajectories.

      (5) For clarity, in the first section, when it is written that "The reversal behavior of trained RNNs was similar to the monkey's behavior on the same task" it would be nice to be more precise, that this is to be expected given the strategy used to train the network.

      We removed this sentence as it makes a blanket statement. Instead, we compared the behavioral outputs of the RNNs and the monkeys one by one.

      We added a sentence in Result Section 1 that the RNN’s abrupt behavioral reversal is expected as they are trained to mimic the target choice outputs of the Bayesian model.

      “Such abrupt reversal behavior was expected as the RNNs were trained to mimic the target outputs of the Bayesian inference model.”

      (6) What is the value of tau used in eq (1), and how does it compare to trial duration?

      We described the value of time constant tau in Eq (1) and also discussed in Result Section 1 that tau=20ms is much faster than trial duration 500ms, thus the persistent behavior seen in trained RNNs is due to learning.

      (7) It would be nice to expand around the notion of « temporally flexible representation » to help readers grasp what this means.

      Instead of stating that the separable dynamic trajectories have “temporally flexible representation”, we break down in what sense it is temporally flexible: separable dynamic trajectories can accommodate the effects that task-related behavior have on generating non-stationary neural dynamics.

      “In sum, our results show that, in a probabilistic reversal learning task, recurrent neural networks encode reversal probability by adopting, not only stationary states as in a line attractor, but also separable dynamic trajectories that can represent distinct probabilistic values while accommodating non-stationary dynamics associated with task-related behavior.”

      Reviewer #3:

      (1) Data:

      It would be useful to describe the experimental task, recording setup, and analyses in much more detail - both in the text and in the methods. What part of PFC are the recordings from? How many neurons were recorded over how many sessions? Which other papers have they been used in? All of these things are important for the reader to know, but are not listed anywhere. There are also some inconsistencies, with the main text e.g. listing the 'typical block length' as 36 trials, and the methods listing the block length as 24 trials (if this is a difference between the biological data and RNN, that should be more explicit and motivated).

      We provided more detailed description of the monkey experimental task and PFC recordings in Result Section 1. We also added a new section in Methods 2.1 to describe the monkey experiment.

      The experimental analyses should be explained in more detail in the methods. There is e.g. no detailed description of the analysis in Figure 6F.

      We added a new section in Methods 6 to describe how the residual PFC activity is computed. It also describes the RNN perturbation experiments.

      Finally, it would be useful for more analyses of monkey behaviour and performance, either in the main text or supplementary figures.

      We did not pursue this comment as it is unclear how additional behavioral analyses would improve the manuscript.

      (2) Model:

      When fitting the network, 'step 1' of training in 2.3 seems superfluous. The posterior update from getting a reward at A is the same as that from not getting a reward at B (and vice versa), and it is therefore completely independent of the network choice. The reversal trial can therefore be inferred without ever simulating the network, simply by generating a sample of which trials have the 'good' option being rewarded and which trials have the 'bad' option being rewarded.

      We respectfully disagree with Reviewer 3’s comment that the reversal trial can be inferred without ever simulating the network. The only way for the network to know about the underlying reward schedule is to perform the task by itself. By simulating the network, it can sample the options and the reward outcomes. 

      Our understanding is that Review 3 described a strategy that a human would use to perform this task. Our goal was to train the RNN to perform the task.

      Do the blocks always start with choice A being optimal? Is everything similar if the network is trained with a variable initial rewarded option? E.g. in Fig 6, would you see the appropriate swap in the effect of the perturbation on choice probability if choice B was initially optimal?

      Thank you for pointing out that the initial high-value option can be random. When setting up the reward schedule, the initial high-value option was chosen randomly from two choice outputs and, at the scheduled reversal, it was switched to the other option. We did not describe this in the original manuscript.

      We added a descrption in Training Scheme Step 4 that the the initial high-value option is selected randomly. This is also explained in Result Section 1 when we give an overview of the RNN training procedure.

      (3) Content:

      It is rarely explained what the error bars represent (e.g. Figures 3B, 4C, ...) - this should be clear in all figures.

      We added that the error bars represent the standard error of mean.

      Figure 2A: this colour scheme is not great. There are abrupt colour changes both before and after the 'reversal' trial, and both of the extremes are hard to see.

      We changed the color scheme to contrast pre- and post-reversal trials without the abrupt color change.

      Figure 3E/F: how is prediction accuracy defined?

      We added that the prediction accuracy is based on Pearson correlation.

      Figure 4B: why focus on the derivative of the dynamics? The subsequent plots looking at the actual trajectories are much easier to understand. Also - what is 'relative trial' relative to?

      The derivative was analyzed to demonstrate stationarity or non-stationarity of the neural activity. We think it will be clearer in the revised manuscript that the derivative allows us to characterize those two activity modes.

      Relative trial number indicate the trial position relative to the behavioral reversal trial. We added this description to the figures when “relative trial” is used.

      Figure 4C: what do these analyses look like if you match the trial numbers for the shift in trajectories? As it is now, there will presumably be more rewarded trials early and late in each block, and more unrewarded trials around the reversal point. Does this introduce biases in the analysis? A related question is (i) why the black lines are different in the top and bottom plots, and (ii) why the ends of the black lines are discontinuous with the beginnings of the red/blue lines.

      We could not understand what Reviewer 3 was asking in this comment. It’d help if Review 3 could clarify the following question:

      “Figure 4C: what do these analyses look like if you match the trial numbers for the shift in trajectories?”

      Question (i): We wanted to look at how the trajectory shifts in the subsequent trial if a reward is or is not received in the current trial. The top panel analyzed all the trials in which the subsquent trial did not receive a reward. The bottom panel analyzed all the trials in which the subsequent trial received a reward. So, the trials analyzed in the top and bottom panels are different, and the black lines (x_rev of “current” trial) in the top and bottom panels are different.

      Question (ii): Black line is from the preceding trial of the red/blue lines, so if trials are designed to be continuous with the inter-trial-interval, then black and red/blue should be continuous. However, in the monkey experiment, the inter-trial-intervals were variable, so the end of current trial does not match with the start of next trial. The neural trajectories presented in the manuscript did not include the activity in this inter-trial-interval.

      Figure 6C: are the individual dots different RNNs? Claiming that there is a decrease in Delta x_choice for a v_+ stimulation is very misleading.

      Yes individual dots are different RNN perturbations. We added explanation about the dots in Figure7C caption. 

      We agree with the comment that \Delta x_choice did not decrease. This sentence was removed. Instead, we revised the manuscript to state that x_choice for v_+ stimulation was smaller than the x_choice for v_- stimulation. We performed KS-test to confirm statistical significance.

      Discussion: "...exhibited behaviour consistent with an ideal Bayesian observer, as found in our study". The RNN was explicitly trained to reproduce an ideal Bayesian observer, so this can only really be considered an assumption (not a result) in the present study.

      We agree that the statement in the original manuscript is inaccurate. It was revised to reflect that, in the other study, behavior outputs similar to a Bayesian observer emerged by simply learning to do the task, intead of directly mimicking the outputs of Bayesian observer as done in our study.

      “Authors showed that trained RNNs exhibited behavior outputs consistent with an ideal Bayesian observer without explicitly learning from the Bayesian observer. This finding shows that the behavioral strategies of monkeys could emerge by simply learning to do the task, instead of directly mimicking the outputs of Bayesian observer as done in our study.”

      Methods: Would the results differ if your Bayesian observer model used the true prior (i.e. the reversal happens in the middle 10 trials) rather than a uniform prior? Given the extensive literature on prior effects on animal behaviour, it is reasonable to expect that monkeys incorporate some non-uniform prior over the reversal point.

      Thank you for pointing out the non-uniform prior. We haven’t conducted this analysis, but would guess that the convergence to the posterior distribution would be faster. We’d have to perform further analysis, which is out of the scope of this paper, to investigate whether the posteior distribution would be different from what we obtained from uniform prior.

      Making the code available would make the work more transparent and useful to the community.

      The code is available in the following Github repository: https://github.com/chrismkkim/LearnToReverse

    1. Author response:

      Reviewer #1 (Public review):

      This study investigates the sex determination mechanism in the clonal ant Ooceraea biroi, focusing on a candidate complementary sex determination (CSD) locus-one of the key mechanisms supporting haplodiploid sex determination in hymenopteran insects. Using whole genome sequencing, the authors analyze diploid females and the rarely occurring diploid males of O. biroi, identifying a 46 kb candidate region that is consistently heterozygous in females and predominantly homozygous in diploid males. This region shows elevated genetic diversity, as expected under balancing selection. The study also reports the presence of an lncRNA near this heterozygous region, which, though only distantly related in sequence, resembles the ANTSR lncRNA involved in female development in the Argentine ant, Linepithema humile (Pan et al. 2024). Together, these findings suggest a potentially conserved sex determination mechanism across ant species. However, while the analyses are well conducted and the paper is clearly written, the insights are largely incremental. The central conclusion - that the sex determination locus is conserved in ants - was already proposed and experimentally supported by Pan et al. (2024), who included O. biroi among the studied species and validated the locus's functional role in the Argentine ant. The present study thus largely reiterates existing findings without providing novel conceptual or experimental advances.

      Although it is true that Pan et al., 2024 demonstrated (in Figure 4 of their paper) that the synteny of the region flanking ANTSR is conserved across aculeate Hymenoptera (including O. biroi), Reviewer 1’s claim that that paper provides experimental support for the hypothesis that the sex determination locus is conserved in ants is inaccurate. Pan et al., 2024 only performed experimental work in a single ant species (Linepithema humile) and merely compared reference genomes of multiple species to show synteny of the region, rather than functionally mapping or characterizing these regions.

      Other comments:

      The mapping is based on a very small sample size: 19 females and 16 diploid males, and these all derive from a single clonal line. This implies a rather high probability for false-positive inference. In combination with the fact that only 11 out of the 16 genotyped males are actually homozygous at the candidate locus, I think a more careful interpretation regarding the role of the mapped region in sex determination would be appropriate. The main argument supporting the role of the candidate region in sex determination is based on the putative homology with the lncRNA involved in sex determination in the Argentine ant, but this argument was made in a previous study (as mentioned above).

      Our main argument supporting the role of the candidate region in sex determination is not based on putative homology with the lncRNA in L. humile. Instead, our main argument comes from our genetic mapping (in Fig. 2), and the elevated nucleotide diversity within the identified region (Fig. 4). Additionally, we highlight that multiple genes within our mapped region are homologous to those in mapped sex determining regions in both L. humile and Vollenhovia emeryi, possibly including the lncRNA.

      In response to the Reviewer’s assertion that the mapping is based on a small sample size from a single clonal line, we want to highlight that we used all diploid males available to us. Although the primary shortcoming of a small sample size is to increase the probability of a false negative, small sample sizes can also produce false positives. We used two approaches to explore the statistical robustness of our conclusions. First, we generated a null distribution by randomly shuffling sex labels within colonies and calculating the probability of observing our CSD index values by chance (shown in Fig. 2). Second, we directly tested the association between homozygosity and sex using Fisher’s Exact Test (shown in Supplementary Fig. S2). In both cases, the association of the candidate locus with sex was statistically significant after multiple-testing correction using the Benjamini-Hochberg False Discovery Rate. These approaches are clearly described in the “CSD Index Mapping” section of the Methods.

      We also note that, because complementary sex determination loci are expected to evolve under balancing selection, our finding that the mapped region exhibits a peak of nucleotide diversity lends orthogonal support to the notion that the mapped locus is indeed a complementary sex determination locus.

      The fourth paragraph of the results and the sixth paragraph of the discussion are devoted to explaining the possible reasons why only 11/16 genotyped males are homozygous in the mapped region. The revised manuscript will include an additional sentence (in what will be lines 384-388) in this paragraph that includes the possible explanation that this locus is, in fact, a false positive, while also emphasizing that we find this possibility to be unlikely given our multiple lines of evidence.

      In response to Reviewer 1’s suggestion that we carefully interpret the role of the mapped region in sex determination, we highlight our careful wording choices, nearly always referring to the mapped locus as a “candidate sex determination locus” in the title and throughout the manuscript. For consistency, the revised manuscript version will change the second results subheading from “The O. biroi CSD locus is homologous to another ant sex determination locus but not to honeybee csd” to “O. biroi’s candidate CSD locus is homologous to another ant sex determination locus but not to honeybee csd,” and will add the word “candidate” in what will be line 320 at the beginning of the Discussion, and will change “putative” to “candidate” in what will be line 426 at the end of the Discussion.

      In the abstract, it is stated that CSD loci have been mapped in honeybees and two ant species, but we know little about their evolutionary history. But CSD candidate loci were also mapped in a wasp with multi-locus CSD (study cited in the introduction). This wasp is also parthenogenetic via central fusion automixis and produces diploid males. This is a very similar situation to the present study and should be referenced and discussed accordingly, particularly since the authors make the interesting suggestion that their ant also has multi-locus CSD and neither the wasp nor the ant has tra homologs in the CSD candidate regions. Also, is there any homology to the CSD candidate regions in the wasp species and the studied ant?

      In response to Reviewer 1’s suggestion that we reference the (Matthey-Doret et al. 2019) study in the context of diploid males being produced via losses of heterozygosity during asexual reproduction, the revised manuscript will include the following sentence: “Therefore, if O. biroi uses CSD, diploid males might result from losses of heterozygosity at sex determination loci (Fig. 1C), similar to what is thought to occur in other asexual Hymenoptera that produce diploid males (Rabeling and Kronauer 2012; Matthey-Doret et al. 2019).”

      We note, however, that in their 2019 study, Matthey-Doret et al. did not directly test the hypothesis that diploid males result from losses of heterozygosity at CSD loci during asexual reproduction, because the diploid males they used for their mapping study came from inbred crosses in a sexual population of that species.

      We address this further below, but we want to emphasize that we do not intend to argue that O. biroi has multiple CSD loci. Instead, we suggest that additional, undetected CSD loci is one possible explanation for the absence of diploid males from any clonal line other than clonal line A. In response to Reviewer 1’s suggestion that we reference the (Matthey-Doret et al. 2019) study in the context of multilocus CSD, the revised manuscript version will include the following additional sentence in the fifth paragraph of the discussion: “Multi-locus CSD has been suggested to limit the extent of diploid male production in asexual species under some circumstances (Vorburger 2013; Matthey-Doret et al. 2019).”

      Regarding Reviewer 2’s question about homology between the putative CSD loci from the (Matthey-Doret et al. 2019) study and O. biroi, we note that there is no homology. The revised manuscript version will have an additional Supplementary Table (which will be the new Supplementary Table S3) that will report the results of this homology search. The revised manuscript will also include the following additional sentence in the Results: “We found no homology between the genes within the O. biroi CSD index peak and any of the genes within the putative L. fabarum CSD loci (Supplementary Table S3).”

      The authors used different clonal lines of O. biroi to investigate whether heterozygosity at the mapped CSD locus is required for female development in all clonal lines of O. biroi (L187-196). However, given the described parthenogenesis mechanism in this species conserves heterozygosity, additional females that are heterozygous are not very informative here. Indeed, one would need diploid males in these other clonal lines as well (but such males have not yet been found) to make any inference regarding this locus in other lines.

      We agree that a full mapping study including diploid males from all clonal lines would be preferable, but as stated earlier in that same paragraph, we have only found diploid males from clonal line A. We stand behind our modest claim that “Females from all six clonal lines were heterozygous at the CSD index peak, consistent with its putative role as a CSD locus in all O. biroi.” In the revised manuscript version, this sentence (in what will be lines 199-201) will be changed slightly in response to a reviewer comment below: “All females from all six clonal lines (including 26 diploid females from clonal line B) were heterozygous at the CSD index peak, consistent with its putative role as a CSD locus in all O. biroi.”

      Reviewer #2 (Public review):

      The manuscript by Lacy et al. is well written, with a clear and compelling introduction that effectively conveys the significance of the study. The methods are appropriate and well-executed, and the results, both in the main text and supplementary materials, are presented in a clear and detailed manner. The authors interpret their findings with appropriate caution.

      This work makes a valuable contribution to our understanding of the evolution of complementary sex determination (CSD) in ants. In particular, it provides important evidence for the ancient origin of a non-coding locus implicated in sex determination, and shows that, remarkably, this sex locus is conserved even in an ant species with a non-canonical reproductive system that typically does not produce males. I found this to be an excellent and well-rounded study, carefully analyzed and well contextualized.

      That said, I do have a few minor comments, primarily concerning the discussion of the potential 'ghost' CSD locus. While the authors acknowledge (line 367) that they currently have no data to distinguish among the alternative hypotheses, I found the evidence for an additional CSD locus presented in the results (lines 261-302) somewhat limited and at times a bit difficult to follow. I wonder whether further clarification or supporting evidence could already be extracted from the existing data. Specifically:

      We agree with Reviewer 2 that the evidence for a second CSD locus is limited. In fact, we do not intend to advocate for there being a second locus, but we suggest that a second CSD locus is one possible explanation for the absence of diploid males outside of clonal line A. In our initial version, we intentionally conveyed this ambiguity by titling this section “O. biroi may have one or multiple sex determination loci.” However, we now see that this leads to undue emphasis on the possibility of a second locus. In the revised manuscript, we will split this into two separate sections: “Diploid male production differs across O. biroi clonal lines” and “O. biroi lacks a tra-containing CSD locus.”

      (1) Line 268: I doubt the relevance of comparing the proportion of diploid males among all males between lines A and B to infer the presence of additional CSD loci. Since the mechanisms producing these two types of males differ, it might be more appropriate to compare the proportion of diploid males among all diploid offspring. This ratio has been used in previous studies on CSD in Hymenoptera to estimate the number of sex loci (see, for example, Cook 1993, de Boer et al. 2008, 2012, Ma et al. 2013, and Chen et al., 2021). The exact method might not be applicable to clonal raider ants, but I think comparing the percentage of diploid males among the total number of (diploid) offspring produced between the two lineages might be a better argument for a difference in CSD loci number.

      We want to re-emphasize here that we do not wish to advocate for there being two CSD loci in O. biroi. Rather, we want to explain that this is one possible explanation for the apparent absence of diploid males outside of clonal line A. We hope that the modifications to the manuscript described in the previous response help to clarify this.

      Reviewer 2 is correct that comparing the number of diploid males to diploid females does not apply to clonal raider ants. This is because males are vanishingly rare among the vast numbers of females produced. We do not count how many females are produced in laboratory stock colonies, and males are sampled opportunistically. Therefore, we cannot report exact numbers. However, we will add the following sentence to the revised manuscript: “Despite the fact that we maintain more colonies of clonal line B than of clonal line A in the lab, all the diploid males we detected came from clonal line A.”

      (2) If line B indeed carries an additional CSD locus, one would expect that some females could be homozygous at the ANTSR locus but still viable, being heterozygous only at the other locus. Do the authors detect any females in line B that are homozygous at the ANTSR locus? If so, this would support the existence of an additional, functionally independent CSD locus.

      We thank the reviewer for this suggestion, and again we emphasize that we do not want to argue in favor of multiple CSD loci. We just want to introduce it as one possible explanation for the absence of diploid males outside of clonal line A.

      The 26 sequenced diploid females from clonal line B are all heterozygous at the mapped locus, and the revised manuscript will clarify this in what will be lines 199-201. Previously, only six of those diploid females were included in Supplementary Table S2, and that will be modified accordingly.

      (3) Line 281: The description of the two tra-containing CSD loci as "conserved" between Vollenhovia and the honey bee may be misleading. It suggests shared ancestry, whereas the honey bee csd gene is known to have arisen via a relatively recent gene duplication from fem/tra (10.1038/nature07052). It would be more accurate to refer to this similarity as a case of convergent evolution rather than conservation.

      In the sentence that Reviewer 2 refers to, we are representing the assertion made in the (Miyakawa and Mikheyev 2015) paper in which, regarding their mapping of a candidate CSD locus that contains two linked tra homologs, they write in the abstract: “these data support the prediction that the same CSD mechanism has indeed been conserved for over 100 million years.” In that same paper, Miyakawa and Mikheyev write in the discussion section: “As ants and bees diverged more than 100 million years ago, sex determination in honey bees and V. emeryi is probably homologous and has been conserved for at least this long.”

      As noted by Reviewer 2, this appears to conflict with a previously advanced hypothesis: that because fem and csd were found in Apis mellifera, Apis cerana, and Apis dorsata, but only fem was found in Mellipona compressipes, Bombus terrestris, and Nasonia vitripennis, that the csd gene evolved after the honeybee (Apis) lineage diverged from other bees (Hasselmann et al. 2008). However, it remains possible that the csd gene evolved after ants and bees diverged from N. vitripennis, but before the divergence of ants and bees, and then was subsequently lost in B. terrestris and M. compressipes. This view was previously put forward based on bioinformatic identification of putative orthologs of csd and fem in bumblebees and in ants [(Schmieder et al. 2012), see also (Privman et al. 2013)]. However, subsequent work disagreed and argued that the duplications of tra found in ants and in bumblebees represented convergent evolution rather than homology (Koch et al. 2014). Distinguishing between these possibilities will be aided by additional sex determination locus mapping studies and functional dissection of the underlying molecular mechanisms in diverse Aculeata.

      Distinguishing between these competing hypotheses is beyond the scope of our paper, but the revised manuscript will include additional text to incorporate some of this nuance. We will include these modified lines below:

      “A second QTL region identified in V. emeryi (V.emeryiCsdQTL1) contains two closely linked tra homologs, similar to the closely linked honeybee tra homologs, csd and fem (Miyakawa and Mikheyev 2015). This, along with the discovery of duplicated tra homologs that undergo concerted evolution in bumblebees and ants (Schmieder et al. 2012; Privman et al. 2013) has led to the hypothesis that the function of tra homologs as CSD loci is conserved with the csd-containing region of honeybees (Schmieder et al. 2012; Miyakawa and Mikheyev 2015). However, other work has suggested that tra duplications occurred independently in honeybees, bumblebees, and ants (Hasselmann et al. 2008; Koch et al. 2014), and it remains to be demonstrated that either of these tra homologs acts as a primary CSD signal in V. emeryi.”

      (4) Finally, since the authors successfully identified multiple alleles of the first CSD locus using previously sequenced haploid males, I wonder whether they also observed comparable allelic diversity at the candidate second CSD locus. This would provide useful supporting evidence for its functional relevance.

      As is already addressed in the final paragraph of the results and in Supplementary Fig. S4, there is no peak of nucleotide diversity in any of the regions homologous to V.emeryiQTL1, which is the tra-containing candidate sex determination locus (Miyakawa and Mikheyev 2015). In the revised manuscript, the relevant lines will be 307-310. We want to restate that we do not propose that there is a second candidate CSD locus in O. biroi, but we simply raise the possibility that multi-locus CSD *might* explain the absence of diploid males from clonal lines other than clonal line A (as one of several alternative possibilities).

      Overall, these are relatively minor points in the context of a strong manuscript, but I believe addressing them would improve the clarity and robustness of the authors' conclusions.

      Reviewer #3 (Public review):

      Summary:

      The sex determination mechanism governed by the complementary sex determination (CSD) locus is one of the mechanisms that support the haplodiploid sex determination system evolved in hymenopteran insects. While many ant species are believed to possess a CSD locus, it has only been specifically identified in two species. The authors analyzed diploid females and the rarely occurring diploid males of the clonal ant Ooceraea biroi and identified a 46 kb CSD candidate region that is consistently heterozygous in females and predominantly homozygous in males. This region was found to be homologous to the CSD locus reported in distantly related ants. In the Argentine ant, Linepithema humile, the CSD locus overlaps with an lncRNA (ANTSR) that is essential for female development and is associated with the heterozygous region (Pan et al. 2024). Similarly, an lncRNA is encoded near the heterozygous region within the CSD candidate region of O. biroi. Although this lncRNA shares low sequence similarity with ANTSR, its potential functional involvement in sex determination is suggested. Based on these findings, the authors propose that the heterozygous region and the adjacent lncRNA in O. biroi may trigger female development via a mechanism similar to that of L. humile. They further suggest that the molecular mechanisms of sex determination involving the CSD locus in ants have been highly conserved for approximately 112 million years. This study is one of the few to identify a CSD candidate region in ants and is particularly noteworthy as the first to do so in a parthenogenetic species.

      Strengths:

      (1) The CSD candidate region was found to be homologous to the CSD locus reported in distantly related ant species, enhancing the significance of the findings.

      (2) Identifying the CSD candidate region in a parthenogenetic species like O. biroi is a notable achievement and adds novelty to the research.

      Weaknesses

      (1) Functional validation of the lncRNA's role is lacking, and further investigation through knockout or knockdown experiments is necessary to confirm its involvement in sex determination.

      See response below.

      (2) The claim that the lncRNA is essential for female development appears to reiterate findings already proposed by Pan et al. (2024), which may reduce the novelty of the study.

      We do not claim that the lncRNA is essential for female development in O. biroi, but simply mention the possibility that, as in L. humile, it is somehow involved in sex determination. We do not have any functional evidence for this, so this is purely based on its genomic position immediately adjacent to our mapped candidate region. We agree with the reviewer that the study by Pan et al. (2024) decreases the novelty of our findings. Another way of looking at this is that our study supports and bolsters previous findings by partially replicating the results in a different species.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      This manuscript presents an interesting new framework (VARX) for simultaneously quantifying effective connectivity in brain activity during sensory stimulation and how that brain activity is being driven by that sensory stimulation. The core idea is to combine the Vector Autoregressive model that is often used to infer Granger-causal connectivity in brain data with an encoding model that maps the features of a sensory stimulus to that brain data. The authors do a nice job of explaining the framework. And then they demonstrate its utility through some simulations and some analysis of real intracranial EEG data recorded from subjects as they watched movies. They infer from their analyses that the functional connectivity in these brain recordings is essentially unaltered during movie watching, that accounting for the driving movie stimulus can protect one against misidentifying brain responses to the stimulus as functional connectivity, and that recurrent brain activity enhances and prolongs the putative neural responses to a stimulus.

      This manuscript presents an interesting new framework (VARX) for simultaneously quantifying effective connectivity in brain activity during sensory stimulation and how that brain activity is being driven by that sensory stimulation. Overall, I thought this was an interesting manuscript with some rich and intriguing ideas. That said, I had some concerns also - one potentially major - with the inferences drawn by the authors on the analyses that they carried out.

      Main comments:

      (1) My primary concern with the way the manuscript is written right now relates to the inferences that can be drawn from the framework. In particular, the authors want to assert that, by incorporating an encoding model into their framework, they can do a better job of accounting for correlated stimulus-driven activity in different brain regions, allowing them to get a clearer view of the underlying innate functional connectivity of the brain. Indeed, the authors say that they want to ask "whether, after removing stimulus-induced correlations, the intrinsic dynamic itself is preserved". This seems a very attractive idea indeed. However, it seems to hinge critically on the idea of fitting an encoding model that fully explains all of the stimulus-driven activity. In other words, if one fits an encoding model that only explains some of the stimulus-driven response, then the rest of the stimulus-driven response still remains in the data and will be correlated across brain regions and will appear as functional connectivity in the ongoing brain dynamics - according to this framework. This residual activity would thus be misinterpreted. In the present work, the authors parameterize their stimulus using fixation onsets, film cuts, and the audio envelope. All of these features seem reasonable and valid. However, they surely do not come close to capturing the full richness of the stimuli, and, as such, there is surely a substantial amount of stimulus-driven brain activity that is not being accounted for by their "B" model and that is being absorbed into their "A" model and misinterpreted as intrinsic connectivity. This seems to me to be a major limitation of the framework. Indeed, the authors flag this concern themselves by (briefly) raising the issue in the first paragraph of their caveats section. But I think it warrants much more attention and discussion.

      We agree. One can never be sure that all stimulus induced correlation is accounted for. We now formulate our question more cautiously: 

      “We will ask here whether, after removing some of the stimulus-induced correlations, the intrinsic dynamic is similar between stimulus and rest conditions.”

      We also highlight that one may expect the opposite result of what we found: 

      “A general observation of these studies is that a portion of the functional connectivity is preserved between rest and stimulus conditions, while some aspects are altered by the perceptual task [12,16], sometimes showing increased connectivity during the stimulus.[15].” 

      We have added a number of additional features (acoustic edges, fixation novelty, and motion) and more carefully characterize how much “connectivity” each one explains in the neural data: 

      “Removing any of the input features increased the effect size of recurrent connections compared to a model with all features (Fig. S4). We then cumulatively added each feature to the VARX model. Effect size monotonically decreases with each feature added (Fig. 3F). Decreases of effect size are significant when adding film cuts (ΔR=-3.6*10<sup>-6</sup>, p<0.0001, N=26, FDR correction, α=0.05) and the sound envelope (ΔR=-3.59*10<sup>-6</sup>, p=0.002, N=26, FDR correction, α=0.05). Thus, adding more input features progressively reduces the strength of recurrent “connections”.”

      We also added more data to the analysis comparing movies vs rest. We now use 4 different movie segments instead of 1 and find reduced recurrent connectivity during movies: 

      “The number of significant recurrent connections in  were significantly reduced during  movie watching compared to rest (Fig. 4C, fixed effect of stimulus: beta = -3.8*10<sup>-3</sup>, t(17) = -3.9, p<0.001), as is the effect size R (Fig. 4D, fixed effect of stimulus: beta = -2.5*10<sup>-4</sup>, t(17) = -4.1, p<0.001).”

      The additional analysis is described in the Methods section:

      “To compare recurrent connectivity between movies and the resting-state, we compute VARX models in four different movie segments of 5 minutes length to match the length of the resting state recording. We use the first and second half of ‘Despicable Me English’, the first half of ‘Inscapes’ and one of the ‘Monkey’ movies. 18 patients include each of these recordings. For each recording in each patient we compute the fraction of significant channels (p<0.001) and average the effect size R across all channel pairs, excluding the diagonal. We test the difference between movies and resting-state with linear mixed-effect models with stimulus as fixed effect (movie vs rest), and patient as random effect, using matlab’s fitlme() routine.”

      We had already seen this trend of decreasing connectivity during movie watching before, and reported on it cautiously as “largely unaltered”. We updated the Abstract correspondingly from “largely unaltered” to “reduced”: 

      “We also find that the recurrent connectivity during rest is reduced during movie watching.”

      We mentioned this possibility in the Discussion before, namely, that additional input features may reduce recurrent connectivity in the model, and therefore show a difference. We discuss this result now as follows: 

      “The stimulus features we included in our model capture mostly low-level visual and auditory input. It is possible that regressing out a richer stimulus characterization would have removed additional stimulus-induced correlation. While we do not expect that this would change the overall effect of a reduced number of “connections” during movie watching compared to resting state, the interpretation of changes in specific connections will be affected by the choice of features. For example, in sensory cortices, higher recurrent connectivity in the LFP during rest would be consistent with the more synchronized state we saw in rest, as reflected by larger oscillatory activity. Synchronization in higher-order cortices, however, is expected to be more strongly influenced by semantic content of external input.”

      In the Discussion we expand on what might happen if additional stimulus features were to be included into the model:  

      “Previous literature does often not distinguish between intrinsic dynamics and extrinsic effects. By factoring out some of the linear effects of the external input we conclude here that recurrent connectivity is reduced in average. From our prior work49, we know that the stimulus features we included here capture a substantial amount of variance across the brain in intracranial EEG. Arguably, however, the video stimuli had rich semantic information that was not captured by the low-level features used here. Adding such semantic features could have further reduced shared variance, and consequently further reduced average recurrent connectivity in the model.”

      “Similarities and differences between rest and movie watching conditions reported previously, do not draw a firm conclusion as to whether overall “functional connectivity” is increased or reduced. Results seem to depend on the time scale of neural activity analyzed, and the specific brain networks [12,16,63]. However, in fMRI, the conclusion seems to be that functional connectivity during movies is stronger than during rest[15], which likely results from stimulus induced correlations. The VARX model can remove some of the effects of these stimuli, revealing that average recurrent connectivity may be reduced rather than increased during stimulus processing.”

      And in the conclusion we now write: 

      “The model revealed a small but significant decrease of recurrent connectivity when watching movies.”

      (2) Related to the previous comment, the authors make what seems to me to be a complex and important point on page 6 (of the pdf). Specifically, they say "Note that the extrinsic effects captured with filters B are specific (every stimulus dimension has a specific effect on each brain area), whereas the endogenous dynamic propagates this initial effect to all connected brain areas via matrix A, effectively mixing and adding the responses of all stimulus dimensions. Therefore, this factorization separates stimulus-specific effects from the shared endogenous dynamic." It seems to me that the interpretation of the filter B (which is analogous to the "TRF") for the envelope, say, will be affected by the fact that the matrix A is likely going to be influenced by all sorts of other stimulus features that are not included in the model. In other words, residual stimulus-driven correlations that are captured in A might also distort what is going on in B, perhaps. So, again, I worry about interpreting the framework unless one can guarantee a near-perfect encoding model that can fully account for the stimulus-driven activity. I'd love to hear the authors' thoughts on this. (On this issue - the word "dominates" on page 12 seems very strong.)

      This is an interesting point we had not thought about. After some theoretical considerations and some empirical testing we conclude that the effect of missing inputs is relevant, but can be easily anticipated. 

      We have added the following to the Results section explaining and demonstrated empirically the effects of adding features and signals to the model: 

      “As with conventional linear regression, the estimate in B for a particular input and output channel is not affected by which other signals are included in or , provided those other inputs are uncorrelated. We confirmed this here empirically by removing dimensions from (Fig. S11A), and by adding uncorrelated input to (Fig. S11B, adding fixation onset does not affect the estimate for auditory envelope responses). In other words, to estimate B, we do not require all possible stimulus features and all brain activity to be measured and included in the model. In contrast, B does vary when correlated inputs are added to (Fig. S11C, adding acoustic edges changes the auditory envelope response). Evidently the auditory envelope and acoustic edges are tightly coupled in time, whereas fixation onset is not. When a correlated input is missing (acoustic edges) then the other input (auditory envelope) absorbs the correlated variance, thus capturing the combined response of both.”

      (3) Regarding the interpretation of the analysis of connectivity between movies and rest... that concludes that the intrinsic connectivity pattern doesn't really differ. This is interesting. But it seems worth flagging that this analysis doesn't really account for the specific dynamics in the network that could differ quite substantially between movie watching and rest, right? At the moment, it is all correlational. But the dynamics within the network could be very different between stimulation and rest I would have thought.

      As discussed above, with more data and additional stimulus features we now see detectable changes in the connectivity. The example in Figure 4G also shows that specific connections may change in different directions, while overall the strength of connections slightly decreases during movie watching compared to rest. We added the following to the results:

      “While the effect size decreases on average, there is some variation across different brain areas (Fig. 4E-G).”

      But even if the connectivity were unchanged, the activity on this network can be different with varying inputs. We actually also saw that there were changes in the variability of activity (Figs. 6 and S13) that may point to non-linear effects. It seems that injecting the input will cause an overall change in power, which can be explained by a relatively simple non-linear gain adaptation. These effects are already discussed at some length in the paper. 

      (4) I didn't really understand the point of comparing the VARX connectivity estimate with the spare-inverse covariance method (Figure 2D). What was the point of this? What is a reader supposed to appreciate from it about the validity or otherwise of the VARX approach?

      We added the following motivation and clarification on this topic: 

      “To test the descriptive validity [43] of the VARX model we follow the approach of recovering structural connectivity from functional activity in simulation. [44] Specifically, we will compare the recurrent connectivity A derived from brain activity simulated assuming a given structural connectivity, i.e. we ask, can the VARX model recover the underlying structural connectivity, at least in a simulated whole-brian model with known connectivity? … For comparison, we also used the sparse-inverse covariance method to recover connectivity from the correlation matrix (functional connectivity). This method is considered state-of-the-art as it is more sensitive than other methods in detecting structural connections [48]”

      (5) I think the VARX model section could have benefitted a bit from putting some dimensions on some of the variables. In particular, I struggled a little to appreciate the dimensionality of A. I am assuming it has to involve both time lags AND electrode channels so that you can infer Granger causality (by including time) between channels. Including a bit more detail on the dimensionality and shape of A might be helpful for others who want to implement the VARX model.

      Your assumption is correct. We added the following to make this easier for readers: 

      “Therefore, A  has dimensions B has dimensions , where are the dimensions of and respectively.”

      (6) A second issue I had with the inferences drawn by the authors was a difficulty in reconciling certain statements in the manuscript. For example, in the abstract, the authors write "We find that the recurrent connectivity during rest is largely unaltered during movie watching." And they also write that "Failing to account for ... exogenous inputs, leads to spurious connections in the intrinsic "connectivity".

      Perhaps this segment of the abstract needed more explanation. To enhance clarity we have also changed the ordering of the findings. Hopefully this is more clear now: 

      “This model captures the extrinsic effect of the stimulus and separates that from the intrinsic effect of the recurrent brain dynamic. We find that the intrinsic dynamic enhances and prolongs the neural responses to scene cuts, eye movements, and sounds. Failing to account for these extrinsic inputs, leads to spurious recurrent connections that govern the intrinsic dynamic. We also find that the recurrent connectivity during rest is reduced during movie watching.”

      Reviewer #2 (Public review):

      Summary:

      The authors apply the recently developed VARX model, which explicitly models intrinsic dynamics and the effect of extrinsic inputs, to simulated data and intracranial EEG recordings. This method provides a directed method of 'intrinsic connectivity'. They argue this model is better suited to the analysis of task neuroimaging data because it separates the intrinsic and extrinsic activity. They show: that intrinsic connectivity is largely unaltered during a movie-watching task compared to eyes open rest; intrinsic noise is reduced in the task; and there is intrinsic directed connectivity from sensory to higher-order brain areas.

      Strengths:

      (1) The paper tackles an important issue with an appropriate method.

      (2) The authors validated their method on data simulated with a neural mass model.

      (3) They use intracranial EEG, which provides a direct measure of neuronal activity.

      (4) Code is made publicly available and the paper is written well.

      Weaknesses:

      It is unclear whether a linear model is adequate to describe brain data. To the author's credit, they discuss this in the manuscript. Also, the model presented still provides a useful and computationally efficient method for studying brain data - no model is 'the truth'.

      We fully agree and have nothing much to add to this, except to highlight the benefit of a linear model even as explanation for non-linear phenomena: 

      “The [noise-quenching] effect we found here can be explained by a VARX model with the addition of a divisive gain adaptation mechanism … The noise-quenching result and its explanation via gain adaptation shows the benefit of using a parsimonious linear model, which can suggest nonlinear mechanisms as simple corrections from linearity.”

      Appraisal of whether the authors achieve their aims:

      As a methodological advancement highlighting a limitation of existing approaches and presenting a new model to overcome it, the authors achieve their aim. Generally, the claims/conclusions are supported by the results.

      The wider neuroscience claims regarding the role of intrinsic dynamics and external inputs in affecting brain data could benefit from further replication with another independent dataset and in a variety of tasks - but I understand if the authors wanted to focus on the method rather than the neuroscientific claims in this manuscript.

      We fully agree. We added the following to the Discussion section:

      “Future studies should test if our findings replicate in an independent iEEG datasets, including active tasks and whether they generalize to other neuroimaging modalities.”

      Impact:

      The authors propose a useful new approach that solves an important problem in the analysis of task neuroimaging data. I believe the work can have a significant impact on the field.

      Recommendations for the authors:  

      Reviewer #1 (Recommendations for the authors):

      Minor comments:

      (1) Did you mean "less" or "fewer" in the following sentence "..larger values lead to overfitting, i.e. less significant connections..."?

      We mean fewer. Thanks for catching this. 

      (2) I didn't see any equations showing how the regularization parameter lambda is incorporated into the framework.

      We prefer the math and details of the algorithm to an earlier paper that has now been published. Instead we added the following clarification: 

      “The VARX models were fitted to data with the matlab version of the code31 using conventional L2-norm regularization. The corresponding regularization parameter was set to 𝜆=0.3.”

      (3) I think some readers of this might struggle to understand the paragraph beginning

      "Connectivity plots are created with nilearn's plot_connectome() function...". It's all quite opaque for the uninitiated.

      Agreed. We now write more simply: 

      “Connectivity plots in Fig. 4 were created with routines from the nilearn toolbox [51].”

      (4) The paragraph beginning "The length of responses for Figure 5..." is also very opaque and could do with being explained more fully. Or this text could be removed from the methods and incorporated into the relevant results section where you actually discuss this analysis.

      Thank you for flagging this. We expand on the details in the Methods as follows: 

      “The length of responses for each channel in B and H to external inputs in Fig. 5 is computed with Matlab's findpeaks() function. This function returns the full-width at half of the peak maximum minus baseline. Power in each channel is computed as the squares of the responses averaged over the time window that was analyzed (0-0.6s).”

      (5) I think adding some comments to the text or caption related to Figures 3C and 3D would be helpful so readers can understand these numbers a bit better. One seems to be the delta log p value and the other is the delta ratio. What does positive or negative mean? Readers might appreciate a little more help.

      We expanded it as follows, hopefully this helps: 

      “C) difference of log for VAX model without minus with inputs (panel A - B). Both models are fit to the same data. D) Thresholding panels A and B at p<0.0001 gives a fraction of significant connections. Here we show the fraction of significant channels for models with and without input. Each line is a patient with color indicating increase or decrease  E) Mean over all channels for VARX models with and without inputs. Each line is a patient.”

      (6) It is not clear what the colors mean in Figures 4 E, F, G.

      We updated the color scheme for those figure panels and carefully explained it in the caption. Please see the manuscript for updated figure 4.   

      (7) It might be nice to slightly unpack what you mean by the "variability of the internal dynamic" and why it can be equated with the power of the innovation process.

      In the methods we added the following clarification right after defining the VARX model: 

      “The innovation process captures the internal variability of the model. Without it, repeating the same input would always result in a fixed deterministic output .”

      In the results section we added the following: 

      “As a metric of internal variability we measured the power of the intrinsic innovation process , which captures the unobserved “random” brain activity which leads to variations in the responses.”

      (8) Typos etc.

      a) "... has been attributed to variability of ongoing dynamic"

      b) The manuscript refers to a Figure 3G, but there is no Figure 3G.

      c) n_a = n_a = 1. Is that a typo?

      d) fiction

      Thank you for catching these. We fixed them. 

      Reviewer #2 (Recommendations for the authors):

      (1) I'm curious about the authors' opinions on the conditions studied. Naively, eyes open rest and passive movie watching seem like similar conditions - were the authors expecting to see a difference with VARX? Do the authors expect that they would see bigger differences when there is a larger difference in sensory input, e.g. eyes closed rest vs movie watching? Given the authors are arguing the need to explicitly model external inputs, a real data example contrasting two very different external inputs might better demonstrate the model's utility.

      Thank you for this suggestion. We added an analysis of eyes-closed rest recordings, available in 8 patients (Fig. S8). The difference between movie and rest is indeed more pronounced than for eyes open rest. The result is described in the methods:

      “In a subset of patients with eyes-closed resting state we find the same effect, that is qualitatively more pronounced (Fig. S8).”

      This complements our updated finding of a difference between movie and eyes-open rest that does show a significant difference after adding more data to this analysis. The results have been updated as following

      “The number of significant recurrent connections in  were significantly reduced during  movie watching compared to rest (Fig. 4C, fixed effect of stimulus:

      beta = -3.8*10<sup>-3</sup>, t(17) = -3.9, p<0.001), as is the effect size R (Fig. 4D, fixed effect of stimulus: beta = -2.5*10<sup>-4</sup>, t(17) = -4.1, p<0.001).”

      The abstract has been updated accordingly:

      “We also find that the recurrent connectivity during rest is reduced during movie watching.”

      (2) It would also have been interesting to see how the proposed model compares to DCM - however, I understand if the authors wanted to focus on their model rather than a comparison with other models.

      We did not try the DCM for a number of reasons. 1) it does not allow for delays in the model dynamic (i.e. the entire time course of the response has to be captured by the recurrent dynamic of a single time step A). 2. It is computationally prohibitive and would not allow us to analyze large channel counts. 3. The available code is custom made for fMRI or EEG analysis with very specified signal generation models that do not obviously apply to iEEG. We added the following to the Discussion of the CDM:  

      “Similar to the VARX model, DCM includes intrinsic and extrinsic effects A and B. However, the modeling is limited to first-order dynamics (i.e. η<sub>a</sub>=η<sub>b</sub>=1). Thus, prolonged responses have to be entirely captured with a first-order recurrent A. … In contrast, here we have analyzed up to 300 channels per subject across the brain, which would be prohibitive with DCM. By analyzing a large number of recordings we were able to draw more general conclusions about whole-brain activity.”

      (3) I believe improving the consistency of the terminology used would improve the manuscript:

      a) Intrinsic dynamics vs intrinsic connectivity vs recurrent connectivity:

      - The term 'intrinsic dynamic' is first introduced in paragraph 3 of the introduction. An explicit definition of is meant by this term would benefit the manuscript.

      - Sometimes the terminology changes to 'intrinsic connectivity' or 'recurrent connectivity'. An explicit definition of these terms (if they refer to different things) would also benefit the manuscript.

      We had used the term “intrinsic” and “recurrent” interchangeably. We now try to mostly say “intrinsic dynamic” when we talk about the more general phenomenon or recurrent brain dynamic, while using “recurrent connectivity” when we refer to the model parameters A. 

      We provide now a definition already at the start of the Abstract: 

      “Sensory stimulation of the brain reverberates in its recurrent neural networks. However, current computational models of brain activity do not separate immediate sensory responses from this intrinsic dynamic. We apply a vector-autoregressive model with external input (VARX), combining the concepts of “functional connectivity” and “encoding models”, to intracranial recordings in humans. This model captures the extrinsic effect of the stimulus and separates that from the intrinsic effect of the recurrent brain dynamic.”

      And at the start of the introduction: 

      “The primate brain is highly interconnected between and within brain areas. … We will refer to the dynamic driven by this recurrent architecture as the intrinsic dynamic of the brain.”

      b) Intrinsic vs Endogenous and Extrinsic vs Exogenous:

      - Footnote 1 defines the 'intrinsic' and 'extrinsic' terminology.

      - However, there are instances where the authors switch back to endogenous/exogenous.

      - Methods section: "Overall system response", paragraph 2.

      - Results section: "Recurrent dynamic enhances and prolongs stimulus responses".

      - Conclusions section.

      With a foot in both neuroscience and systems identification, it’s a hard habit to break. Thanks for catching it. We searched and replaced all instances of endogenous and exogenous.  

      (4) Methods:

      a) The model equation would be clearer if the convolution was written out fully. (I had to read reference 1 to understand the model.).

      We now spell out the full equation and hope it's not too cumbersome to read:  

      “For the th signal channel the recurrence of the VARX model is given by: 

      b) How is an individual dimension omitted in the reduced model, are the values in the y, x set to zero?

      No, it is actually removed from the linear prediction. We added: 

      “… omitted from the prediction …”

      c) "The p-value quantifies the probability that a specific connection in A or B is zero" - for each of n_a/n_b filters?

      d) It should be clarified that D is a vector.

      We hope the following clarification addresses both these questions: 

      “The p-value quantifies the probability that a specific connection in either A or B is zero. Therefore, D,P and R<sup>2</sup> all have dimensions or for A or B  respectively.”

      (5) Results:

      a) Stimulus-induced reduction of noise in the intrinsic activity: would be good to define the frequency range for theta and beta in paragraph 2.

      Added. 

      b) Neural mass model simulation:

      - A brief description of what was simulated is needed.

      We basically ran the sample code of the neurolib library. With that in mind maybe the description we already provide is sufficient:  

      “We used the default model simulation of the neurolib python library (using their sample code for the “ALNModel”), which is a mean-field approximation of adaptive exponential integrate-and-fire neurons. This model can generate simulated mean firing rates in 80 brain areas based on connectivity and delay matrices determined with diffusion tensor imaging (DTI). We used 5 min of “resting state” activity (no added stimulus, simulated at 0.1ms resolution, subsequently downsampled to 100Hz).”

      - It's not clear to me why the A matrix should match the structural connectivity.

      We added the following introduction to make the purpose of this simulation clear:

      “To test the descriptive validity [43] of the VARX model we follow the approach of recovering structural connectivity from functional activity in simulation. [44] Specifically, we will compare the “connectivity” A derived from brain activity simulated assuming a given structural connectivity, i.e. we ask, can the VARX model recover the underlying structural connectivity, at least in a simulated whole-brian model with known connectivity?”

      - It would be interesting to see the inferred A matrix.

      We added a Supplement figure for this and the following: 

      “The VARX model was estimated with n<sub>a</sub>=2, and no input. The resulting estimate for A is dominated by the diagonal elements that capture the autocorrelation within brain areas (Fig. S1).”

      - How many filters were used here?

      No input filters were used for this simulation:

      We used 5 min of “resting state” activity (no added stimulus, simulated at 0.1ms resolution, subsequently downsampled to 100Hz). 

      c) Intracranial EEG:

      - It's not clear how overfitting was measured and how the selection of the number of filters (n_a and n_b) was done.

      We have removed the statement about overfitting. Mostly the word is used in the context of testing on a separate dataset, which we did not do here. So this “overfitting” can be confusing. Instead we used the analytic p-value as indication that a larger model order is not supported by the data. We write this now as follows: 

      “Increasing the number of delays n<sub>a</sub>, increases estimated effect size R (Fig. S3A,B), however, larger values lead to fewer significant connections (Fig. S3C). Significance (p-value) is computed analytically, i.e. non-parametrically, based on deviance. Values around n<sub>a</sub>=6 time delays appear to be the largest model order supported by this statistical analysis.”

      d) Figure 1:

      - Typo: "auto-regressive"

      Fixed. Thanks for catching that. 

      - LFP and BHA in C are defined much later in the text, would be useful to define these in the caption. o Shouldn't B (the VARX model parameter) be a 2x3 matrix for different time lags?

      Hopefully the following clarifications address both these points: 

      “C) Example of neural signal y(t) recorded at a single location in the brain. We will analyze local field potentials (LFP) and broad-band high frequency activity (BHA) in separate analyses.  D) Examples of filters B for individual feed-forward connections between an extrinsic input and a specific recording location in the brain.”

      (6) Discussion:

      I could not find Muller et al 2016 listed in the references.

      Added. Thanks for catching that omission. 

      Additional edits prompted by reviewers, but not in the context of any particular comment.

      While reviewers did not raise this following point, we felt the need clarify the terminology in the Methods to make sure there is not misunderstanding in the proposed interpretation of the model: 

      “We will refer to the filters in matrix A and B and as recurrent and feed-forward “connections”, but avoid the use of the word “causal” which can be misleading.”

      In addressing questions to Figure 4, we noticed that there is quite a bit of variability across patients, so the analysis for Figure 4 and 7 which combines data across patients now accounts for a random effect of patient (previously we have used mean values for repeated measures). We added the following to the Methods to explain this:

      “To compare recurrent connectivity between movies and the resting-state (in Fig. 4), we compute VARX models in four different movie segments of 5 minutes length to match the length of the resting state recording. We use the first and second half of ‘Despicable Me English’, the first half of ‘Inscapes’ and one of the ‘Monkey’ movies. 18 patients include each of these recordings. For each recording in each patient we compute the fraction of significant channels (p<0.001) and average the effect size R across all channel pairs, excluding the diagonal. We test the difference between movies and resting-state with linear mixed-effect models with stimulus as fixed effect (movie vs rest), and patient as random effect (to account for the repeated measures for the different video segments), using matlab’s fitlme() routine. For the analysis of asymmetry of recurrent connectivity (in Fig. 4) we also used a mixed-effect model with T1w/T2w ratio as fixed effect and patients as random effect (to account for the repeated measures in multiple brain locations).”

      All analyses were rerun with more data (eyes closed resting) and 2 additional patients that have become available since the first submission. Therefore all figures and statistics have been updated throughout the paper. Other than the difference between movies and resting state which was trending before and is now significant, no results changed.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1:

      Comment 0: Summary: This work presents an Interpretable protein-DNA Energy Associative (IDEA) model for predicting binding sites and affinities of DNA-binding proteins. Experimental results demonstrate that such an energy model can predict DNA recognition sites and their binding strengths across various protein families and can capture the absolute protein-DNA binding free energies.

      We appreciate the reviewer’s careful assessment of the paper, and we thank the reviewer for the insightful suggestions and comments.

      Comment 1: Strengths: (1) The IDEA model integrates both structural and sequence information, although such an integration is not completely original. (2) The IDEA predictions seem to have agreement with experimental data such as ChIP-seq measurements.

      We appreciate the reviewer’s positive comments on the strength of the paper.

      Comment 2: Weaknesses: (1) The authors claim that the binding free energy calculated by IDEA, trained using one MAX-DNA complex, correlates well with experimentally measured MAX-DNA binding free energy (Figure 2) based on the reported Pearson Correlation of 0.67. However, the scatter plot in Figure 2A exhibits distinct clustering of the points and thus the linear fit to the data (red line) may not be ideal. As such. the use of the Pearson correlation coefficient that measures linear correlation between two sets of data may not be appropriate and may provide misleading results for non-linear relationships.

      We thank the reviewer for the insightful comments and agree that a linear fit between our predictions and the experimental data may not be the best measure of performance. The primary utility of the IDEA model is to predict high-affinity DNA-binding sequences for a given DNA-binding protein by assessing the relative binding affinities across different DNA sequences. In this regard, the ranked order of predicted sequence binding affinities serves as a better metric for evaluating the success of this model. To evaluate this, we calculated both Spearman’s rank correlation coefficient, which does not rely on linear correlation, and the Pearson correlation coefficient between our predictions and the experimental results. As shown in Figure 2, our computation shows a Spearman’s rank correlation coefficient of 0.65 for the MAX-based predictions using one MAX-DNA complex (PDB ID: 1HLO), supporting the model’s capability to effectively distinguish strong from weak binders.

      Although our model generally captures the relative binding affinities across different DNA sequences, its predictive accuracy diminishes for low-affinity sequences (Figure 2).

      This could be due to two limitations of the current modeling framework: (1) The model is residue-based and estimates binding free energy as the additive sum of contributions from individual contacting amino-acid-nucleotide pairs. This assumption does not account for cooperative effects caused by simultaneous changes at multiple nucleotide positions. One potential direction to further improve the model would be to use a finergrained representation by incorporating more atom types within contacting residues, and to use a many-body potential to better capture cooperative effects from multiple mutations. (2) The model assumes that the target DNA adopts the same binding interface as in the reference crystal structure. However, sequence-dependent DNA shape has been shown to be important in determining protein-DNA binding affinity [1]. To address this limitation, a future direction is to use deep-learning-based methods to incorporate predicted DNA shape or protein-DNA complex structures based on their sequences [2, 3] into our model prediction.

      To fully evaluate the predictive power of IDEA, we have included Spearman’s rank correlation coefficient for every correlation plot in this manuscript and have updated the relevant texts. Across all our analyses, the Spearman’s rank correlation coefficients reveal similar predictive performance as the Pearson correlation coefficients. Additionally, we have included in our discussion the current limitations of our model and potential directions for future improvement.

      We have edited our Discussion Section to include a discussion on the limitations of the current model. Specifically, the added texts are:

      “Although IDEA has proved successful in many examples, it can be improved in several aspects. The model currently assumes the training and testing sequences share the same protein-DNA structure. While double-stranded DNA is generally rigid, recent studies have shown that sequence-dependent DNA shape contributes to their binding specificity [1, 2, 4]. To improve predictive accuracy, one could incorporate predicted DNA shapes or structures into the IDEA training protocol. In addition, the model is residue-based and evaluates the binding free energy as the additive sum of contributions from individual amino-acid-nucleotide contacts. This assumption does not account for cooperative effects that may arise from multiple nucleotide changes. A potential refinement could utilize a finer-grained model that includes more atom types within contacting residues and employs a many-body potential to account for such cooperative effects.”

      Comment 3: (2) In the same vein, the linear Pearson Correlation analysis performed in Figure 5A and the conclusion drawn may be misleading.

      We thank the reviewer for the insightful comments. As noted in our response to the previous comment, we have added Spearman’s rank correlation coefficient in addition to the Pearson correlation coefficient to all correlation plots, including Figure 5A.

      Comment 4: (3) The authors included the sequences of the protein and DNA residues that form close contacts in the structure in the training dataset, whereas a series of synthetic decoy sequences were generated by randomizing the contacting residues in both the protein and DNA sequences. In particular, synthetic decoy binders were generated by randomizing either the DNA (1000 sequences) or protein sequences (10,000 sequences) from the strong binders. However, the justification for such randomization and how it might impact the model’s generalizability and transferability remain unclear.

      We thank the reviewer for the insightful comments. The number of randomizing sequences was chosen to strike a balance between sufficient sequence coverage and computational feasibility. Because proteins have more types of amino acids than four nucleotides in DNA, we utilized more protein decoy sequences than DNA decoys. To examine the robustness of our choice against different number of decoy sequences, we repeated the transferability analysis within the bHLH superfamily (Figure 3A) and the generalizability analysis across 12 protein families (Figure 2E) using two additional decoy sequence combinations: (1) 1000 DNA sequences and 1000 protein sequences; (2) 100 DNA sequences and 1000 protein sequences. As shown in Figure S15, we achieved similar results to those reported using the original decoy set, demonstrating the robustness of our model prediction against the variations in the number of decoys. We have included this figure as Figure S15.

      Comment 5: (4) The authors performed Receiver Operating Characteristic (ROC) analysis and reported the Area Under the Curve (AUC) scores in order to quantitate the successful identification of the strong binders by IDEA. It would be beneficial to analyze the precision-recall (PR) curve and report the PRAUC metric which could be more robust.

      We agree with the reviewer that more robust statistical metrics should be used to evaluate our model’s performance. We have included the PRAUC score as an additional evaluation metric of the model’s performance. Due to a significant imbalance in the number of strong and weak binders from the experimental data [5], where the experimentally identified strong binders are far fewer than the weak binders, we reweighted the sample to achieve a balanced evaluation [6], using 0.5 as the baseline for randomized prediction. As shown in Figure S5, IDEA achieves successful predictions in 18 out of 22 cases, demonstrating its predictive accuracy.

      The updated PRAUC result has been included as Figure S5 in the manuscript. We have also included the detailed precision-recall curves for each case in Figure S4.

      In addition, we have provided PRAUC scores for comparing the performance of IDEA with other models, and have summarized these results in Table S2.

      Reviewer #2:

      Comment 0: Summary: Zhang et al. present a methodology to model protein-DNA interactions via learning an optimizable energy model, taking into account a representative bound structure for the system and binding data. The methodology is sound and interesting. They apply this model for predicting binding affinity data and binding sites in vivo. However, the manuscript lacks discussion of/comparison with state-of-the-art and evidence of broad applicability. The interpretability aspect is weak, yet over-emphasized.

      We appreciate the reviewer’s excellent summary of the paper, and we thank the reviewer for the insightful suggestions and comments.

      Comment 1: Strengths: The manuscript is well organized with good visualizations and is easy to follow. The methodology is discussed in detail. The IDEA energy model seems like an interesting way to study a protein-DNA system in the context of a given structure and binding data. The authors show that an IDEA model trained on one system can be transferred to other structurally similar systems. The authors show good performance in discriminating between binding-vs-decoy sequences for various systems, and binding affinity prediction. The authors also show evidence of the ability to predict genome-wide binding sites.

      We appreciate the reviewer’s strong assessment of the strengths of this paper. We have further refined our Methods Section to ensure all modeling details are clearly presented.

      Comment 2: Weaknesses: An energy-based model that needs to be optimized for specific systems is inherently an uncomfortable idea. Is this kind of energy model superior to something like Rosetta-based energy models, which are generally applicable? Or is it superior to family-specific knowledge-based models? It is not clear.

      We thank the reviewer for the insightful comments. The protein-DNA energy model facilitates the calculation of protein-DNA binding free energy based on protein-DNA structures and sequences. Because this model is optimized using the structure-sequence relationship of given protein-DNA complexes, it features specificity based on the conserved structural interface characteristic of each protein family. Because of that, its predictive accuracy depends on the degree of protein-DNA interface similarity between the training and target protein-DNA pairs, and is distinct from a general protein-DNA energy model, such as a Rosetta-based energy model. The model has some connections to the familyspecific energy model. As shown in Author response image 1, systems belonging to the same protein superfamily (MAX and PHO4) exhibit similar patterns in their learned energy models, in contrast to those from a different superfamily (PDX1).

      Author response image 1:

      Comparison of learned energy models for different protein-DNA complexes: MAX (A), PHO4 (B), and PDX1 (C). MAX and PHO4 are members of the Helixloop-helix (HLH) CATH protein superfamily (4.10.280.100), while PDX1 belongs to another Homeodomain-like CATH protein superfamily (1.10.10.60).

      To compare our approach with both general and family-specific knowledge-based energy models, we conducted two studies. First, we incorporated a knowledge-based generic protein-DNA energy model (DBD-Hunter) learned from the protein-DNA database, reported by Skoinick and coworkers [7], into our prediction protocol. This model assigns interaction energies to different functional groups within each DNA nucleotide (e.g., phosphate (PP), sugar (SU), pyrimidine (PY), and imidazole (IM) groups). For our comparison, we averaged the energy contributions of these groups within each nucleotide and replaced the IDEA-learned energy model with this generic one to test its ability to differentiate strong binders from weak binders in the HT-SELEX dataset [5]. As shown in Figure S6, the IDEA model generally achieves better performance than the generic energy model.

      Additionally, we compared IDEA with rCLAMPS, a family-specific energy model developed to predict protein-DNA binding specificity in the C2H2 and homeodomain families.

      As shown in Table S1 and Table S2, IDEA also shows better performance than rCLAMPS in most cases across the C2H2 and homeodomain families, demonstrating that it has better predictive accuracy than both state-of-the-art family-specific and generic knowledgebased models.

      We have included relevant texts in Appendix Section Comparison of IDEA predictive performance Using HT-SELEX data to clarify this point. The added texts are:

      In addition, we compared the performance of IDEA with both general and family-specific knowledge-based energy models. First, we incorporated a knowledgebased generic protein-DNA energy model (DBD-Hunter) learned from the protein-DNA database, reported by Skoinick and coworkers [7], into our prediction protocol. This model assigns interaction energies to different functional groups within each DNA nucleotide, including phosphate (PP), sugar (SU), pyrimidine (PY), and imidazole (IM) groups. For our comparison, we averaged the energy contributions of these groups within each nucleotide and replaced the IDEA-learned energy model with the DBD-Hunter model to assess its ability to differentiate strong binders from weak binders in the HTSELEX dataset [5]. Additionally, we compared IDEA with rCLAMPS, a familyspecific energy model developed to predict protein-DNA binding specificity in the C2H2 and homeodomain families. rCLAMPS learns a position-dependent amino-acid-nucleotide interaction energy model. To incorporate this model into the binding free energy calculation, we averaged the energy contributions across all occurrences of each amino-acid-nucleotide pair, which resulted in a 20-by-4 residue-type-specific energy matrix. This matrix is structurally analogous to the IDEA-trained energy model and can be directly integrated into the binding free energy calculations. As shown in Figure S6, Table S1, and Table S2, the IDEA model generally outperforms DBD-Hunter and rCLAMPS, demonstrating that it can achieve better predictive accuracy than both generic and family-specific knowledge-based models.

      Comment 3: Prediction of binding affinity is a well-studied domain and many competitors exist, some of which are well-used. However, no quantitative comparison to such methods is presented. To understand the scope of the presented method, IDEA, the authors should discuss/compare with such methods (e.g. PMID 35606422).

      We thank the reviewer for the insightful comments. As detailed in our response to Comment 5, we previously misused the term “binding specificity”, and would like to clarify that our model is designed to predict protein-DNA binding affinity. To compare the performance of IDEA with state-of-the-art protein-DNA predictive models, we examined the predictive accuracies of two additional popular computational models: ProBound [8] and DeepBind [9]. ProBound has been shown to have a better performance than several earlier predictive protein-DNA models, including JASPAR 2018 [11], HOCOMOCO [12], Jolma et al. [13], and DeepSELEX [14]. To benchmark these models’ performance, we examine each method’s capability to identify strong binders with the HT-SELEX datasets covering 22 proteins from 12 protein families [5]. As suggested by Reviewer 1, we also calculated the PRAUC score, reweighted to account for data imbalance [6], as a complementary metric for evaluating the model performance.

      As shown in Figure S6, Table S1, and Table S2, IDEA ranked second among the three predictive methods. It is important to note that both ProBound and DeepBind were trained on a curated version of the HT-SELEX data [13], which overlaps with the testing data [5]. Compared with them, IDEA was trained only on the given structural and sequence information from a single protein-DNA complex, thus independent of the testing data. In order to assess how IDEA performs when incorporating knowledge from HT-SELEX data, we augmented the training by randomly including half of the HT-SELEX data (see the Methods Section Enhanced Modeling Prediction with SELEX Data). The augmented IDEA model achieved the best performance among all the models. Overall, IDEA can be used to predict protein-DNA affinities in the absence of known binding sequence data, thereby filling a critical gap when such experimental datasets are unavailable.

      Additionally, we have conducted a 10-fold cross-validation using the same HT-SELEX data [5] and found that IDEA outperformed a recent regression model that considers the shape of DNA with different sequences [5].

      We have revised our text to include the comparison between IDEA and other predictive models. Specifically, we revised the text in Section: IDEA Generalizes across Various Protein Families.

      The revised text reads:

      “To examine IDEA’s predictive accuracy across different DNA-binding protein families, we applied it to calculate protein-DNA binding affinities using a comprehensive HT-SELEX dataset [5]. We focused on evaluating the capability of IDEA to distinguish strong binders from weak binders for each protein with an experimentally determined structure. We calculated the probability density distribution of the top and bottom binders identified in the SELEX experiment. A well-separated distribution indicates the successful identification of strong binders by IDEA (Figure 2D and S4). Receiver Operating Characteristic (ROC) analysis was performed to calculate the Area Under the Curve (AUC) and the precision-recall curve (PRAUC) scores for these predictions. Further details are provided in the Methods Section Evaluation of IDEA Prediction Using HT-SELEX Data. Our analysis shows that IDEA successfully differentiates strong from weak binders for 80% of the 22 proteins across 12 protein families, achieving AUC and balanced PRAUC scores greater than 0.5 (Figure 2D and S5). To benchmark IDEA’s performance against other leading methods, we compared its predictions with several popular models, including the sequence-based predictive models ProBound [8] and DeepBind [9], the familybased energy model rCLAMPS [10], and the knowledge-based energy model DBD-Hunter [7]. IDEA demonstrates performance comparable to these stateof-the-art approaches, and incorporating sequence features further improves its prediction accuracy (Figure S6, Table S1, and Table S2). We also performed 10-fold cross-validation on the binding affinities of protein–DNA pairs in this dataset and found that IDEA outperforms a recent regression model that considers the shape of DNA with different sequences [5] (Figure S7). Details are provided in Section: Comparison of IDEA predictive performance Using HT-SELEX data.”

      We also added one section Comparison of IDEA predictive performance Using HT-SELEX data in the Appendix to fully explain the comparison between IDEA and other popular models. The added texts are:

      “To benchmark the performance of IDEA against state-of-the-art protein-DNA predictive models, we evaluated its ability to recognize strong binders with the HT-SELEX datasets across 22 proteins from 12 families [5]. Specifically, we compare IDEA with two widely used sequence-based models: ProBound [8] and DeepBind [9]. ProBound has demonstrated superior performance over many other predictive protein-DNA models, including JASPAR 2018 [11], HOCOMOCO [12], Jolma et al. [13], and DeepSELEX [14]. To use ProBound, we retrieved the trained binding model for each protein from motifcentral.org and used the GitHub implementation of ProBoundTools to infer the binding scores between protein and target DNA sequences. Except for POU3F1, binding models are available for all proteins. Therefore, we excluded POU3F1 and evaluated the protein-DNA binding affinities for the remaining 21 proteins. To use DeepBind, sequence-specific binding affinities were predicted directly with its web server. The Area Under the Curve (AUC) and the Precision-Recall AUC (PRAUC) scores were used as metrics for comparison. An AUC score of 1.0 indicates a perfect separation between the strong- and weak-binder distributions, while an AUC score of 0.5 indicates no separation. Because there is a significant imbalance in the number of strong and weak binders from the experimental data [5], where the strong binders are far fewer than the weak binders, we reweighted the samples to achieve a balanced evaluation, using 0.5 as the baseline for randomized prediction [6]. As summarized in Figure S6, Table S1, and Table S2, IDEA ranked second among the three predictive models. In order to assess the performance of IDEA when augmented with additional protein-DNA binding data, we augmented IDEA using randomly selected half of the HT-SELEX data (see the Methods Section Enhanced Modeling Prediction with SELEX Data). The augmented IDEA model achieved the best performance among all the models.”

      “We also performed 10-fold cross-validation using the same HT-SELEX datasets, following the protocol described in the Methods Section Enhanced Modeling Prediction with SELEX Data. For each protein, we divided the entire dataset into 10 equal, randomly assigned folds. In each iteration, we used randomly selected 9 of the 10 folds as the training dataset and the remaining fold as the testing dataset. This process was repeated 10 times so that each fold served as the test set once. We then reported the average R2 scores across these iterations to evaluate IDEA’s predictive performance. Our results are compared with the 1mer and 1mer+shape methods from [5], the latest regression model that considers the shape of DNA with different sequences (Figure S7). This comparative analysis shows IDEA achieved higher predictive accuracy than the state-of-the-art sequence-based protein-DNA binding predictors for proteinDNA complexes that have available experimentally resolved structures.”

      “Overall, these results demonstrate that IDEA can be used to predict the proteinDNA pairs in the absence of known binding sequence data, thus filling an important gap in protein-DNA predictions when experimental binding sequence data are unavailable.”

      Comment 4: The term “interpretable” has been used lavishly in the manuscript while providing little evidence on the matter. The only evidence shown is the family-specific residue-nucleotide interaction/energy matrix and speculations on how these values are biologically sensible. Recent works already present more biophysical, fine-grained, and sometimes family-independent interpretability (e.g. PMID 39103447, 36656856, 38352411, etc.). The authors should put into context the scope of the interpretability of IDEA among such works.

      We thank the reviewer for the insightful comment and agree that “interpretability” should be discussed in a relevant context. In our work, interpretability refers to the familyspecific amino-acid-nucleotide interaction energies identified from the model training, which reveal interaction preferences within protein-DNA binding interfaces. As detailed in our response to Comment 6, we performed principal component analysis (PCA) on the learned energy models and observed clustering of learned energy models corresponding to protein families. Therefore, the IDEA-learned energy models can be used as a signature to capture the energetic preferences of amino-acid-nucleotide interactions within a given protein family. This preference can be used to infer preferred sequence binding motifs, similar to those identified by other computational tools [10, 4, 15, 16].

      We have revised the text to clarify the “interpretability” as the family-specific aminoacid-nucleotide interactions that govern sequence-dependent protein-DNA binding, and to discuss IDEA’s interoperability within the context of recent works, including those suggested by the reviewers.

      We have revised the text in Introduction. The new text reads:

      “Here, we introduce the Interpretable protein-DNA Energy Associative (IDEA) model, a predictive model that learns protein-DNA physicochemical interactions by fusing available biophysical structures and their associated sequences into an optimized energy model (Figure 1). We show that the model can be used to accurately predict the sequence-specific DNA binding affinities of DNA-binding proteins and is transferrable across the same protein superfamily. Moreover, the model can be enhanced by incorporating experimental binding data and can be generalized to enable base-pair resolution predictions of genomic DNA-binding sites. Notably, IDEA learns a family-specific interaction matrix that quantifies energetic interactions between each amino acid and nucleotide, allowing for a direct interpretation of the “molecular grammar” governing sequence-specific protein-DNA binding affinities. This interpretable energy model is further integrated into a simulation framework, facilitating mechanistic studies of various biomolecular functions involving protein-DNA dynamics.”

      We have revised the text in Results. The new text reads:

      “IDEA is a coarse-grained biophysical model at the residue resolution for investigating protein-DNA binding interactions (Figure 1). It integrates both structures and corresponding sequences of known protein-DNA complexes to learn an interpretable energy model based on the interacting amino acids and nucleotides at the protein-DNA binding interface. The model is trained using available protein-DNA complexes curated from existing databases [17, 18].

      Unlike existing deep-learning-based protein-DNA binding prediction models, IDEA aims to learn a physicochemical-based energy model that quantitatively characterizes sequence-specific interactions between amino acids and nucleotides, thereby interpreting the “molecular grammar” driving the binding energetics of protein-DNA interactions. The optimized energy model can be used to predict the binding affinity of any given protein-DNA pair based on its structures and sequences. Additionally, it enables the prediction of genomic DNA binding sites by a given protein, such as a transcription factor. Finally, the learned energy model can be incorporated into a simulation framework to study the dynamics of DNA-binding processes, revealing mechanistic insights into various DNA-templated processes. Further details of the optimization protocol are provided in Methods Section Energy Model Optimization.”

      The revised text in Section: Discussion now reads:

      “Another highlight of IDEA is its ability to present an interpretable, familyspecific amino acid-nucleotide interaction energy model for given proteinDNA complexes. The optimized IDEA energy model can not only predict sequence-specific binding affinities of protein-DNA pairs but also provide a residue-specific interaction matrix that dictates the preferences of amino acidnucleotide interactions within specific protein families (Figure S11). This interpretable energy matrix would facilitate the discovery of sequence binding motifs for target DNA-binding proteins, complementing both sequencebased [24, 16, 25] and structure-based approaches [10, 26, 4, 15]. Additionally, we integrated this physicochemical-based energy model into a simulation framework, thereby improving the characterization of protein-DNA binding dynamics. IDEA-based simulation enables the investigation into dynamic interactions between various proteins and DNA, facilitating molecular-level understanding of the physical mechanisms underlying many DNA-binding processes, such as transcription, epigenetic regulations, and their modulation by sequence variations, such as single-nucleotide polymorphisms (SNPs) [22, 23].”

      Comment 5: The manuscript disregards subtle yet important differences in commonly used terminology in the field. For example, the authors use the term ”specificity” and ”affinity” almost interchangeably (for example, the caption for Figure 3A uses ”specificity” although the Methods text describes the prediction as about ”affinity”). If the authors are looking to predict specificity, IDEA needs to be put in the context of the corresponding state-of-the-art (PMID 36123148, 39103447, 38867914, 36124796, etc).

      We really appreciate the reviewer for pointing out the conflation of “specificity” and “affinity” in our manuscript. To clarify, the primary function of IDEA is to predict the binding affinities of protein-DNA pairs in a sequence-specific manner. We have revised the text to clarify the distinction between affinity and specificity and acknowledge prior works, including those provided by the reviewers, that focus on predicting protein-DNA binding specificity.

      We have revised the Section title IDEA Accurately Predicts Protein-DNA Binding Specificity to IDEA Accurately Predicts Sequence-Specific Protein-DNA Binding Affinity; and ResidueLevel Protein-DNA Energy Model for Predicting Protein-DNA Recognition Specificities to Predictive Protein-DNA Energy Model at Residue Resolution.

      We have revised the text in Introduction. The revised text reads:

      “Computational methods complement experimental efforts by providing the initial filter for assessing sequence-specific protein-DNA binding affinity. Numerous methods have emerged to enable predictions of binding sites and affinities of DNA-binding proteins [27, 9, 1, 5, 28, 29, 30, 31, 8]. These methods often utilized machine-learning-based training to extract sequence preference information from DNA or protein by utilizing experimental high-throughput (HT) assays [27, 9, 1, 5, 28, 8], which rely on the availability and quality of experimental binding assays. Additionally, many approaches employ deep neural networks [29, 30, 31], which could obscure the interpretation of interaction patterns governing protein-DNA binding specificities. Understanding these patterns, however, is crucial for elucidating the molecular mechanisms underlying various DNA-recognition processes, such as those seen in TFs [32].”

      We have revised the text in Section: IDEA Demonstrates Transferability across Proteins in the Same CATH Superfamily.

      The revised text reads:

      “Since IDEA relies on the sequence-structure relationship of given protein-DNA complexes to reach predictive accuracy, we inquired whether the trained energy model from one protein-DNA complex could be generalized to predict the sequence-specific binding affinities of other complexes. To test this, we assessed the transferability of IDEA predictions across all 11 structurally available protein-DNA complexes within the MAX TF-associated CATH superfamily (CATH ID: 4.10.280.10, Helix-loop-helix DNA-binding domain). We trained IDEA based on each of these 11 complexes and then used the trained model to predict the MAX-based MITOMI binding affinity. Our results show that IDEA generally makes correct predictions of the binding affinity when trained on proteins that are homologous to MAX, with Pearson and Spearman Correlation coefficients larger than 0.5 (Figure 3A and Figure S10).”

      We have revised the caption of Figure 3: The revised text reads:

      “IDEA prediction shows transferability within the same CATH superfamily. (A) The predicted MAX binding affinity, trained on other protein-DNA complexes within the same protein CATH superfamily, correlates well with experimental measurement. The proteins are ordered by their probability of being homologous to the MAX protein, determined using HHpred [33]. Training with a homologous protein (determined as a hit by HHpred) usually leads to better predictive performance (Pearson Correlation coefficient > 0.5) compared to non-homologous proteins. (B) Structural alignment between 1HLO (white) and 1A0A (blue), two protein-DNA complexes within the same CATH Helix-loop-helix superfamily. The alignment was performed based on the Ebox region of the DNA [34]. (C) The optimized energy model for 1A0A, a protein-DNA complex structure of the transcription factor PHO4 and DNA, with 33.41% probability of being homologous to the MAX protein. The optimized energy model is presented in reduced units, as explained in the Methods Section: Training Protocol.”

      We have revised the text in Section Discussion: The revised text now reads:

      “The protein-DNA interaction landscape has evolved to facilitate precise targeting of proteins towards their functional binding sites, which underlie essential processes in controlling gene expression. These interaction specifics are determined by physicochemical interactions between amino acids and nucleotides. By integrating sequences and structural data from available proteinDNA complexes into an interaction matrix, we introduce IDEA, a data-driven method that optimizes a system-specific energy model. This model enables high-throughput in silico predictions of protein-DNA binding specificities and can be scaled up to predict genomic binding sites of DNA-binding proteins, such as TFs. IDEA achieves accurate de novo predictions using only proteinDNA complex structures and their associated sequences, but its accuracy can be further enhanced by incorporating available experimental data from other binding assay measurements, such as the SELEX data [35, 36, 37], achieving accuracy comparable or better than state-of-the-art methods (Figures S2 and S7, Table S1 and S2). Despite significant progress in genome-wide sequencing techniques [38, 39, 40, 41], determining sequence-specific binding affinities of DNA-binding biomolecules remains time-consuming and expensive. Therefore, IDEA presents a cost-effective alternative for generating the initial predictions before pursuing further experimental refinement.”

      We have revised the text in Discussion to clarify that the acquired binding affinities of target DNA sequences can be used to help existing models to infer specific DNA binding motifs.

      The revised text now reads:

      Another highlight of IDEA is its ability to present an interpretable, familyspecific amino acid-nucleotide interaction energy model for given proteinDNA complexes. The optimized IDEA energy model can not only predict sequence-specific binding affinities of protein-DNA pairs but also provide a residue-specific interaction matrix that dictates the preferences of amino acidnucleotide interactions within specific protein families (Figure S11). This interpretable energy matrix would facilitate the discovery of sequence binding motifs for target DNA-binding proteins, complementing both sequencebased [24, 16, 25] and structure-based approaches [10, 26, 4, 15]. Additionally, we integrated this physicochemical-based energy model into a simulation framework, thereby improving the characterization of protein-DNA binding dynamics. IDEA-based simulation enables the investigation into dynamic interactions between various proteins and DNA, facilitating molecular-level understanding of the physical mechanisms underlying many DNA-binding processes, such as transcription, epigenetic regulations, and their modulation by sequence variations, such as single-nucleotide polymorphisms (SNPs) [22, 23].

      Comment 6: It is not clear how much the learned energy model is dependent on the structural model used for a specific system/family. It would be interesting to see the differences in learned model based on different representative PDB structures used. Similarly, the supplementary figures show a lack of discriminative power for proteins like PDX1 (homeodomain family), POU, etc. Can the authors shed some light on why such different performances?

      We thank the reviewer for the insightful comments and agree that the trained energy model should be presented in the context of protein families. To further analyze the dependence of the energy model on protein family, we visualized the trained energy models for 24 proteins, including all proteins from the HT-SELEX dataset as well as PHO4 (PDB ID: 1A0A) and CTCF (PDB ID: 8SSQ), spanning 12 distinct protein families. To quantitatively assess similarities and differences among these energy models, we flattened each normalized energy model into an 80-dimensional vector and performed principal component analysis (PCA). As shown in Author response image 1 and Figure S11, energy models optimized from the same protein family fall within the same cluster, while those from different protein families exhibit distinct patterns. Moreover, the relative distance between energy models in PCA space reflects the degree of transferability. For example, PHO4 (PDB ID: 1A0A) is positioned close to MAX (PDB ID: 1HLO), whereas USF1 (PDB ID: 1AN4) and TCF4 (PDB ID: 6OD3) are farther away. This is consistent with the results shown in Figure 3A, where the energy model trained from PHO4 has better transferability than those from the other two systems.

      We also greatly appreciate the reviewer’s suggestion to examine cases where IDEA failed to demonstrate strong discriminative power. When evaluating the model’s ability to distinguish between strong and weak binders, we used the available experimental structure most similar to the protein employed in the HT-SELEX experiments. In some instances, only the structure of the same protein from a different organism is available. For example, the HT-SELEX data for PDX1-DNA used the human PDX1 protein, but no human PDX1–DNA complex structure is available. Therefore, we used the mouse PDX1–DNA complex (PDB ID: 2H1K) for model training. The differences between species may limit the predictive accuracy of the model. A similar limitation applies to POU3F1, where an available mouse complex (PDB ID: 4Y60) was used to predict human protein–DNA interactions. Notably, DeepBind [9], a sequence-based prediction tool, also failed to distinguish strong from weak binders when using the mouse POU3F1 protein (AUC score: 0.457), but this was corrected with the human POU3F1 protein (AUC score: 0.956).

      We also examined the remaining cases where IDEA did not show a clear distinction between strong and weak binders: USF1, Egr1, and PROX1. For PROX1, we initially used the structure of a protein-DNA complex (PDB ID: 4Y60) in training. However, upon closer inspection, we discovered that this structure does not include the PROX1 protein, but SOX-18, a different transcription factor. This explains the inaccurate prediction made by IDEA. Since no experimental PROX1-DNA complex structure is currently available, we have removed this case from our HT-SELEX evaluation.

      IDEA also fails to fully resolve the binding preference of USF1. A closer examination of the HT-SELEX data reveals a lack of distinction among the sequences, as most sequences, including those with the lowest M-word (binding affinity) scores, contain the DNA-binding E-box sequence CACGTG. Therefore, USF1 represents a challenging example where the experimental data only consists of strong binders with limited variations in binding affinity, which likely results from differences in flanking sequences of the E-box motif.

      Egr1 stands as a peculiar example. Whereas IDEA does not effectively distinguish between the strong and weak binders in the current HT-SELEX dataset, its predictions are consistent with other experimental datasets, including binding affinities measured by kMITOMI [42] (Figure S8A, B), preferred binding sequences from protein-binding microarray, an earlier HT-SELEX experiment, and bacterial one-hybrid data [43]. Therefore, further investigation of the current HT-SELEX data is needed to reconcile these differences.

      We have included additional text in Section: IDEA Demonstrates Transferability across Proteins in the Same CATH Superfamily to discuss the PCA analysis and the dependence of the model’s transferability on the similarity among the learned energy models.

      The revised text now reads:

      “The transferability of IDEA within the same CATH superfamily can be understood from the similarities in protein-DNA binding interfaces, which determine similar learned energy models. For example, the PHO4 protein (PDB I”D: 1A0A) shares a highly similar DNA-binding interface with the MAX protein (PDB ID: 1HLO) (Figure 3B), despite sharing only a 33.41% probability of being homologous. Consequently, the energy model derived from the PHO4DNA complex (Figure 3C) exhibits a similar amino-acid-nucleotide interactive pattern as that learned from the MAX-DNA complex (Figure 2B). To further evaluate the similarity between the learned energy models and their connection to protein families, we performed principal component analysis (PCA) on the normalized energy models across 24 proteins from 12 protein families [5]. Our analysis (Figure S11) reveals that most of the energy models from the same protein family fall within the same cluster, while those from different protein families exhibit distinct patterns. Moreover, the relative distance between energy models in PCA space reflects the degree of transferability between them. For example, PHO4 (PDB ID: 1A0A) is positioned close to MAX (PDB ID: 1HLO), whereas USF1 (PDB ID: 1AN4) and TCF4 (PDB ID: 6OD3) are farther away. This is consistent with the results in Figure 3A, where the energy model trained on PHO4 has better transferability than those trained on USF1 or TCF4.”

      We have also added an Appendix section titled Analysis of examples where IDEA fails to recognize strong DNA binders to discuss the examples in which IDEA did not perform well:

      “We examine IDEA’s capability in identifying strong binders from the HT-SELEX dataset across 12 protein families [5]. The model successfully predicts 18 out of 22 protein-DNA systems, but the performance is reduced in 4 cases. Closer investigations revealed the source of these limitations. In some instances, only the protein from a different organism is available. For example, the PDX1 HT-SELEX data utilized the human PDX1 protein, but no human PDX1–DNA complex structure is available. Therefore, the mouse PDX1–DNA complex structure (PDB ID: 2H1K) was used for model training. Differences between model organisms may reduce predictive accuracy. A similar limitation applies to POU3F1, where an available mouse complex (PDB ID: 4Y60) was used to predict human protein–DNA interactions. Notably, DeepBind [9], a sequence-based prediction tool, also failed to distinguish strong from weak binders when using the mouse POU3F1 protein (AUC score: 0.457), but this was corrected with the human POU3F1 protein (AUC score: 0.956).

      IDEA also fails to fully resolve the binding preference of USF1. A closer examination of the HT-SELEX data reveals a lack of distinction among the sequences, as most sequences, including those with the lowest M-word (binding affinity) scores, contain the DNA-binding E-box sequence CACGTG. Therefore, USF1 represents a challenging example where the experimental data only consists of strong binders with limited variations in binding affinity, which likely results from differences in flanking sequences of the E-box motif.

      Egr1 stands as a peculiar example. Whereas IDEA does not effectively distinguish between the strong and weak binders in the current HT-SELEX dataset, its predictions are consistent with other experimental datasets, including binding affinities measured by k-MITOMI [42] (Figure S8A, B), preferred binding sequences from protein-binding microarray, an earlier HT-SELEX experiment, and bacterial one-hybrid data [43]. Therefore, further investigation of the current HT-SELEX data is needed to reconcile these differences.”

      Comment 7: It is also not clear if IDEA’s prediction for reverse complement sequences is the same for a given sequence. If so, how is this property being modelled? Either this description is lacking or I missed it.

      We thank the reviewer for the insightful comments. Given a target protein-DNA sequence, the IDEA protocol substitutes it into a known protein-DNA complex structure to evaluate the binding free energy, which can be converted into binding affinity. IDEA uses sequence identity to determine whether the forward or reverse strand of the DNA should be replaced. Only the strand most similar to the target sequence is substituted. As a result, the model treats reverse-complement sequences differently. As the orientations of test sequences are specified from 5’ to 3’ in all datasets used in this study (e.g., processed MITOMI, HT-SELEX, and ChIP-seq data), this approach ensures that the target sequences are replaced and evaluated correctly. In cases where sequence orientation is not provided (though this was not an issue in this study), we recommend replacing both the forward and reverse strands with the target sequence separately and evaluating the corresponding protein–DNA binding free energies. Since strong binders are likely to dominate the experimental signals, the higher predicted binding affinity, with stronger binding free energies, should be taken as the model’s final prediction.

      We have added one section to the Methods Section titled Treatment of Complementary DNA Sequences to clarify these modeling details.

      The specific text reads:

      To replace the DNA sequence in the protein-DNA complex structure with a target sequence, IDEA uses sequence identity to determine whether the target sequence belongs to the forward or reverse strand of the DNA in the proteinDNA structure. The more similar strand is selected and replaced with the target sequence. As the orientations of test sequences are specified from 5’ to 3’ in all datasets used in this study (e.g., processed MITOMI, HT-SELEX, and ChIP-seq data), this approach ensures that the target sequences are replaced and evaluated correctly. In cases where sequence orientation is not provided (though this was not an issue in this study), we recommend replacing both the forward and reverse strands with the target sequence separately and evaluating the corresponding protein–DNA binding free energies. Since strong binders are likely to dominate the experimental signals, the higher predicted binding affinity, with stronger binding free energy, should be taken as the model’s final prediction.”

      “Comment 8: Page 21 line 403, the E-box core should be CACGTG instead of CACGTC.

      We apologize for our oversight and have corrected the relevant text.

      Comment 9: The citation for DNAproDB is outdated and should be updated (PMID 39494533).

      We thank the reviewer for pointing this out and have updated our citation accordingly.

      Reviewer #3:

      Comment 0: Summary: Protein-DNA interactions and sequence readout represent a challenging and rapidly evolving field of study. Recognizing the complexity of this task, the authors have developed a compact and elegant model. They have applied well-established approaches to address a difficult problem, effectively enhancing the information extracted from sparse contact maps by integrating artificial sequences decoy set and available experimental data. This has resulted in the creation of a practical tool that can be adapted for use with other proteins.

      We appreciate the reviewer’s excellent summary of the paper, and we thank the reviewer for the insightful suggestions and comments.

      Comment 1: Strengths: (1) The authors integrate sparse information with available experimental data to construct a model whose utility extends beyond the limited set of structures used for training. (2) A comprehensive methods section is included, ensuring that the work can be reproduced. Additionally, the authors have shared their model as a GitHub project, reflecting their commitment to transparency of research.

      We appreciate the reviewer’s strong assessment of the strengths of this paper. In addition to sharing our model on GitHub, we have also uploaded the original data and the essential scripts required to reproduce the results presented in the manuscript. We hope this further demonstrates our commitment to transparency and reproducibility.

      Comment 2: Weaknesses: (1) The coarse-graining procedure appears artificial, if not confusing, given that full-atom crystal structures provide more detailed information about residue-residue contacts. While the selection procedure for distance threshold values is explained, the overall motivation for adopting this approach remains unclear. Furthermore, since this model is later employed as an empirical potential for molecular modeling, the use of P and C5 atoms raises concerns, as the interactions in 3SPN are modeled between Cα and the nucleic base, represented by its center of mass rather than P or C5 atoms.

      We appreciate the reviewer’s insightful comments. The selection of P and C5 atoms was based on different relative positions of protein and DNA across various complex structures, each with distinctive protein-DNA structural interfaces. To illustrate this, we selected two representative structures where our algorithm selected C5 and P atoms, respectively: MAX-DNA (PDB ID: 1HLO) and FOXP3 (PDB ID: 7TDW). As shown in Author response image 2, in the case of 1HLO, more C5 atoms are within the cutoff distance of 10 A from˚ the protein Cα atoms, thus capturing essential contacting interactions. In contrast, 7TDW has more P atoms within this cutoff. Importantly, several P atoms are distributed on the minor groove of the DNA, which were not captured by the C5 atoms. To maximize the inclusion of relevant structural contacts, we employed a filtering scheme that selectively chooses either P or C5 atoms based on their proximity to the protein to enhance the model prediction. We note that while this scheme is helpful, the IDEA predictions remain robust across different atom selections. To assess this robustness, we performed binding affinity predictions using only P atoms on the HT-SELEX dataset across 12 protein families [5]. Our predictions (Author response table 1) show comparable performance to that achieved using our filtering scheme.

      Author response image 2.

      Comparison between P and C5 atoms in proximity to the protein 3D structures of MAX–DNA (A) and FOXP-DNA (B) complexes, where P atoms (red sphere) and C5 atoms (blue sphere) that are within 10 A of Cα atoms are highlighted.

      When incorporating the trained IDEA energy model into a simulation model, we acknowledge a potential mismatch between the resolution of the data-driven model (one coarse-grained site per nucleotide) and the 3SPN simulation model (three coarse-grained sites per nucleotide). The selection of nucleic base sites for molecular interactions in the 3SPN model follows our previous work [44] and its associated code implementation. While revisiting this part of the manuscript, we identified an inconsistency in the reported results in Figure 5A of our initial version: Specifically, we previously used the protein side-chain atoms, rather than only the Cα atoms, in model training. Retraining the data using the Cα atoms results in reduced prediction performance for the IDEA model (Figure 5A). Nonetheless, incorporating this updated energy model into simulations still yielded high accuracy in the predicted absolute binding free energies (Author response image 3A), demonstrating the robustness of our simulation framework in predicting absolute binding free energies against variations in atom selection during the IDEA model training. Following the reviewer’s suggestion, we also incorporated the IDEA-trained energy model as short-range van der Waals interactions between protein Cα atoms and DNA P atoms. As shown in Author response image 3B, our simulation reveals a slightly improved performance over our original implementation, with higher Pearson and Spearman correlation coefficients and a fitted slope closer to 1.0. This result suggests that a more consistent atom selection scheme between the data-driven and simulation models can improve the overall predictions. Accordingly, we have updated Figure 5 with this improved setup, using the simulation model with short-range vdW interactions implemented between protein Cα atoms and DNA P atoms (Figure 5C), ensuring consistency between the IDEA model and simulation framework.

      Author response table 1.

      Comparison of IDEA performance using two DNA atom selection schemes: the filtering scheme presented in the manuscript (C5 and P atoms) versus using only P atoms. Cases where the two schemes result in different atom selections are highlighted in bold.

      We acknowledge that a gap still exists between the resolution of the data-driven and simulation models. To ensure a completely consistent coarse-grained level between these two models, we will work on implementing the IDEA model output for 1-bead-per-nucleotide DNA simulation models in the future.

      Comment 3: (2) Although the authors use a standard set of metrics to assess model quality and predictive power, some ∆∆G predictions compared to MITOMI-derived ∆∆G values appear nonlinear, which casts doubt on the interpretation of the correlation coefficient.

      Author response image 3.

      Comparison of simulations using different representative atoms (A) Protein-DNA binding simulation with the IDEA-model incorporated as short-range van der Waals between protein Cα atom and nucleic base site. (B) Protein-DNA binding simulation with the IDEA-model incorporated as short-range van der Waals between protein Cα atom and DNA P atoms. The predicted free energies are robust to the choice of DNA representative atoms. The predicted binding free energies are presented in physical units, and error bars represent the standard deviation of the mean.

      We thank the reviewer for the insightful comments and agree that the linear fit between our model’s prediction and the experimental data may not be the best measure of performance. The primary utility of the IDEA model is to predict high-affinity DNA-binding sequences for a given DNA-binding protein by assessing the relative binding affinities across different DNA sequences. In this regard, the ranked order of predicted sequence binding affinities serves as a better metric for evaluating the success of this model. To evaluate this, we calculated both Spearman’s rank correlation coefficient, which does not rely on linear correlation, and the Pearson correlation coefficient between our predictions and the experimental results. As shown in Figure 2, our computation shows a Spearman’s rank correlation coefficient of 0.65 for the MAX-based predictions using one MAX-DNA complex (PDB ID: 1HLO), supporting the model’s capability to effectively distinguish strong from weak binders.

      As reflected in Figure 2 of the main text, although our model generally captures the relative binding affinities across different DNA sequences, its predictive accuracy diminishes for low-affinity sequences (Figure 2). This could be due to two limitations of the current modeling framework: (1) The model is residue-based and estimates binding free energy as the additive sum of contributions from individual contacting amino-acid-nucleotide pairs. This assumption does not account for cooperative effects caused by simultaneous changes at multiple nucleotide positions. One potential direction to further improve the model would be to use a finer-grained representation by incorporating more atom types within contacting residues, and to use a many-body potential to better capture cooperative effects from multiple mutations. (2) The model assumes that the target DNA adopts the same binding interface as in the reference crystal structure. However, sequencedependent DNA shape has been shown to be important in determining protein-DNA binding affinity [1]. To address this limitation, a future direction is to use deep-learningbased methods to incorporate predicted DNA shape or protein-DNA complex structures based on their sequences [2, 3] into our model prediction.

      To fully evaluate the predictive power of IDEA, we have included Spearman’s rank correlation coefficient for every correlation plot in this manuscript. Across all our analyses, the Spearman’s rank correlation coefficients reveal similar predictive performance as the Pearson correlation coefficients. Additionally, we have included in our discussion the current limitations of our model and potential directions for future improvement.

      We have edited our Discussion Section to include a discussion on the limitations of the current model. Specifically, the added texts are:

      “Although IDEA has proved successful in many examples, it can be improved in several aspects. The model currently assumes the training and testing sequences share the same protein-DNA structure. While double-stranded DNA is generally rigid, recent studies have shown that sequence-dependent DNA shape contributes to their binding specificity [1, 2, 4]. To improve predictive accuracy, one could incorporate predicted DNA shapes or structures into the IDEA training protocol. In addition, the model is residue-based and evaluates the binding free energy as the additive sum of contributions from individual amino-acid-nucleotide contacts. This assumption does not account for cooperative effects that may arise from multiple nucleotide changes. A potential refinement could utilize a finer-grained model that includes more atom types within contacting residues and employs a many-body potential to account for such cooperative effects.”

      Comment 4: (3) The discussion section lacks information about the model’s limitations and a comprehensive comparison with other models. Additionally, differences in model performance across various proteins and their respective predictive powers are not addressed.

      We thank the reviewer for the insightful comments. As discussed in the response to Comment 3, the current structural model has several limitations, which may reduce predictive accuracy for weak DNA binders. We have noted these limitations in the Discussion section.

      To compare the performance of IDEA with state-of-the-art protein-DNA predictive models, we examined the predictive accuracies of two additional popular computational models: ProBound [8] and DeepBind [9]. ProBound has been shown to have a better performance than several earlier predictive protein-DNA models, including JASPAR 2018 [11], HOCOMOCO [12], Jolma et al. [13], and DeepSELEX [14]. To benchmark these models’ performance, we examine each method’s capability to identify strong binders with the HT-SELEX datasets covering 22 proteins from 12 protein families [5]. As suggested by Reviewer 1, we also calculated the PRAUC score, reweighted to account for data imbalance [6], as a complementary metric for evaluating the model performance.

      As shown in Figure S6, Table S1, and Table S2, IDEA ranked second among the three predictive methods. It is important to note that both ProBound and DeepBind were trained on a curated version of the HT-SELEX data [13], which overlaps with the testing data [5]. Compared with them, IDEA was trained only on the given structural and sequence information from a single protein-DNA complex, thus independent of the testing data. In order to assess how IDEA performs when incorporating knowledge from HT-SELEX data, we augmented the training by randomly including half of the HT-SELEX data (see the Methods Section Enhanced Modeling Prediction with SELEX Data). The augmented IDEA model achieved the best performance among all the models. We further benchmarked IDEA using a 10-fold cross-validation on the same HT-SELEX data [5] and found that IDEA outperformed a recent regression model that considers the shape of DNA with different sequences [5]. Overall, IDEA can be used to predict protein-DNA affinities in the absence of known binding sequence data, thereby filling a critical gap when such experimental datasets are unavailable.

      In addition, we compared the performance of IDEA with both general and family-specific knowledge-based energy models. First, we incorporated a knowledge-based generic protein-DNA energy model (DBD-Hunter) learned from the protein-DNA database, reported by Skoinick and coworkers [7], into our prediction protocol. This model assigns interaction energies to different functional groups within each DNA nucleotide (e.g., phosphate (PP), sugar (SU), pyrimidine (PY), and imidazole (IM) groups). For our comparison, we averaged the energy contributions of these groups within each nucleotide and replaced the IDEA-learned energy model with this generic one to test its ability to differentiate strong binders from weak binders in the HT-SELEX dataset [5]. As shown in Figure S6, the IDEA model generally achieves better performance than the generic energy model. Additionally, we compared IDEA with rCLAMPS, a family-specific energy model developed to predict protein-DNA binding specificity in the C2H2 and homeodomain families. As shown in Table S1 and Table S2, IDEA also shows better performance than rCLAMPS in most cases across the C2H2 and homeodomain families, demonstrating that it has better predictive accuracy than both family-specific and generic knowledge-based models.

      We have revised our text to include the comparison between IDEA and other predictive models. Specifically, we revised the text in Section: IDEA Generalizes across Various Protein Families.

      The revised text reads:

      “To examine IDEA’s predictive accuracy across different DNA-binding protein families, we applied it to calculate protein-DNA binding affinities using a comprehensive HT-SELEX dataset [5]. We focused on evaluating the capability of IDEA to distinguish strong binders from weak binders for each protein with an experimentally determined structure. We calculated the probability density distribution of the top and bottom binders identified in the SELEX experiment. A well-separated distribution indicates the successful identification of strong binders by IDEA (Figure 2D and S4). Receiver Operating Characteristic (ROC) analysis was performed to calculate the Area Under the Curve (AUC) and the precision-recall curve (PRAUC) scores for these predictions. Further details are provided in the Methods Section Evaluation of IDEA Prediction Using HT-SELEX Data. Our analysis shows that IDEA successfully differentiates strong from weak binders for 80% of the 22 proteins across 12 protein families, achieving AUC and balanced PRAUC scores greater than 0.5 (Figure 2E and S5). To benchmark IDEA’s performance against other leading methods, we compared its predictions with several popular models, including the sequence-based predictive models ProBound [8] and DeepBind [9], the familybased energy model rCLAMPS [10], and the knowledge-based energy model DBD-Hunter [7]. IDEA demonstrates performance comparable to these stateof-the-art approaches (Figure S6, Table S1, and Table S2), and incorporating sequence features further improves its prediction accuracy. We also performed 10-fold cross-validation on the binding affinities of protein–DNA pairs in this dataset and found that IDEA outperforms a recent regression model that considers the shape of DNA with different sequences [5] (Figure S7). Details are provided in Section: Comparison of IDEA predictive performance Using HT-SELEX data.”

      We also added one section Comparison of IDEA predictive performance Using HT-SELEX data in the Appendix to fully explain the comparison between IDEA and other popular models.

      The added texts are:

      “To benchmark the performance of IDEA against state-of-the-art protein-DNA predictive models, we evaluated its ability to recognize strong binders with the HT-SELEX datasets across 22 proteins from 12 families [5]. Specifically, we compare IDEA with two widely used sequence-based models: ProBound [8] and DeepBind [9]. ProBound has demonstrated superior performance over many other predictive protein-DNA models, including JASPAR 2018 [11], HOCOMOCO [12], Jolma et al. [13], and DeepSELEX [14]. To use ProBound, we retrieved the trained binding model for each protein from motifcentral.org and used the GitHub implementation of ProBoundTools to infer the binding scores between protein and target DNA sequences. Except for POU3F1, binding models are available for all proteins. Therefore, we excluded POU3F1 and evaluated the protein-DNA binding affinities for the remaining 21 proteins. To use DeepBind, sequence-specific binding affinities were predicted directly with its web server. The Area Under the Curve (AUC) and the Precision-Recall AUC (PRAUC) scores were used as metrics for comparison. An AUC score of 1.0 indicates a perfect separation between the strong- and weak-binder distributions, while an AUC score of 0.5 indicates no separation. Because there is a significant imbalance in the number of strong and weak binders from the experimental data [5], where the strong binders are far fewer than the weak binders, we reweighted the samples to achieve a balanced evaluation, using 0.5 as the baseline for randomized prediction [6]. As summarized in Figure S6, Table S1, and Table S2, IDEA ranked second among the three predictive models. In order to assess the performance of IDEA when augmented with additional protein-DNA binding data, we augmented IDEA using randomly selected half of the HT-SELEX data (see the Methods Section Enhanced Modeling Prediction with SELEX Data). The augmented IDEA model achieved the best performance among all the models.”

      “In addition, we compared the performance of IDEA with both general and family-specific knowledge-based energy models. First, we incorporated a knowledgebased generic protein-DNA energy model (DBD-Hunter) learned from the protein-DNA database, reported by Skoinick and coworkers [7], into our prediction protocol. This model assigns interaction energies to different functional groups within each DNA nucleotide, including phosphate (PP), sugar (SU), pyrimidine (PY), and imidazole (IM) groups. For our comparison, we averaged the energy contributions of these groups within each nucleotide and replaced the IDEA-learned energy model with the DBD-Hunter model to assess its ability to differentiate strong binders from weak binders in the HTSELEX dataset [5]. Additionally, we compared IDEA with rCLAMPS, a familyspecific energy model developed to predict protein-DNA binding specificity in the C2H2 and homeodomain families. rCLAMPS learns a position-dependent amino-acid-nucleotide interaction energy model. To incorporate this model into the binding free energy calculation, we averaged the energy contributions across all occurrences of each amino-acid-nucleotide pair, which resulted in a 20-by-4 residue-type-specific energy matrix. This matrix is structurally analogous to the IDEA-trained energy model and can be directly integrated into the binding free energy calculations. As shown in Figure S6, Table S1, and Table S2, the IDEA model generally outperforms DBD-Hunter and rCLAMPS, demonstrating that it can achieve better predictive accuracy than both generic and family-specific knowledge-based models.”

      “We also performed 10-fold cross-validation using the same HT-SELEX datasets, following the protocol described in the Methods Section Enhanced Modeling Prediction with SELEX Data. For each protein, we divided the entire dataset into 10 equal, randomly assigned folds. In each iteration, we used randomly selected 9 of the 10 folds as the training dataset and the remaining fold as the testing dataset. This process was repeated 10 times so that each fold served as the test set once. We then reported the average R2 scores across these iterations to evaluate IDEA’s predictive performance. Our results are compared with the 1mer and 1mer+shape methods from [5], the latest regression model that considers the shape of DNA with different sequences (Figure S7). This comparative analysis shows IDEA achieved higher predictive accuracy than the state-of-the-art sequence-based protein-DNA binding predictors for proteinDNA complexes that have available experimentally resolved structures.”

      “Overall, these results demonstrate that IDEA can be used to predict the proteinDNA pairs in the absence of known binding sequence data, thus filling an important gap in protein-DNA predictions when experimental binding sequence data are unavailable.”

      We also greatly appreciate the reviewer’s suggestion to examine the model’s performance across different proteins. To do this, we first evaluated the dependence of IDEA prediction on the availability of experimental structures similar to the target protein-DNA complexes. To quantitatively assess similarities and differences among the IDEA-derived energy models, we flattened each normalized energy model into an 80-dimensional vector and performed principal component analysis (PCA). As shown in Author response image 1 and Figure S11, energy models optimized from the same protein family fall within the same cluster, while those from different protein families exhibit distinct patterns. Moreover, the relative distance between energy models in PCA space reflects the degree of transferability. For example, PHO4 (PDB ID: 1A0A) is positioned close to MAX (PDB ID: 1HLO), whereas USF1 (PDB ID: 1AN4) and TCF4 (PDB ID: 6OD3) are farther away. This is consistent with the results shown in Figure 3A, where the energy model trained from PHO4 has better transferability than those from the other two systems. Therefore, the availability of experimental structures from protein-DNA complexes more similar to the target can lead to better predictive performance.

      We also examine cases in which the IDEA model failed to show strong discriminative power for protein-DNA complexes in the HT-SELEX datasets [5] (Figures 2E and S5). When evaluating the model’s ability to distinguish between strong and weak binders, we used the available experimental structure most similar to the protein employed in the HT-SELEX experiments. In some instances, only the structure of the same protein from a different organism is available. For example, the HT-SELEX data for PDX1-DNA used the human PDX1 protein, but no human PDX1–DNA complex structure is available. Therefore, we used the mouse PDX1–DNA complex (PDB ID: 2H1K) for model training. The differences between species may limit the predictive accuracy of the model. A similar limitation applies to POU3F1, where an available mouse complex (PDB ID: 4Y60) was used to predict human protein–DNA interactions. Notably, DeepBind [9], a sequencebased prediction tool, also failed to distinguish strong from weak binders when using the mouse POU3F1 protein (AUC score: 0.457), but this was corrected with the human POU3F1 protein (AUC score: 0.956).

      We also examined the remaining cases where IDEA did not show a clear distinction between strong and weak binders: USF1, Egr1, and PROX1. For PROX1, we initially used the structure of a protein-DNA complex (PDB ID: 4Y60) in training. However, upon closer inspection, we discovered that this structure does not include the PROX1 protein, but SOX-18, a different transcription factor. This explains the inaccurate prediction made by IDEA. Since no experimental PROX1-DNA complex structure is currently available, we have removed this case from our HT-SELEX evaluation.

      IDEA also fails to fully resolve the binding preference of USF1. A closer examination of the HT-SELEX data reveals a lack of distinction among the sequences, as most sequences, including those with the lowest M-word (binding affinity) scores, contain the DNA-binding E-box sequence CACGTG. Therefore, USF1 represents a challenging example where the experimental data only consists of strong binders with limited variations in binding affinity, which likely results from differences in flanking sequences of the E-box motif.

      Egr1 stands as a peculiar example. Whereas IDEA does not effectively distinguish between the strong and weak binders in the current HT-SELEX dataset, its predictions are consistent with other experimental datasets, including binding affinities measured by kMITOMI [42] (Figure S8A, B), preferred binding sequences from protein-binding microarray, an earlier HT-SELEX experiment, and bacterial one-hybrid data [43]. Therefore, further investigation of the current HT-SELEX data is needed to reconcile these differences.

      In summary, IDEA’s predictive performance depends on the availability of experimental structures closely related to the target protein-DNA complexes, both in terms of protein sequences and model organisms.

      We have included additional text in Section: IDEA Demonstrates Transferability across Proteins in the Same CATH Superfamily to discuss the PCA analysis and the dependence of the model’s transferability on the similarity among the learned energy models.

      The revised text now reads:

      “The transferability of IDEA within the same CATH superfamily can be understood from the similarities in protein-DNA binding interfaces, which determine similar learned energy models. For example, the PHO4 protein (PDB ID: 1A0A) shares a highly similar DNA-binding interface with the MAX protein (PDB ID: 1HLO) (Figure 3B), despite sharing only a 33.41% probability of being homologous. Consequently, the energy model derived from the PHO4DNA complex (Figure 3C) exhibits a similar amino-acid-nucleotide interactive pattern as that learned from the MAX-DNA complex (Figure 2B). To further evaluate the similarity between the learned energy models and their connection to protein families, we performed principal component analysis (PCA) on the normalized energy models across 24 proteins from 12 protein families [5]. Our analysis (Figure S11) reveals that most of the energy models from the same protein family fall within the same cluster, while those from different protein families exhibit distinct patterns. Moreover, the relative distance between energy models in PCA space reflects the degree of transferability between them. For example, PHO4 (PDB ID: 1A0A) is positioned close to MAX (PDB ID: 1HLO), whereas USF1 (PDB ID: 1AN4) and TCF4 (PDB ID: 6OD3) are farther away. This is consistent with the results in Figure 3A, where the energy model trained on PHO4 has better transferability than those trained on USF1 or TCF4.”

      We have also added an Appendix section titled Analysis of examples where IDEA fails to recognize strong DNA binders to discuss the examples in which IDEA did not perform well:

      “We examine IDEA’s capability in identifying strong binders from the HT-SELEX dataset across 12 protein families [5]. The model successfully predicts 18 out of 22 protein-DNA systems, but the performance is reduced in 4 cases. Closer investigations revealed the source of these limitations. In some instances, only the protein from a different organism is available. For example, the PDX1 HT-SELEX data utilized the human PDX1 protein, but no human PDX1–DNA complex structure is available. Therefore, the mouse PDX1–DNA complex structure (PDB ID: 2H1K) was used for model training. Differences between model organisms may reduce predictive accuracy. A similar limitation applies to POU3F1, where an available mouse complex (PDB ID: 4Y60) was used to predict human protein–DNA interactions. Notably, DeepBind [9], a sequence-based prediction tool, also failed to distinguish strong from weak binders when using the mouse POU3F1 protein (AUC score: 0.457), but this was corrected with the human POU3F1 protein (AUC score: 0.956).

      IDEA also fails to fully resolve the binding preference of USF1. A closer examination of the HT-SELEX data reveals a lack of distinction among the sequences, as most sequences, including those with the lowest M-word (binding affinity) scores, contain the DNA-binding E-box sequence CACGTG. Therefore, USF1 represents a challenging example where the experimental data only consists of strong binders with limited variations in binding affinity, which likely results from differences in flanking sequences of the E-box motif.

      Egr1 stands as a peculiar example. Whereas IDEA does not effectively distinguish between the strong and weak binders in the current HT-SELEX dataset, its predictions are consistent with other experimental datasets, including binding affinities measured by k-MITOMI [42] (Figure S8A, B), preferred binding sequences from protein-binding microarray, an earlier HT-SELEX experiment, and bacterial one-hybrid data [43]. Therefore, further investigation of the current HT-SELEX data is needed to reconcile these differences.”

      Comment 5: The authors provide an implementation of their model via GitHub, which is commendable. However, it unexpectedly requires the Modeller suite, despite no details about homology modeling being included in the methods section.

      We thank the reviewer for the helpful comments. We did not use the homology modeling module of Modeller. Instead, we only used a single Python script, buildseq.py, from the Modeller package to extract the protein and DNA sequences from the given PDB structure. We have clarified this in the README file on our GitHub repository.

      Comment 6: While the manuscript is written in clear and accessible English, some sentences are quite long and could benefit from rephrasing (e.g., lines 49-52).

      Thank you for the helpful suggestion. We agree that the original sentence was overly long and have revised it by splitting it into two for improved clarity and readability.

      The revised version reads:

      “The very robustness of evolution [46, 47, 48, 49] provides an opportunity to extract the sequence-structure relationships embedded in existing complexes. Guided by this principle, we can learn an interpretable binding energy landscape that governs the recognition processes of DNA-binding proteins.”

      Comment 7: In line 82, the citations appear out of place, as the context seems to suggest the use of the newly developed model.

      Thank you for this insightful suggestion. We have rephrased the sentence to better connect with the context of this section.

      The revised text now reads:

      “Finally, the learned energy model can be incorporated into a simulation framework to explore the dynamics of DNA-binding processes, revealing mechanistic insights into various DNA-templated processes.”

      Comment 8: Line 143 ”different structure from the bHLH TFs and thus requires a different atom” This is the first instance in the manuscript where the atom selection for distance thresholding is mentioned, making the text somewhat confusing.

      We thank the reviewer for the insightful comment and agree that the atom selection scheme appears abruptly in this section. To improve clarity, we have moved the detailed atom selection scheme and its rationale to the Methods Section titled Structural Modeling of Protein and DNA.

      Comment 9: Figures: Overall, the figures are visually appealing but could be further improved.

      We appreciate the positive feedback regarding the visual presentation of our figures. Following the reviewer’s suggestions and to further enhance clarity, we have revised several figures to improve labeling, layout, and annotations.

      Comment 10: Figure 1: The description ”highlighted in blue” considers changing to ”highlighted in blue on the structure.”.

      We have revised the text based on your suggestion.

      Comment 11: Figure 2: Panel B is missing a color bar legend and units, as is the case in Figure 3C. Additionally, the placement of Panel C is unconventional - it appears it should be Panel D. The color scheme for the spheres is not fully described. Panel E: There are too many colors used; consider employing different markers to improve clarity.

      Thank you for the helpful suggestions.

      For Figure 2B and Figure 3C, we would like to clarify that the predicted energies are presented in reduced units due to an undetermined prefactor introduced during the model optimization. This point has now been clarified in the figure captions and is also explained in the Methods section titled Training Protocol.

      Additionally, we have rearranged Panels C and D to improve the figure layout and have fully described the color coding used in the structural representations.

      We have updated it to read:

      “Results for MAX-based predictions. (A) The binding free energies calculated by IDEA, trained using a single MAX–DNA complex (PDB ID: 1HLO), correlate well with experimentally measured MAX–DNA binding free energies [50]. ∆∆G represents the changes in binding free energy relative to that of the wild-type protein–DNA complex. (B) The heatmap, derived from the optimized energy model, illustrates key amino acid–nucleotide interactions governing MAX–DNA recognition, showing pairwise interaction energies between 20 amino acids and the four DNA bases—DA (deoxyadenosine), DT (deoxythymidine), DC (deoxycytidine), and DG (deoxyguanosine). Both the predicted binding free energies and the optimized energy model are expressed in reduced units, as explained in the Methods Section Training Protocol. Each cell represents the optimized energy contribution, where blue indicates more favorable (lower) energy values, and red indicates less favorable (higher) values. (C) The 3D structure of the MAX–DNA complex (zoomed in with different views) highlights key amino acid–nucleotide contacts at the protein–DNA interface. Notably, several DNA deoxycytidines (red spheres) form close contacts with arginines (blue spheres). Additional nucleotide color coding: adenine (yellow spheres), guanine (green spheres), thymine (pink spheres). (D) Probability density distributions of predicted binding free energies for strong (blue) and weak (red) binders of the protein ZBTB7A. The mean of each distribution is marked with a dashed line. (E) Summary of AUC scores for protein–DNA pairs across 12 protein families, calculated based on the predicted probability distributions of binding free energies.”

      We fully agree that Panel E was visually overwhelming. We have revised the plot by using a combination of color and marker shapes to more clearly distinguish between different protein families, as suggested.

      Comment 12: Typos:

      Line 18: Gene expressions → Gene expression?

      Line 28: performed → utilized ?

      We really appreciate the suggestions and have corrected the text accordingly.

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    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors have used full-length single-cell sequencing on a sorted population of human fetal retina to delineate expression patterns associated with the progression of progenitors to rod and cone photoreceptors. They find that rod and cone precursors contain a mix of rod/cone determinants, with a bias in both amounts and isoform balance likely deciding the ultimate cell fate. Markers of early rod/cone hybrids are clarified, and a gradient of lncRNAs is uncovered in maturing cones. Comparison of early rods and cones exposes an enriched MYCN regulon, as well as expression of SYK, which may contribute to tumor initiation in RB1 deficient cone precursors.

      Strengths:

      (1) The insight into how cone and rod transcripts are mixed together at first is important and clarifies a long-standing notion in the field.

      (2) The discovery of distinct active vs inactive mRNA isoforms for rod and cone determinants is crucial to understanding how cells make the decision to form one or the other cell type. This is only really possible with full-length scRNAseq analysis.

      (3) New markers of subpopulations are also uncovered, such as CHRNA1 in rod/cone hybrids that seem to give rise to either rods or cones.

      (4) Regulon analyses provide insight into key transcription factor programs linked to rod or cone fates.

      (5) The gradient of lncRNAs in maturing cones is novel, and while the functional significance is unclear, it opens up a new line of questioning around photoreceptor maturation.

      (6) The finding that SYK mRNA is naturally expressed in cone precursors is novel, as previously it was assumed that SYK expression required epigenetic rewiring in tumors.

      We thank the reviewer for describing the study’s strengths, reflecting the major conclusions of the initially submitted manuscript.  However, based on new analyses – including the requested analyses of other scRNA-seq datasets, our revision clarifies that:

      -  related to point (1), cone and rod transcripts do not appear to be mixed together at first (i.e., in immediately post-mitotic immature cone and rod precursors) but appear to be coexpressed in subsequent cone and rod precursor stages; and 

      - related to point (3), CHRNA1 appears to mark immature cone precursors that are distinct from the maturing cone and rod precursors that co-express cone- and rod-related RNAs (despite the similar UMAP positions of the two populations in our dataset). 

      Weaknesses:

      (1) The writing is very difficult to follow. The nomenclature is confusing and there are contradictory statements that need to be clarified.

      (2) The drug data is not enough to conclude that SYK inhibition is sufficient to prevent the division of RB1 null cone precursors. Drugs are never completely specific so validation is critical to make the conclusion drawn in the paper.

      We thank the reviewer for noting these important issues. Accordingly, in the revised manuscript:

      (1) We improve the writing and clarify the nomenclature and contradictory statements, particularly those noted in the Reviewer’s Recommendations for Authors. 

      (2) We scale back claims related to the role of SYK in the cone precursor response to RB1 loss, with wording changes in the Abstract, Results, and Discussion, which now recognize that the inhibitor studies only support the possibility that cone-intrinsic SYK expression contributes to retinoblastoma initiation, as detailed in our responses to Reviewer’s Recommendations for Authors. We agree and now mention that genetic perturbation of SYK is required to prove its role.  

      Reviewer #2 (Public review):

      Summary:

      The authors used deep full-length single-cell sequencing to study human photoreceptor development, with a particular emphasis on the characteristics of photoreceptors that may contribute to retinoblastoma.

      Strengths:

      This single-cell study captures gene regulation in photoreceptors across different developmental stages, defining post-mitotic cone and rod populations by highlighting their unique gene expression profiles through analyses such as RNA velocity and SCENIC. By leveraging fulllength sequencing data, the study identifies differentially expressed isoforms of NRL and THRB in L/M cone and rod precursors, illustrating the dynamic gene regulation involved in photoreceptor fate commitment. Additionally, the authors performed high-resolution clustering to explore markers defining developing photoreceptors across the fovea and peripheral retina, particularly characterizing SYK's role in the proliferative response of cones in the RB loss background. The study provides an in-depth analysis of developing human photoreceptors, with the authors conducting thorough analyses using full-length single-cell RNA sequencing. The strength of the study lies in its design, which integrates single-cell full-length RNA-seq, longread RNA-seq, and follow-up histological and functional experiments to provide compelling evidence supporting their conclusions. The model of cell type-dependent splicing for NRL and THRB is particularly intriguing. Moreover, the potential involvement of the SYK and MYC pathways with RB in cone progenitor cells aligns with previous literature, offering additional insights into RB development.

      We thank the reviewer for summarizing the main findings and noting the compelling support for the conclusions, the intriguing cell type-dependent splicing of rod and cone lineage factors, and the insights into retinoblastoma development.  

      Weaknesses:

      The manuscript feels somewhat unfocused, with a lack of a strong connection between the analysis of developing photoreceptors, which constitutes the bulk of the manuscript, and the discussion on retinoblastoma. Additionally, given the recent publication of several single-cell studies on the developing human retina, it is important for the authors to cross-validate their findings and adjust their statements where appropriate.

      We agree that the manuscript covers a range of topics resulting from the full-length scRNAseq analyses and concur that some studies of developing photoreceptors were not well connected to retinoblastoma. However, we also note that the connection to retinoblastoma is emphasized in several places in the Introduction and throughout the manuscript and was a significant motivation for pursuing the analyses. We suggest that it was valuable to highlight how deep, fulllength scRNA-seq of developing retina provides insights into retinoblastoma, including i) the similar biased expression of NRL transcript isoforms in cone precursors and RB tumors, ii) the cone precursors’ co-expression of rod- and cone-related genes such as NR2E3 and GNAT2, which may explain similar co-expression in RB cells, and iii) the expression of  SYK in early cones and RB cells.  While the earlier version had mainly highlighted point (iii), the revised Discussion further refers to points (i) and (ii) as described further in the response to the Reviewer’s Recommendations for Authors. 

      We address the Reviewer’s request to cross-validate our findings with those of other single-cell studies of developing human retina by relating the different photoreceptor-related cell populations identified in our study to those characterized by Zuo et al (PMID 39117640), which was specifically highlighted by the reviewer and is especially useful for such cross-validation given the extraordinarily large ~ 220,000 cell dataset covering a wide range of retinal ages (pcw 8–23) and spatiotemporally stratified by macular or peripheral retina location. Relevant analyses of the Zuo et al dataset are shown in Supplementary Figures S3G-H, S10B, S11A-F, and S13A,B. 

      Reviewer #3 (Public review):

      Summary:

      The authors use high-depth, full-length scRNA-Seq analysis of fetal human retina to identify novel regulators of photoreceptor specification and retinoblastoma progression.

      Strengths:

      The use of high-depth, full-length scRNA-Seq to identify functionally important alternatively spliced variants of transcription factors controlling photoreceptor subtype specification, and identification of SYK as a potential mediator of RB1-dependent cell cycle reentry in immature cone photoreceptors.

      Human developing fetal retinal tissue samples were collected between 13-19 gestational weeks and this provides a substantially higher depth of sequencing coverage, thereby identifying both rare transcripts and alternative splice forms, and thereby representing an important advance over previous droplet-based scRNA-Seq studies of human retinal development.

      Weaknesses:

      The weaknesses identified are relatively minor. This is a technically strong and thorough study, that is broadly useful to investigators studying retinal development and retinoblastoma.

      We thank the reviewer for describing the strengths of the study. Our revision addresses the concerns raised separately in the Reviewer’s Recommendations for Authors, as detailed in the responses below.  

      Recommendations for the authors:

      Reviewing Editor Comments:

      The reviewers have completed their reviews. Generally, they note that your work is important and that the evidence is generally convincing. The reviewers are in general agreement that the paper adds to the field. The findings of rod/cone fate determination at a very early stage are intriguing. Generally, the paper would benefit from clarifications in the writing and figures. Experimentally, the paper would benefit from validation of the drug data, for example using RNAi or another assay. Alternatively, the authors could note the caveats of the drug experiments and describe how they could be improved. In terms of analysis, the paper would be improved by additional comparisons of the authors' data to previously published datasets.

      We thank the reviewing editor for this summary. As described in the individual reviewer responses, we clarify the writing and figures and provide comparisons to previously published datasets (in particular, the large snRNA-seq dataset of Zuo et al., 2024 (PMID 39117640).  With regard to the drug (i.e., SYK inhibitor) studies, we opted to provide caveats and describe the need for genetic approaches to validate the role of SYK, owing to the infeasibility of completing genetic perturbation experiments in the appropriate timeframe.  We are grateful for the opportunity to present our findings with appropriate caveats. 

      Reviewer #1 (Recommendations for the authors):

      Shayler cell sort human progenitor/rod/cone populations then full-length single cell RNAseq to expose features that distinguish paths towards rods or cones. They initially distinguish progenitors (RPCs), immature photoreceptor precursors (iPRPs), long/medium wavelength (LM) cones, late-LM cones, short wavelength (S) cones, early rods (ER) and late rods (LR), which exhibit distinct transcription factor regulons (Figures 1, 2). These data expose expected and novel enriched genes, and support the notion that S cones are a default state lacking expression of rod (NRL) or cone (THRB) determinants but retaining expression of generic photoreceptor drivers (CRX/OTX2/NEUROD1 regulons). They identify changes in regulon activity, such as increasing NRL activity from iPRP to ER to LR, but decreasing from iPRP to cones, or increasing RAX/ISL2/THRB regulon activity from iPRP to LM cones, but decreasing from iPRP to S cones or rods.

      They report co-expression of rod/cone determinants in LM and ER clusters, and the ratios are in the expected directions (NRLTHRB or RXRG in ER). A novel insight from the FL seq is that there are differing variants generated in each cell population. Full-length NRL (FL-NRL) predominates in the rod path, whereas truncated NRL (Tr-NRL) does so in the cone path, then similar (but opposite) findings are presented for THRB (Fig 3, 4), whereas isoforms are not a feature of RXRG expression, just the higher expression in cones.

      The authors then further subcluster and perform RNA velocity to uncover decision points in the tree (Figure 5). They identify two photoreceptor precursor streams, the Transitional Rods (TRs) that provide one source for rod maturation and (reusing the name from the initial clustering) iPRPs that form cones, but also provide a second route to rods. TR cells closest to RPCs (immediately post-mitotic) have higher levels of the rod determinant NR2E3 and NRL, whereas the higher resolution iPRPs near RPCs lack NR2E3 and have higher levels of ONECUT1, THRB, and GNAT2, a cone bias. These distinct rod-biased TR and cone-biased high-resolution iPRPs were not evident in published scRNAseq with 3′ end-counting (i.e. not FL seq). Regulon analysis confirmed higher NRL activity in TR cells, with higher THRB activity in highresolution iPRP cells.

      Many of the more mature high-resolution iPRPs show combinations of rod (GNAT1, NR2E3) and cone (GNAT2, THRB) paths as well as both NRL and THRB regulons, but with a bias towards cone-ness (Figure 6). Combined FISH/immunofluorescence in fetal retina uncovers cone-biased RXRG-protein-high/NR2E3-protein-absent cone-fated cells that nevertheless expressed NR2E3 mRNA. Thus early cone-biased iPRP cells express rod gene mRNA, implying a rod-cone hybrid in early photoreceptor development. The authors refer to these as "bridge region iPRP cells".

      In Figure 7, they identify CHRNA1 as the most specific marker of these bridge cells (overlapping with ATOH7 and DLL3, previously linked to cone-biased precursors), and FISH shows it is expressed in rod-biased NRL protein-positive and cone-biased RXRG proteinpositive cones at fetal week 12.

      Figure 8 outlines the graded expression of various lncRNAs during cone maturation, a novel pattern.

      Finally (Figure 9), the authors identify differential genes expressed in early rods (ER cluster from Figure 1) vs early cones (LM cluster, excluding the most mature opsin+ cells), revealing high levels of MYCN targets in cones. They also find SYK expression in cones. SYK was previously linked to retinoblastoma, so intrinsic expression may predispose cone precursors to transformation upon RB loss. They finish by showing that a SYK inhibitor blocks the proliferation of dividing RB1 knockdown cone precursors in the human fetal retina.

      Overall, the authors have uncovered interesting patterns of biased expression in cone/rod developmental paths, especially relating to the isoform differences for NRL and THRB which add a new layer to our understanding of this fate choice. The analyses also imply that very soon after RPCs exit the cell cycle, they generate post-mitotic precursors biased towards a rod or cone fate, that carry varying proportions of mixed rod/cone determinants and other rod/cone marker genes. They also introduce new markers that may tag key populations of cells that precede the final rod/cone choice (e.g. CHRNA1), catalogue a new lncRNA gradient in cone maturation, and provide insight into potential genes that may contribute to retinoblastoma initiation, like SYK, due to intrinsic expression in cone precursors. However, as detailed below, the text needs to be improved considerably, and overinterpretations need to be moderated, removed, or tested more rigorously with extra data.

      Major Comments

      The manuscript is very difficult to follow. The nomenclature is at times torturous, and the description of hybrid rod/cone hybrid cells is confusing in many aspects.

      (1) A single term, iPRP, is used to refer to an initial low-resolution cluster, and then to a subset of that cluster later in the paper.

      We agree that using immature photoreceptor precursor (iPRP) for both high-resolution and lowresolution clusters was confusing. We kept this name for the low-resolution cluster (which includes both immature cone and immature rod precursors), renamed the high-resolution iPRP cluster immature cone precursors (iCPs). and renamed their transitional rod (TR) counterparts immature rod precursors (iRPs). These designations are based on 

      - the biased expression of THRB, ONECUT1, and the THRB regulon in iCPs (Fig. 5D,E);

      - the biased expression of NRL, NR2E3, and NRL regulon iRPs (Fig. 5D,E);

      - the partially distinct iCP and iRP UMAP positions (Figure 5C); and 

      - the evidence of similar immature cone versus rod precursor populations in the Zuo et al 3’ snRNA-seq dataset, as noted below and described in two new paragraphs starting at the bottom of p. 12.

      (2) To complicate matters further, the reader needs to understand the subset within the iPRP referred to as bridge cells, and we are told at one point that the earliest iPRPs lack NR2E3, then that they later co-express NR2E3, and while the authors may be referring to protein and RNA, it serves to further confuse an already difficult to follow distinction. I had to read and re-read the iPRP data many times, but it never really became totally clear.

      We agree that the description of the high-resolution iPRP (now “iCP”) subsets was unclear, although our further analyses of a large 3’ snRNA-seq dataset in Figure S11 support the impression given in the original manuscript that the earliest iCPs lack NR2E3 and then later coexpress NR2E3 while the earliest iRPs lack THRB and then later express THRB. As described in new text in the Two post-mitotic immature photoreceptor precursor populations section (starting on line 7 of p. 13): 

      When considering only the main cone and rod precursor UMAP regions, early (pcw 8 – 13) cone precursors expressed THRB and lacked NR2E3 (Figure S11D,E, blue arrows), while early (pcw 10 – 15) rod precursors expressed NR2E3 and lacked THRB (Figure S11D,E, red arrows), similar to RPC-localized iCPs and iRPs in our study (Figure 5D).

      Next, as summarized in new text in the Early cone and rod precursors with rod- and conerelated RNA co-expression section (new paragraph at top of p. 16): 

      Thus, a 3’ snRNA-seq analysis confirmed the initial production of immature photoreceptor precursors with either L/M cone-precursor-specific THRB or rod-precursor-specific NR2E3 expression, followed by lower-level co-expression of their counterparts, NR2E3 in cone precursors and THRB in rod precursors. However, in the Zuo et al. analyses, the co-expression was first observed in well-separated UMAP regions, as opposed to a region that bridges the early cone and early rod populations in our UMAP plots. These findings are consistent with the notion that cone- and rod-related RNA co-expression begins in already fate-determined cone and rod precursors, and that such precursors aberrantly intermixed in our UMAP bridge region due to their insufficient representation in our dataset.  

      Importantly, and as noted in our ‘Public response’ to Reviewer 1, “CHRNA1 appears to mark immature cone precursors that are distinct from the maturing cone and rod precursors that coexpress cone- and rod-related RNAs (despite the similar UMAP positions of the two populations in our dataset).” In support of this notion, the immature cone precursors expressing CHRNA1  and other  populations did not overlap in UMAP space in the Zuo et al dataset. We hope the new text cited above along with other changes will significantly clarify the observations.

      (3) The term "cone/rod precursor" shows up late in the paper (page 12), but it was clear (was it not?) much earlier in this manuscript that cone and rod genes are co-expressed because of the coexpressed NRL and THRB isoforms in Figures 3/4.

      We thank the reviewer for noting that the differential NRL and THRB isoform expression already implies that cone and rod genes are co-expressed. However, as we now state, the co-expression of RNAs encoding an additional cone marker (GNAT2) and rod markers (GNAT1, NR2E3) was 

      “suggestive of a proposed hybrid cone/rod precursor state more extensive than implied by the coexpression of different THRB and NRL isoforms” (first paragraph of “Early cone and rod …” section on p. 14; new text underlined). 

      (4) The (incorrect) impression given later in the manuscript is that the rod/cone transcript mixture applies to just a subset of the iPRP cells, or maybe just the bridge cells (writing is not clear), but actually, neither of those is correct as the more abundant and more mature LM and ER populations analyzed earlier coexpress NRL and THRB mRNAs (Figures 2, 3). Overall, the authors need to vastly improve the writing, simplify/clarify the nomenclature, and better label figures to match the text and help the reader follow more easily and clearly. As it stands, it is, at best, obtuse, and at worst, totally confusing.

      We thank the reviewer for bringing the extent of the confusing terminology and wording to our attention. We revised the terminology (as in our response to point 1) and extensively revised the text.  We also performed similar analyses of the Zuo et al. data (as described in more detail in our response to Reviewer 2), which clarifies the distinct status of cells with the “rod/cone transcript mixture” and cells co-expressing early cone and rod precursor markers.  

      To more clearly describe data related to cells with rod- and cone-related RNA co-expression, we divided the former Figure 6 into two figures, with Figure 6 now showing the cone- and rodrelated RNA co-expression inferred from scRNA-seq and Figure 7 showing GNAT2 and NR2E3 co-expression in FISH analyses of human retina plus a new schematic in the new panel 7E.

      To separate the conceptually distinct analyses of cone and rod related RNA co-expression and the expression of early photoreceptor precursor markers (which were both found in the so-called bridge region – yet now recognized to be different subpopulations), we separated the analyses of the early photoreceptor precursor markers to form a new section, “Developmental expression of photoreceptor precursor markers and fate determinants,” starting on p. 16. 

      Additionally, we further review the findings and their implications in four revised Discussion paragraphs starting at the bottom of p. 23).

      (5) The data showing that overexpressing Tr-NRL in murine NIH3T3 fibroblasts blocks FL-NRL function is presented at the end of page 7 and in Figure 3G. Subsequent analysis two paragraphs and two figures later (end page 8, Figure 5C + supp figs) reveal that Tr-NRL protein is not detectable in retinoblastoma cells which derive from cone precursors cells and express Tr-NRL mRNA, and the protein is also not detected upon lentiviral expression of Tr-NRL in human fetal retinal explants, suggesting it is unstable or not translated. It would be preferable to have the 3T3 data and retinoblastoma/explant data juxtaposed. E.g. they could present the latter, then show the 3T3 that even if it were expressed (e.g. briefly) it would interfere with FL-NRL. The current order and spacing are somewhat confusing.

      We thank the reviewer for this suggestion and moved the description of the luciferase assays to follow the retinoblastoma and explant data and switched the order of Figure panels 3G and 3H.  

      (6) On page 15, regarding early rod vs early cone gene expression, the authors state: "although MYCN mRNA was not detected....", yet on the volcano plot in Figure S14A MYCN is one of the marked genes that is higher in cones than rods, meaning it was detected, and a couple of sentences later: "Concordantly, the LM cluster had increased MYCN RNA". The text is thus confusing.

      With respect, we note that the original text read, “although MYC RNA was not detected,” which related to a statement in the previous sentence that the gene ontology analysis identified “MYC targets.” However, given that this distinction is subtle and may be difficult for readers to recognize, we revised the text (now on p. 19) to more clearly describe expression of MYCN (but not MYC) as follows:

      “The upregulation of MYC target genes was of interest given that many MYC target genes are also targets of MYCN, that MYCN protein is highly expressed in maturing (ARR3+) cone precursors but not in NRL+ rods (Figure 10A), and that MYCN is critical to the cone precursor proliferative response to pRB loss8–10.  Indeed, whereas MYC RNA was not detected, the LM cone cluster had increased MYCN RNA …”

      (7) The authors state that the SYK drug is "highly specific". They provide no evidence, but no drug is 100% specific, and it is possible that off-target hits are important for the drug phenotype. This data should be removed or validated by co-targeting the SYK gene along with RB1.

      We agree that our data only show the potential for SYK to contribute to the cone proliferative response; however, we believe the inhibitor study retains value in that a negative result (no effect of the SYK inhibitor) would disprove its potential involvement. To reflect this, we changed wording related to this experiment as follows:

      In the Abstract, we changed:

      (1) “SYK, which contributed to the early cone precursors’ proliferative response to RB1 loss” To: “SYK, which was implicated in the early cone precursors’ proliferative response to RB1 loss.”  

      (2) “These findings reveal … and a role for early cone-precursor-intrinsic SYK expression.” To:  “These findings reveal … and suggest a role for early cone-precursor-intrinsic SYK expression.”

      In the last paragraph of the Results, we changed:

      (1) “To determine if SYK contributes…” To:  “To determine if SYK might contribute…”

      (2) “the highly specific SYK inhibitor” To:  “the selective SYK inhibitor”  

      (3)  “indicating that cone precursor intrinsic SYK activity is critical to the proliferative response” To: “consistent with the notion that cone precursor intrinsic SYK activity contributes to the proliferative response.”

      In the Results, we added a final sentence: 

      “However, given potential SYK inhibitor off-target effects, validation of the role of SYK in retinoblastoma initiation will require genetic ablation studies.”

      In the Discussion (2nd-to-last paragraph), we changed: 

      “SYK inhibition impaired pRB-depleted cone precursor cell cycle entry, implying that native SYK expression rather than de novo induction contributes to the cone precursors’ initial proliferation.” To: “…the pRB-depleted cone precursors’ sensitivity to a SYK inhibitor suggests that native SYK expression rather than de novo induction contributes to the cone precursors’ initial proliferation, although genetic ablation of SYK is needed to confirm this notion.” In the Discussion last sentence, we changed:

      “enabled the identification of developmental stage-specific cone precursor features that underlie retinoblastoma predisposition.” To: “enabled the identification of developmental stage-specific cone precursor features that are associated with the cone precursors’ predisposition to form retinoblastoma tumors.”

      Minor/Typos

      Figure 7 legend, H should be D.

      We corrected the figure legend (now related to Figure 8).

      Reviewer #2 (Recommendations for the authors):

      (1) The author should take advantage of recently published human fetal retina data, such as PMID:39117640, which includes a larger dataset of cells that could help validate the findings. Consequently, statements like "To our knowledge, this is the first indication of two immediately post-mitotic photoreceptor precursor populations with cone versus rod-biased gene expression" may need to be revised.

      We thank the reviewer for noting the evidence of distinct immediately post-mitotic rod and cone populations published by others after we submitted our manuscript. In response, we omitted the sentence mentioned and extensively cross-checked our results including:

      - comparison of our early versus late cone and rod maturation states to the cone and rod precursor versus cone and rod states identified by Zuo et al (new paragraph on the top half of p. 6 and new figure panels S3G,H);

      - detection of distinct immediately post-mitotic versus later cone and rod precursor populations (two new paragraphs on pp. 12-13 and new Figures S10B and S11A-E); 

      - identification of cone and rod precursor populations that co-express cone and rod marker genes (two new paragraphs starting at the bottom of p. 15 and new Figures S11D-F);

      - comparison of expression patterns of immature cone precursor (iCP) marker genes in our and the Zuo et al dataset (new paragraph on top half of p. 17 and new Figure S13).

      We also compare the cell states discerned in our study and the Zuo et al. study in a new Discussion paragraph (bottom of p. 23) and new Figure S17.

      (2) The data generated comes from dissociated cells, which inherently lack spatial context. Additionally, it is unclear whether the dataset represents a pool of retinas from multiple developmental stages, and if so, whether the developmental stage is known for each cell profiled. If this information is available, the authors should examine the distribution of developmental stages on the UMAP and trajectory analysis as part of the quality control process. 

      We thank the reviewer for highlighting the importance of spatial context and developmental stage. 

      Related to whether the dataset represents a pool of retinae from multiple developmental stages, the different cell numbers examined at each time point are indicated in Figure S1A. To draw the readers’ attention to this detail, Figure S1A is now cited in the first sentence of the Results. 

      Related to the age-related cell distributions in UMAP plots, the distribution of cells from each retina and age was (and is) shown in Fig. S1F. In addition, we now highlight the age distributions by segregating the FW13, FW15-17, and FW17-18-19 UMAP positions in the new Figure 1C. We describe the rod temporal changes in a new sentence at the top of  p. 5:

      “Few rods were detected at FW13, whereas both early and late rods were detected from FW15-19 (Figure 1C), corroborating prior reports [15,20].”  

      We describe the cone temporal changes and note the likely greater discrimination of cell state changes that would be afforded by separately analyzing macula versus peripheral retina at each age in a new sentence at the bottom of p. 5:

      “L/M cone precursors from different age retinae occupied different UMAP regions, suggesting age-related differences in L/M cone precursor maturation (Figure 1C).”

      Moreover, they should assess whether different developmental stages impact gene expression and isoform ratios. It is well established that cone and rod progenitors typically emerge at different developmental times and in distinct regions of the retina, with minimal physical overlap. Grouping progenitor cells based solely on their UMAP positioning may lead to an oversimplified interpretation of the data.

      (2a) We agree that different developmental stages may impact gene expression and isoform ratios, and evaluated stages primarily based on established Louvain clustering rather than UMAP position. However, we also used UMAP position to segregate so-called RPC-localized and nonRPC-localized iCPs and iRPs, as well as to characterize the bridge region iCP sub-populations. In the revision, we examine whether cell groups defined by UMAP positions helped to identify transcriptomically distinct populations and further examine the spatiotemporal gene expression patterns of the same genes in the Zuo et al. 3’ snRNA-seq dataset. 

      (2b) Related to analyses of immediately post-mitotic iRPs and iCPs, the new Figure S10A expanded the violin plots first shown in Figure 5D to compare gene expression in RPC-localized versus non-RPC-localized iCPs and iRPs and subsequent cone and rod precursor clusters (also presented in response to Reviewer 3). The new Figure S10C, shows a similar analysis of UMAP region-specific regulon activities. These figures support the idea that there are only subtle UMAP region-related differences in the expression of the selected gene and regulons. 

      To further evaluate early cone and rod precursors, we compared expression patterns in our cluster- and UMAP-defined cell groups to those of the spatiotemporally defined cell groups in the Zuo et al. 3’ snRNA-seq study. The results revealed similar expression timing of the genes examined, although the cluster assignments of a subset of cells were brought into question, especially the assigned rod precursors at pcw 10 and 13, as shown in new Figures S10B (grey columns) and S11, and as described in two new paragraphs starting near the bottom of p.12. 

      (2c) Related to analyses of iCPs in the so-called bridge region, our analyses of the Zuo et al dataset helped distinguish early cone and rod precursor populations (expressing early markers such as ATOH7 and CHRNA1) from the later stages exhibiting rod- and cone-related gene coexpression, which had intermixed in the UMAP bridge region in our dataset. Further parsing of early cone precursor marker spatiotemporal expression revealed intriguing differences as now described in the second half of a new paragraph at the top of p. 17, as follows:

      “Also, different iCP markers had different spatiotemporal expression: CHRNA1 and ATOH7 were most prominent in peripheral retina with ATOH7 strongest at pcw 10 and CHRNA1 strongest at pcw 13; CTC-378H22.2 was prominently expressed from pcw 10-13 in both the macula and the periphery; and DLL3 and ONECUT1 showed the earliest, strongest, and broadest expression (Figure S13B). The distinct patterns suggest spatiotemporally distinct roles for these factors in cone precursor differentiation.”

      (3) I would commend the authors for performing a validation experiment via RNA in situ to validate some of the findings. However, drawing conclusions from analyzing a small number of cells can still be dangerous. Furthermore, it is not entirely clear how the subclustering is done. Some cells change cell type identities in the high-resolution plot. For example, some iPRP cells from the low-resolution plots in Figure 1 are assigned as TR in high-resolution plots in Figure 5.

      The authors should provide justification on the identifies of RPC localized iPRP and TR.

      Comparison of their data with other publicly available data should strengthen their annotation

      We agree that drawing conclusions from scRNA-seq or in situ hybridization analysis of a small number of cells can be dangerous and have followed the reviewer’s suggestion to compare our data with other publicly available data, focusing on the 3’ snRNA-seq of Zuo et al. given its large size and extensive annotation. Our analysis of  the Zuo et al. dataset helped clarify cell identities by segregating cone and rod precursors with similar gene expression properties in distinct UMAP regions. However, we noted that the clustering of early cone and rod precursors likely gave numerous mis-assigned cells (as noted in response 2b above and shown in the new Figure S11). It would appear that insights may be derived from the combination of relatively shallow sequencing of a high number of cells and deep sequencing of substantially fewer cells. 

      Related to how subclustering was done, the Methods state, “A nearest-neighbors graph was constructed from the PCA embedding and clusters were identified using a Louvain algorithm at low and high resolutions (0.4 and 1.6)[70],” citing the Blondel et al reference for the Louvain clustering algorithm used in the Seurat package.  To clarify this, the results text was revised such that it now indicates the levels used to cluster at low resolution (0.4, p. 4, 2nd paragraph) and at high resolution (1.6, top of p. 11) .

      Related to the assignment of some iPRP cells from the low-resolution plots in Figure 1 to the TR cluster (now called the ‘iRP’ ‘cluster) in the high-resolution plots in Figure 5, we suggest that this is consistent with Louvain clustering, which does not follow a single dendrogram hierarchy. 

      The justification for referring to these groups as RPC-localized iCPs and iRPs relates to their biased gene and regulon expression in Fig. 5D and 5E, as stated on p. 12: 

      “In the RPC-localized region, iCPs had higher ONECUT1, THRB, and GNAT2, whereas iRPs trended towards higher NRL and NR2E3 (p= 0.19, p=0.054, respectively).”

      (4) Late-stage LM5 cluster Figure 9 is not defined anywhere in previous figures, in which LM clusters only range from 1 to 4. The inconsistency in cluster identification should be addressed.

      We revised the text related to this as follows: 

      “Indeed, our scRNA-seq analyses revealed that SYK RNA expression increased from the iCP stage through cluster LM4, in contrast to its minimal expression in rods (Figure 10E).  Moreover, SYK expression was abolished in the five-cell group with properties of late maturing cones (characterized in Figure 1E), here displayed separately from the other LM4 cells and designated LM5 (Figure 10E).”  (p. 19-20)

      (5) Syk inhibitor has been shown to be involved in RB cell survival in previous studies. The manuscript seems to abruptly make the connection between the single-cell data to RB in the last figure. The title and abstract should not distract from the bulk of the manuscript focusing on the rod and cone development, or the manuscript should make more connection to retinoblastoma.

      We appreciate the reviewer’s concern that the title may seem to over-emphasize the connection to retinoblastoma based solely on the SYK inhibitor studies. However, we suggest the title also emphasizes the identification and characterization of early human photoreceptor states, per se, and that there are a number of important connections beyond the SYK studies that could warrant the mention of cell-state-specific retinoblastoma-related features in the title.

      Most importantly, a prior concern with the cone cell-of-origin theory was that retinoblastoma cells express RNAs thought to mark retinal cell types other than cones, especially rods. The evidence presented here, that cone precursors also express the rod-related genes helps resolve this issue. The issue is noted numerous times in the manuscript, as follows:  

      In the Introduction, we write:

      “However, retinoblastoma cells also express rod lineage factor NRL RNAs, which – along with other evidence – suggested a heretofore unexplained connection between rod gene expression and retinoblastoma development[12,13]. Improved discrimination of early photoreceptor states is needed to determine if co-expression of rod- and cone-related genes is adopted during tumorigenesis or reflects the co-expression of such genes in the retinoblastoma cell of origin.” (bottom, p. 2) And: 

      “In this study, we sought to further define the transcriptomic underpinnings of human  photoreceptor development and their relationship to retinoblastoma tumorigenesis.” (last paragraph, p. 3)

      The Discussion also alluded to this issue and in the revised Discussion, we aimed to make the connection clearer.  We previously ended the 3rd-to-last paragraph with,  

      “iPRP [now iCP] and early LM cone precursors’ expression of NR2E3 and NRL RNAs suggest that their presence in retinoblastomas[12,13] reflects their normal expression in the L/M cone precursor cells of origin.” 

      We now separate and elaborate on this point in a new paragraph as follows: 

      “Our characterization of cone and rod-related RNA co-expression may help resolve questions about the retinoblastoma cell of origin. Past studies suggested that retinoblastoma cells co-express RNAs associated with rods, cones, or other retinal cells due to a loss of lineage fidelity[12]. However, the early L/M cone precursors’ expression of NR2E3 and NRL RNAs suggest that their presence in retinoblastomas[12,13] reflects their normal expression in the L/M cone precursor cells of origin. This idea is further supported by the retinoblastoma cells’ preferential expression of cone-enriched NRL transcript isoforms (Figure S5B).” (middle of p. 24) Based on the above, we elected to retain the title.  

      Minor comments:

      (1) It is difficult to see the orange and magenta colors in the Fig 3E RNA-FISH image. The colors should be changed, or the contrast threshold needs to be adjusted to make the puncta stand out more.

      We re-assigned colors, with red for FL-NRL puncta and green for Tr-NRL puncta. 

      (2) Figure 5C on page 8 should be corrected to Supplementary Figure 5C.

      We thank the reviewer for noting this error and changed the figure citation.

      Reviewer #3 (Recommendations for the authors):

      (1) Minor concerns

      a. Abbreviation of some words needs to be included, example: FW. 

      We now provide abbreviation definitions for FW and others throughout the manuscript.  

      b. Cat # does not matches with the 'key resource table' for many reagents/kits. Some examples are: CD133-PE mentioned on Page # 22 on # 71, SMART-Seq V4 Ultra Low Input RNA Kit and SMARTer Ultra Low RNA Kit for the Fluidigm C1 Sytem on Page # 22 on # 77, Nextera XT DNA Library preparation kit on Page # 23 on # 77.

      We thank the reviewer for noting these discrepancies. We have now checked all catalog numbers and made corrections as needed.

      c. Cat # and brand name of few reagents & kits is missing and not mentioned either in methods or in key resource table or both. Eg: FBS, Insulin, Glutamine, Penicillin, Streptomycin, HBSS, Quant-iT PicoGreen dsDNA assay, Nextera XT DNA LibraryPreparation Kit, 5' PCR Primer II A with CloneAmp HiFi PCR Premix. 

      Catalog numbers and brand names are now provided for the tissue culture and related reagents within the methods text and for kits in the Key Resources Table. Additional descriptions of the primers used for re-amplification and RACE were added to the Methods (p. 28-29).

      d. Spell and grammar check is needed throughout the manuscript is needed. Example. In Page # 46 RXRγlo is misspelled as RXRlo.

      Spelling and grammar checks were reviewed.

      (2) Methods & Key Resource table.

      a. In Page # 21, IRB# needs to be stated.      

      The IRB protocols have been added, now at top of p. 26.

      b. In Page # 21, Did the authors dissociate retinae in ice-cold phosphate-buffered saline or papain?   

      The relevant sentence was corrected to “dissected while submerged in ice-cold phosphatebuffered saline (PBS) and dissociated as described10.” ( p. 26)

      c. In Page # 21, How did the authors count or enumerate the cell count? Provide the details.

      We now state, “… a 10 µl volume was combined with 10 µl trypan blue and counted using a hemocytometer” (top of p. 27)

      d. Why did the authors choose to specifically use only 8 cells for cDNA preparation in Page # 22? State the reason and provide the details.

      The reasons for using 8 cells (to prevent evaporation and to manually transfer one slide-worth of droplets to one strip of PCR tubes) and additional single cell collection details are now provided as follows (new text underlined): 

      “Single cells were sorted on a BD FACSAria I at 4°C using 100 µm nozzle in single-cell mode into each of eight 1.2 µl lysis buffer droplets on parafilm-covered glass slides, with droplets positioned over pre-defined marks … .  Upon collection of eight cells per slide, droplets were transferred to individual low-retention PCR tubes (eight tubes per strip) (Bioplastics K69901, B57801) pre-cooled on ice to minimize evaporation. The process was repeated with a fresh piece of parafilm for up to 12 rounds to collect 96 cells). (p. 27, new text underlined)

      e. Key resource table does not include several resources used in this study. Example - NR2E3 antibody.

      We added the NR2E3 antibody and checked for other omissions.

      (3) Results & Figures & Figure Legends

      a. Regulon-defined RPC and photoreceptor precursor states

      i. On page # 4, 1 paragraph - Clarify the sentence 'Exclusion of all cells with <100,000 cells read and 18 cells.........Emsembl transcripts inferred'. Did the authors use 18 cells or 18FW retinae? 

      The sentence was changed to:

      “After sequencing, we excluded all cells with <100,000 read counts and 18 cells expressing one or more markers of retinal ganglion, amacrine, and/or horizontal cells (POU4F1, POU4F2, POU4F3, TFAP2A, TFAP2B, ISL1) and concurrently lacking photoreceptor lineage marker OTX2. This yielded 794 single cells with averages of 3,750,417 uniquely aligned reads, 8,278 genes detected, and 20,343 Ensembl transcripts inferred (Figure S1A-C).” (p. 4, new words underlined)

      To clarify that 18 retinae were used, the first sentence of the Results was revised as follows:

      “To interrogate transcriptomic changes during human photoreceptor development, dissociated RPCs and photoreceptor precursors were FACS-enriched from 18 retinae, ages FW13-19 …” (p. 4).

      Why did the authors 'exclude cells lacking photoreceptor lineage marker OTX2' from analysis especially when the purpose here was to choose photoreceptor precursor states & further results in the next paragraph clearly state that 5 clusters were comprised of cells with OTX2 and CRX expression. This is confusing.

      We apologize for the imprecise diction. We divided the evidently confusing sentence into two sentences to more clearly indicate that we removed cells that did not express OTX2, as in the first response to the previous question.

      ii. In Page # 5, the authors reported the number of cell populations (363 large and 5 distal) identified in the THRB+ L/M-cone cluster. What were the # of cell populations identified in the remaining 5 clusters of the UMAP space?

      We added the cell numbers in each group to Fig. 1B. We corrected the large LM group to 366 cells (p. 5) and note 371 LM cells , which includes the five distal cells, in Figure 1B.

      b. Differential expression of NRL and THRB isoforms in rod and cone precursors

      i. In Figure 3B, the authors compare and show the presence of 5 different NRL isoforms for all the 6 clusters that were defined in 3A. However, in the results, the ENST# of just 2 highly assigned transcript isoforms is given. What are the annotated names of the three other isoforms which are shown in 3B? Please explain in the Results.

      As requested, we now annotate the remaining isoforms as encoding full-length or truncated NRL in Fig. 3B and show isoform structures in new Supplementary Figure S4B.  We also refer to each transcript isoform in the Results (p. 7, last paragraph) and similarly evaluate all isoforms in RB31 cells (Fig. S5B).

      ii. What does the Mean FPM in the y-axis of Fig 3C refer to?

      Mean FPM represents mean read counts (fragments per million, FPM) for each position across Ensembl NRL exons for each cluster, as now stated in the 6th line of the Fig. 3 legend.

      iii. A clear explanation of the results for Figures 3E-3F is missing.

      We revised the text to more clearly describe the experiment as follows:

      “The cone cells’ higher proportional expression of Tr-NRL first exon sequences was validated by RNA fluorescence in situ hybridization (FISH) of FW16 fetal retina in which NRL immunofluorescence was used to identify rod precursors, RXRg immunofluorescence was used to identify cone precursors, and FISH probes specific to truncated Tr-NRL exon 1T or FL-NRL exons 1 and 2 were used to assess Tr-NRL and FL-NRL expression (Figure 3E,F).” (p. 8, new text underlined).

      c. Two post-mitotic photoreceptor precursor populations

      i. Although deep-sequencing and SCENIC analysis clarified the identities of four RPC-localized clusters as MG, RPC, and iPRP indicative of cone-bias and TR indicative of rod-bias. It would be interesting to see the discriminating determinant between the TR and ER by SCENIC and deep-sequencing gene expression violin/box plots.

      We agree it is of interest to see the discriminating determinant between the TR [now termed iRP] and ER clusters by SCENIC and deep-sequencing gene expression violin/box plots. We now provide this information for selected genes and regulons of interest in the new Supplementary Figures S10A and S10C, along with a similar comparison between the prior high-resolution iPRP (now termed iCP) cluster and the first high-resolution LM cluster, LM1, as described for gene expression on p. 12:

      “Notably, THRB and GNAT2 expression did not significantly change while ONECUT1 declined in the subsequent non-RPC-localized iCP and LM1 stages, whereas NR2E3 and NRL dramatically increased on transitioning to the ER state (Figure S10A).”

      And as described for regulon activities on pp. 13-14:

      “Finally, activities of the cone-specific THRB and ISL2 regulons, the rod-specific NRL regulon, and the pan-photoreceptor LHX3, OTX2, CRX, and NEUROD1 regulons increased to varying extents on transitioning from the immature iCP or iRP states to the early-maturing LM1 or ER states (Figure 10C).”

      We also show expression of the same genes for spatiotemporally grouped cells from the Zuo et al. dataset in the new Figure S10B, which displays a similar pattern (apart from the possibly mixed pcw 10 and pcw13 designated rod precursors).

      d. Early cone precursors with cone- and rod-related RNA expression

      i. On page #12, the last paragraph where the authors explain the multiplex RNA FISH results of RXRγ and NR2E3 by citing Figure S8E. However, in Fig S8E, the authors used NRL to identify the rods. Please clarify which one of the rod markers was used to perform RNA FISH?

      Figure S8E (where NRL was used as a rod marker) was cited to remind readers that RXRg has low expression in rods and high expression in cones, rather than to describe the results of this multiplex FISH section. To avoid confusion on this point, Figure S8E is now cited using “(as earlier shown in Figure S8E).” With this issue clarified, we expect the markers used in the FISH + IF analysis will be clear from the revised explanation, 

      “… we examined GNAT2 and NR2E3 RNA co-expression in RXRg+ cone precursors in the outermost NBL and in RXRg+ rod precursors in the middle NBL … .” (p. 14-15).

      To provide further clarity, we provide a diagram of the FISH probes, protein markers, and expression patterns in the new Figure 7E.

      ii. The Y-axis of Fig 6G-6H needs to be labelled.

      The axes have been re-labeled from “Nb of cells” to “Number of RXRg+ outermost NBL cells in each region” (original Fig. 6G, now Fig. 7C) and “Number of RXRg+ middle NBL cells in each region” (original Fig. 6H, now Fig. 7D).

      iii. The legends of Figures 6G and 6H are unclear. In the Figure 6G legend, the authors indicate 'all cells are NR2E3 protein-'. Does that imply the yellow and green bars alone? Similarly, clarify the Figure 6H legend, what does the dark and light magenta refer to? What does the light magenta color referring to NR2E3+/ NR2E3- and the dark magenta color referring to NR2E3+/ NR2E3+ indicate? 

      We regret the insufficient clarity. We revised the Fig. 6G (now Fig. 7C) key, which now reads

      “All outermost NBL cells are NR2E3 protein-negative.”  We added to the figure legend for panel 7C,D “(n.b., italics are used for RNAs, non-italics for proteins).”  The new scheme in Figure 7E shows the RNAs in italics proteins in non-italics. We hope these changes will clarify when RNA or protein are represented in each histogram category.

      Overall, the results (on page # 13) reflecting Figures 6E-6H & Figure S11 are confusing and difficult to understand. Clear descriptions and explanations are needed.

      We revised this results section described in the paragraph now spanning p. 14:

      -  We now refer to the bar colors in Figures 7C and 7D that support each statement. 

      -  We provide an illustration of the findings in Figure 7E.

      iv. Previously published literature has shown that cells of the inner NBL are RXRγ+ ganglion cells. So, how were these RXRγ+ ganglion cells in the inner NBL discriminated during multiplex RNA FISH (in Fig 6E-6H and in Fig S11)?

      We thank the reviewer for requesting this clarification. We agree that “inner NBL” is the incorrect term for the region in which we examined RXRg+ photoreceptor precursors, as this could include RXRγ+ nascent RGCs. We now clarify that 

      “we examined GNAT2 and NR2E3 RNA co-expression in RXRg+ cone precursors in the outermost NBL and in RXRg+ rod precursors in the middle NBL … .”  (p. 14-15) We further state, 

      “Limiting our analysis to the outer and middle NBL allowed us to disregard RXRγ+ retinal ganglion cells in the retinal ganglion cell layer or inner NBL (top of p. 15)”

      Figure 7E is provided to further aid the reader in understanding the positions examined, and the legend states “RXRg+ retinal ganglion cells in the inner NBL and ganglion cell layer not shown. 

      v. In Figure 6E, what marker does each color cell correspond to?

      In this figure (now panel 7A), we declined to provide the color key since the image is not sufficiently enlarged to visualize the IF and FISH signals. The figure is provided solely to document the regions analyzed and readers are now referred to “see Figure S12 for IF + FISH images” (2nd line, p. 15), where the marker colors are indicated.

      vi. In Figure S11 & 6E, Protein and RNA transcript color of NR2E3, GNAT2 are hard to distinguish. Usage of other colors is recommended.  

      We appreciate the reviewer’s concern related to the colors (in the now redesignated Figure S12 and 7A); however, we feel this issue is largely mitigated by our use of arrows to point to the cells needed to illustrate the proposed concepts in Figure S12B. All quantitation was performed by examining each color channel separately to ensure correct attribution, which is now mentioned in the Methods (2nd-to-last line of Quantitation of FISH section, p. 35).

      vii. 

      With due respect, we suggest that labeling each box (now in Figure 8B) makes the figure rather busy and difficult to infer the main point, which is that boxed regions were examined at various distanced from the center (denoted by the “C” and “0 mm”) with distances periodically indicated. We suggest the addition of such markers would not improve and might worsen the figure for most readers.    

      e. An early L/M cone trajectory marked by successive lncRNA expression

      i. In Figure 8C - color-coded labelling of LM1-4 clusters is recommended.

      We note Fig. 8C (now 9C) is intended to use color to display the pseudotemporal positions of each cell. We recognize that an additional plot with the pseudotime line imposed on LM subcluster colors could provide some insights, yet we are unaware of available software for this and are unable to develop such software at present. To enable readers to obtain a visual impression of the pseudotime vs subcluster positions, we now refer the reader to Figure 5A in the revised figure legend, as follows:  (“The pseudotime trajectory may be related to LM1-LM4 subcluster distributions in Figure 5A.”).

      ii. In Figure 8G - what does the horizontal color-coded bar below the lncRNAs name refer to? These bars are similar in all four graphs of the 8G figure.

      As stated in the Fig. 8G (now 9G) legend, “Colored bars mark lncRNA expression regions as described in the text.”  We revised the text to more clearly identify the color code. (p. 18-19)   

      f. Cone intrinsic SYK contributions to the proliferative response to pRB loss

      i. In Fig 9F - The expression of ARR3+ cells (indicated by the green arrow in FW18) is poorly or rarely seen in the peripheral retina.

      We thank the reviewer for finding this oversight. In panel 9F (now 10F), we removed the green arrows from the cells in the periphery, which are ARR3- due to the immaturity of cones in this region. 

      ii. In Figure 9F - Did the authors stain the FW16 retina with ARR3?

      Unfortunately, we did not stain the FW16 retina for ARR3 in this instance.

      iii. Inclusion of DAPI staining for Fig 9F is recommended to justify the ONL & INL in the images.

      We regret that we are unable to merge the DAPI in this instance due to the way in which the original staining was imaged.  A more detailed analysis corroborating and extending the current results is in progress. 

      iv. Immunostaining images for Figure 9G are missing & are required to be included. What does shSCR in Fig 9G refer to?

      We now provide representative immunostaining images below the panel (now 10G). The legend was updated: “Bottom: Example of Ki67, YFP, and RXRg co-immunostaining with DAPI+ nuclei (yellow outlines). Arrows: Ki67+, YFP+, RXRg+ nuclei.”  The revised legend now notes that shSCR refers to the scrambled control shRNA.

      v. For Figure 9H - Is the presence and loss of SYK activity consistent with all the subpopulations (S & LM) of early maturing and matured cones?

      We appreciate the reviewer’s question and interest (relating to the redesignated Figure 10H); however, we have not yet completed a comprehensive evaluation of SYK expression in all the subpopulations (S & LM) of early maturing and matured cones and will reserve such data for a subsequent study. We suggest that this information is not critical to the study’s major conclusions.

      vi. Figure 9A is not explained in the results. Why were MYCN proteins assessed along with ARR3 and NRL? What does this imply?

      We thank the reviewer for noting that this figure (now Figure 10A) was not clearly described. 

      As per the response to Reviewer 1, point 6 , the text now states,  

      “The upregulation of MYC target genes was of interest given that many MYC target genes are also MYCN targets, that MYCN protein is highly expressed in maturing (ARR3+) cone precursors but not in NRL+ rods (Figure 10A), and that MYCN is critical to the cone precursor proliferative response to pRB loss [8–10].” (middle, p. 19, new text underlined).

      Hence, the figure demonstrates the cone cell specificity of high MYCN protein.  This is further noted in the Fig. 10a legend: “A. Immunofluorescent staining shows high MYCN in ARR3+ cones but not in NRL+ rods in FW18 retina.”

    1. Author response:

      Reviewer #1 (Public review):

      Functional lateralization between the right and left hemispheres is reported widely in animal taxa, including humans. However, it remains largely speculative as to whether the lateralized brains have a cognitive gain or a sort of fitness advantage. In the present study, by making use of the advantages of domestic chicks as a model, the authors are successful in revealing that the lateralized brain is advantageous in the number sense, in which numerosity is associated with spatial arrangements of items. Behavioral evidence is strong enough to support their arguments. Brain lateralization was manipulated by light exposure during the terminal phase of incubation, and the left-to-right numerical representation appeared when the distance between items gave a reliable spatial cue. The light-exposure induced lateralization, though quite unique in avian species, together with the lack of intense inter-hemispheric direct connections (such as the corpus callosum in the mammalian cerebrum), was critical for the successful analysis in this study. Specification of the responsible neural substrates in the presumed right hemisphere is expected in future research. Comparable experimental manipulation in the mammalian brain must be developed to address this general question (functional significance of brain laterality) is also expected.

      We sincerely appreciate the Reviewer's insightful feedback and his/her recognition of the key contributions of our study.

      Reviewer #2 (Public review):

      Summary:

      This is the first study to show how a L-R bias in the relationship between numerical magnitude and space depends on brain lateralisation, and moreover, how is modulated by in ovo conditions.

      Strengths:

      Novel methodology for investigating the innateness and neural basis of an L-R bias in the relationship between number and space.

      We would like to thank the Reviewer for their valuable feedback and for highlighting the key contributions of our study.

      Weaknesses:

      I would query the way the experiment was contextualised. They ask whether culture or innate pre-wiring determines the 'left-to-right orientation of the MNL [mental number line]'.

      We thank the Reviewer for raising this point, which has allowed us to provide a more detailed explanation of this aspect. Rather than framing the left-to-right orientation of the mental number line (MNL) as exclusively determined by either cultural influences or innate pre-wiring, our study highlights the role of environmental stimulation. Specifically, prenatal light exposure can shape hemispheric specialization, which in turn contributes to spatial biases in numerical processing. Please see lines 115-118.

      The term, 'Mental Number Line' is an inference from experimental tasks. One of the first experimental demonstrations of a preference or bias for small numbers in the left of space and larger numbers in the right of space, was more carefully described as the spatialnumerical association of response codes - the SNARC effect (Dehaene, S., Bossini, S., & Giraux, P. (1993). The mental representation of parity and numerical magnitude. Journal of Experimental Psychology: General, 122, 371-396).

      We have refined our description of the MNL and SNARC effect to ensure conceptual accuracy in the revised manuscript; please see lines 53-59.

      This has meant that the background to the study is confusing. First, the authors note, correctly, that many other creatures, including insects, can show this bias, though in none of these has neural lateralisation been shown to be a cause. Second, their clever experiment shows that an experimental manipulation creates the bias. If it were innate and common to other species, the experimental manipulation shouldn't matter. There would always be an LR bias. Third, they seem to be asserting that humans have a left-to-right (L-R) MNL. This is highly contentious, and in some studies, reading direction affects it, as the original study by Dehaene et al showed; and in others, task affects direction (e.g. Bachtold, D., Baumüller, M., & Brugger, P. (1998). Stimulus-response compatibility in representational space. Neuropsychologia, 36, 731-735, not cited). Moreover, a very careful study of adult humans, found no L-R bias (Karolis, V., Iuculano, T., & Butterworth, B. (2011), not cited, Mapping numerical magnitudes along the right lines: Differentiating between scale and bias. Journal of Experimental Psychology: General, 140(4), 693-706). Indeed, Rugani et al claim, incorrectly, that the L-R bias was first reported by Galton in 1880. There are two errors here: first, Galton was reporting what he called 'visualised numerals', which are typically referred to now as 'number forms' - spontaneous and habitual conscious visual representations - not an inference from a number line task. Second, Galton reported right-to-left, circular, and vertical visualised numerals, and no simple left-to-right examples (Galton, F. (1880). Visualised numerals. Nature, 21, 252-256.). So in fact did Bertillon, J. (1880). De la vision des nombres. La Nature, 378, 196-198, and more recently Seron, X., Pesenti, M., Noël, M.-P., Deloche, G., & Cornet, J.-A. (1992). Images of numbers, or "When 98 is upper left and 6 sky blue". Cognition, 44, 159-196, and Tang, J., Ward, J., & Butterworth, B. (2008). Number forms in the brain. Journal of Cognitive Neuroscience, 20(9), 1547-1556.

      We sincerely appreciate the opportunity to discuss numerical spatialization in greater detail. We have clarified that an innate predisposition to spatialize numerosity does not necessarily exclude the influence of environmental stimulation and experience. We have proposed an integrative perspective, incorporating both cultural and innate factors, suggesting that numerical spatialization originates from neural foundations while remaining flexible and modifiable by experience and contextual influences. Please see lines 69–75.

      We have incorporated the Reviewer’s suggestions and cited all the recommended papers; please see lines 47–75.

      If the authors are committed to chicks' MN Line they should test a series of numbers showing that the bias to the left is greater for 2 and 3 than for 4, etc. 

      What does all this mean? I think that the paper should be shorn of its misleading contextualisation, including the term 'Mental Number Line'. The authors also speculate, usefully, on why chicks and other species might have a L-R bias. I don't think the speculations are convincing, but at least if there is an evolutionary basis for the bias, it should at least be discussed.

      In the revised version of the manuscript, we have resorted to adopt the Spatial Numerical Association (SNA). We thank the Reviewer for this valuable comment.

      We appreciated the Reviewer’s suggestion regarding the evolutionary basis of lateralization and have included considerations of its relevance in chicks and other species; please see lines 143-151 and 381-386.

      This paper is very interesting with its focus on why the L-R bias exists, and where and why it does not.

      We wish to thank the Reviewer again for his/her work.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1:

      “EGFRvIII is mainly associated with the classical subtype, so the mesenchymal subtype might be unexpected here. This could be commented on.” 

      We acknowledge that EGFRvIII is most often associated with the classical subtype of glioblastoma and agree that mesenchymal subtype classification may be unexpected given the use of her4.1:EGFRvIII as a driver in our model. We would like to highlight the fact that our brain tumors do also express certain markers associated with the classical subtype including neural precursor and neural stem cell markers like sox2, ascl1b, and gli2 (Supplementary Fig 4, 5; Supplementary Table 1-3). However, our transcriptomic data was not found to significantly enrich for classical subtype gene expression, compared to normal brains. This could be due to a significant contribution of normal brain tissue to our analyses (bulk tumor burdened brains were harvested for RNA sequencing), as well as the significant contribution of mesenchymal subtype signatures and/or inflammatory gene expression in our brain tumor-positive samples. Because signatures associated with inflammation consist of some of the most highly upregulated genes in our samples, this could potentially dilute out and/or lessen alterative subtype and/or signature gene expression. Importantly, it is now widely appreciated that patient tumors simultaneously consist of heterogenous tumor cells reflecting multiple molecular subtypes (Couturier et al., 2020; Darmanis et al., 2017; Neftel et al., 2019), providing glioblastoma with a high level of phenotypic plasticity. We also demonstrate that the contribution of additional drivers not always present with EGFRvIII in patient glioblastoma enhances primary brain tumors in vivo. This result is consistent with more aggressive glioblastomas seen in patients with EGFRvIII variants and TP53 loss-of-function mutations (Ruano et al., 2009). It will therefore be interesting in the future to consider how single or multiple driver mutations contribute to subtype-specific gene expression in our model, as well as histopathology, relative to patients. We have included some of these discussion points to our revised manuscript.     

      “Some more histologic characterization of the tumors would be helpful. Are they invasive, do larger tumors show necrosis and microvascular proliferation? This would help with understanding the full potential of the new model.”

      We have updated our manuscript to include more histolopathological characterization and images (Supplementary Fig 2).

      “Current thinking in established glioblastoma is that the M1/M2 designations for macrophages are not relevant, with microglia macrophage populations showing a mixture of pre- and anti-inflammatory features. Ideally, there would be a much more detailed characterization of the intratumoral microglia/macrophage population here, as single markers can’t be relied upon.”

      We performed additional gene set enrichment analyses (GSEA) using our sequencing datasets and compared p53EPS gene expression to M1/M2 macrophage expression signatures and expression signatures from MCSF-stimulated macrophages at early and late (M2 polarized) time-points. From this analysis, we detected enrichment for markers of both pro- and antiinflammatory features, however, with stronger and significant enrichment for gene expression signatures associated with classical pro-inflammatory M1 macrophages. We have included these GSEA plots and gene set enrichment lists as supplementary materials (Supplementary Fig 6, Supplementary Table 6). We also performed GSEA against a broad curated set of immunologic gene sets (C7: immunologic signature gene sets, Molecular Signatures Database, (Liberzon et al., 2011)) and have included the list of signatures and enrichment scores as a supplementary table (Supplementary Table 6). 

      “Phagocytosis could have anti-tumor effects through removal of live cancer cells or could be cancer-promoting if apoptotic cells are being rapidly cleared with concomitant activation of an immunosuppressive phenotype in the phagocytes (ie. efferocytosis).” 

      We looked at efferocytosis-associated gene expression in our sequencing dataset (124 “efferocytosis” genes, GeneCards), and while we detected upregulation of certain genes associated with efferocytosis in p53EPS brains, we did not detect significant enrichment for the entire gene set. Furthermore, we did not detect up-regulation of key efferocytosis receptors including Axl and Tyro3 (Supplementary Table 1, 2), compared to normal brains. While efferocytosis may contribute to tumor growth and evolution, this GSEA combined with our functional data supporting an inhibitory role for phagocytes in p53EPS tumor initiation and engraftment following transplantation (Fig 4, Fig 5, Supplementary Fig 7), suggests that efferocytosis is not a major driver of tumor formation in our model. However, how efferocytosis affects tumor progression in our model and/or relapse following therapy will be an interesting feature to explore in the future using temporal manipulations of phagocytes and/or treatments with chemical inhibitors.

      Author response image 1.

      Gene Set Enrichment Analysis (GSEA) for efferocytosis-associated gene expression (124 “efferocytosis” genes in GeneCards) in tp53EPS tumor brains, compared to normal zebrafish brains. Normalized enrichment score (NES) and p-value are indicated. 

      “Do the irf7/8 and chlodronate experiments distinguish between effects on microglia/macrophages and dendritic cells?”

      In addition to microglia/macrophages, the IRF8 transcription factor has been shown to control survival and function of dendritic cells (Sichien et al., 2016). Chlodronate treatments are also used to deplete both macrophages and dendritic cells in vivo. Therefore, we cannot distinguish the effects of these manipulations in our experiments and have updated our manuscript throughout to reflect this.     

      Reviewer #2:

      “The authors state that oncogenic MAPK/AKT pathway activation drives glial-derived tumor formation. It would be important to include a wild-type or uninjected control for the pERK and pAKT staining shown in Fig1 I-K to aid in the interpretation of these results. Likewise, quantification of the pERK and pAKT staining would be useful to demonstrate the increase over WT, and would also serve to facilitate comparison with the similar staining in the KPG model (Supp Fig 2D).”

      We have updated Fig 1 and Supplementary Fig 3D (formerly Fig 2D), to include histology from tumor-free uninjected control animals, as well as quantifications of p-ERK and p-AKT staining to highlight increased MAPK/AKT signaling pathway activation in our tumor model.  

      “The authors use a transplantation assay to further test the tumorigenic potential of dissociated cells from glial-derived tumors. Listing the percentage of transplants that generate fluorescent tumor would be helpful to fully interpret these data. Additionally, it was not clear based on the description in the results section that the transplantation assay was an “experimental surrogate” to model the relapse potential of the tumor cell. This is first mentioned in the discussion. The authors may consider adding a sentence for clarity earlier in the manuscript as it helps the reader better understand the logic of the assay.” 

      We have clarified in the text the percentage of transplants that generated fluorescent tumor (1625%, n=3 independent screens). This is also represented in Fig 5C,D. We also added text when introducing the transplantation assay, explaining that transplantation is frequently used as an experimental surrogate to assess relapse potential, and that our objective was to assess tumor cell propagation in the context of specific manipulations within the TME.  

      “The authors nicely show high levels of immune cell infiltration and associations between microglia/macrophages and tumor cells. However, a quantification of the emergence of macrophages over time in relation to tumor initiation and growth would provide significant support to the observations of tumor suppressive activity of the phagocytes. Along these lines, the inclusion of a statement about when leukocytes emerge during normal development would be informative for those not familiar with the zebrafish model.”

      In zebrafish, microglia colonize the neural retina by 48 hpf, and the optic tectum by 84 hpf (Herbomel et al., 2001), prior to when we typically observe lesions in our p53EPS brains. To validate the emergence of microglia prior to tumor formation in p53EPS, we have now used live confocal imaging through the brains of uninjected control and p53EPS injected zebrafish at 5, 7 and 9 dpf. As expected, microglia were present throughout the cephalic region and in the brain at 5 dpf (120 hpf). At this stage, p53EPS injected zebrafish brains displayed mosaic cellular expression of her4.1:mScarlet; however, cells were sparse and diffuse, and no large intensely fluorescent tumor-like clusters were detected at this stage (n=12/12 tumor negative). At 7 dpf, microglia were observed in the brains of control and p53EPS zebrafish; however, at this stage we detected clusters of her4.1:mScarlet+ cells (n=5/9), indicative of tumor formation. Lesions were found to be surrounded and/or infiltrated by mpeg:_EGFP+ microglia. Finally, at 9 dpf _her4.1:mScarlet+ expression became highly specific to tumor lesions, and these lesions were associated with _mpeg:_EGFP+ microglia/macrophages (n=8/8 of tumor-positive zebrafish). These descriptions along with representative images has been added to Figure 3.

      “From the data provided in Figure 4G and Supp Fig 7b, the authors suggest that “increased p53EPS tumor initiation following Irf gene knock-down is a consequence of irf7 and irf8 loss-of-function in the TME.” Given the importance of the local microenvironment highlighted in this study, spatial information on the form of in situ hybridization to identify the relevant location of the expression change would be important to support this conclusion.”

      We performed fluorescent in situ hybridization (using HCR RNA-FISH, Molecular Instruments) on whole mount control and irf7 CRISPR-injected p53EPG animals (her4.1:EGFRvIII +her4.1:PI3KCAH1047R + her4.1:GFP, GFP was used in this case because of probe availability).

      Representative confocal projections through tumors, as well as single optical sections are presented and discussed in Figure 4, highlighting the location of irf7 expression change following gene knock-down. We found significant irf7 signal in and surrounding p53EPS tumors at early stages of tumor formation_. This expression was reduced and/or lost following _irf7 CRISPR gene targeting, consistent with RT-PCR data (Supplementary Fig 7).          

      “The authors used neutral red staining that labels lysosomal-rich phagocytes to assess enrichment at the early stages of tumor initiation. The images in Figure 3 panel A should be labeled to denote the uninjected controls to aid in the interpretation of the data. In Supplemental Figure 6, the neutral red staining in the irf8 CRISPR-injected larvae looks to be increased, counter to the quantification. Can the authors comment if the image is perhaps not representative?”

      We have updated Figure 3 and Supplementary Figure 6 to aid in the interpretation of our results. In Fig 3A, we used tumor-negative controls from our injected cohorts. This was done to control for exogenous transgene presence and/or over-expression prior to (or in the absence of) malignant transformation. In Supplementary Fig 6, our images are representative, but we have now used unprocessed images with arrowheads to highlight neutral-red positive foci for clarity. In our original manuscript the images contained software generated markers, which could have obscured and/or confused the neutral red staining we were trying the highlight.    

      Recommendations For the Authors:

      Reviewer #1: 

      “The PI 3-kinase does a lot more than just activating mTOR and Akt – I would suggest modifying that sentence in the introduction.”

      We have adjusted text in the introduction to reflect the broad role for PI3K signaling.

      Reviewer #2:

      “In Supplemental Fig 1, it would be helpful for the authors to provide a co-stain, such as DAPI to label all nuclei, which would allow the reader to assess the morphology of the cells in the context of the surrounding tissue.”

      We have included brightfield images in Supplementary Fig 1, that together with her4.1:mScarlet fluorescence, should help readers assess tumor location and morphology in the context of surrounding tissue. Tumor cell morphology at high-resolution can be visualized in Fig 3, Movie 1 and Movie 2.

      “The authors state that oncogenic MAPK/AKT pathway activation drives glial-derived tumor formation. The authors may consider testing if the addition of an inhibitor of MAPK signaling may prevent or decrease the formation of glial-derived tumors in this context to further support their results.” 

      To further assess the role for MAPK activation, we decided to test the effect of 50uM AZD6244 MAPK inhibitor following transplantation of dissociated primary p53EPS cells into syngeneic CG1 strain zebrafish embryos, similar to as previously described (Modzelewska et al., 2016). Following 5 days of drug treatments, we did not detect significant differences in tumor engraftment or in tumor size between DMSO control and AZD6244-treated cohorts, suggesting that MAPK inhibition is not sufficient to prevent p53EPS engraftment and growth in our model. In the future, assessments of on-target drug effects, possible resistance mechanisms, and/or testing MAPK inhibitors in combination with other targeted agents including Akt and/or mTOR inhibitors (Edwards et al., 2006; McNeill et al., 2017; Schreck et al., 2020) will enhance our understanding of potential therapeutic strategies.

      Author response image 2.

      Dorsal views of 8 dpf zebrafish larvae engrafted with her4.1:mScarlet+ p53EPS tumor cells following treatment from 3-8dpf with 0.1% DMSO (control) or 50uM AZD6244. Tumor cell injections were performed at 2 dpf into syngeneic CG1 strain embryos. The percentage of total animals with persisting engraftment following drug treatments, as well as tumor size (microns squared, quantified using Carl Zeiss ZEN software) are shown for control and AZD6244 treated larvae. 

      “Have the authors tested if EGFR and PI3KCA driven by other neural promoters produce similar results, or not? This would help support the specificity of her4.1 neural progenitors and glia as the cell of origin in this model.”

      At this time, we have not tested other neural promoters. However, previous reports describe a zebrafish zic4-driven glioblastoma model with mesenchymal-like gene expression (Mayrhofer et al., 2017), supporting neural progenitors as a cell of origin. In the future it will be interesting to test sox2, nestin, and gfap promoters to further define and support her4.1-expressing neural progenitors and glia as the cell of origin in our model.

      “Other leukocyte populations, such as neutrophils, can also respond to inflammatory cues. Can the authors comment if neutrophils are also observed in the TME?”

      We performed initial assessments of neutrophils in the TME using our expression datasets as well as her4.1:EGFRvIII + her4.1:PI3KCAH1047R co-injection into Tg(mpx:EGFP) strain zebrafish. We observed tumor formation without significant infiltration of mpx:EGFP+ neutrophils. Future investigations will be important to assess differences in the contributions of different myeloidderived lineages in the TME of p53EPS, as well as how heterogeneity may be altered depending on different oncogenic drivers and/or stage of tumor progression, as seen in human glioblastoma (Friedmann-Morvinski and Hambardzumyan, 2023). We have added text in the disscussion section of our manuscript to indicate the possibility of neutrophils and/or other immune cell types contributing to p53EPS tumor biology. 

      Author response image 3.

      Control-injected tumornegative and tumor-positive Tg(mpx:EGFP) zebrafish at 10 dpf. Tg(mpx:EGFP) strain embryos were injected at the one-cell stage with her4.1:EGFRvIII + her4.1:PI3KCAH1047R + her4.1:mScarlet.

      “It is not clear if the transcriptomics data has been deposited in a publicly available database, such as the Gene Expression Omnibus (GEO). Sharing of these data would be a benefit to the field and facilitate use in other studies.”

      We have uploaded all transcriptomic data to GEO under accession GSE246295.

    1. Author response:

      Reviewer #1 (Public Review):

      Summary:

      In this manuscript, the authors investigated the effect of chronic activation of dopamine neurons using chemogenetics. Using Gq-DREADDs, the authors chronically activated midbrain dopamine neurons and observed that these neurons, particularly their axons, exhibit increased vulnerability and degeneration, resembling the pathological symptoms of Parkinson's disease. Baseline calcium levels in midbrain dopamine neurons were also significantly elevated following the chronic activation. Lastly, to identify cellular and circuit-level changes in response to dopaminergic neuronal degeneration caused by chronic activation, the authors employed spatial genomics (Visium) and revealed comprehensive changes in gene expression in the mouse model subjected to chronic activation. In conclusion, this study presents novel data on the consequences of chronic hyperactivation of midbrain dopamine neurons.

      Strengths:

      This study provides direct evidence that the chronic activation of dopamine neurons is toxic and gives rise to neurodegeneration. In addition, the authors achieved the chronic activation of dopamine neurons using water application of clozapine-N-oxide (CNO), a method not commonly employed by researchers. This approach may offer new insights into pathophysiological alterations of dopamine neurons in Parkinson's disease. The authors also utilized state-of-the-art spatial gene expression analysis, which can provide valuable information for other researchers studying dopamine neurons. Although the authors did not elucidate the mechanisms underlying dopaminergic neuronal and axonal death, they presented a substantial number of intriguing ideas in their discussion, which are worth further investigation.

      We thank the reviewer for these positive comments.

      Weaknesses:

      Many claims raised in this paper are only partially supported by the experimental results. So, additional data are necessary to strengthen the claims. The effects of chronic activation of dopamine neurons are intriguing; however, this paper does not go beyond reporting phenomena. It lacks a comprehensive explanation for the degeneration of dopamine neurons and their axons. While the authors proposed possible mechanisms for the degeneration in their discussion, such as differentially expressed genes, these remain experimentally unexplored.

      We thank the reviewer for this review. We do believe that the manuscript has a mechanistic component, as the central experiments involve direct manipulation of neuronal activity, and we show an increase in calcium levels and gene expression changes in dopamine neurons that coincide with the degeneration. However, we agree that deeper mechanistic investigation would strengthen the conclusions of the paper. We have planned several important revisions, including the addition of CNO behavioral controls, manipulation of intracellular calcium using isradipine, additional transcriptomics experiments and further validation of findings. We anticipate that these additions will significantly bolster the conclusions of the paper.

      Reviewer #2 (Public Review):

      Summary:

      Rademacher et al. present a paper showing that chronic chemogenetic excitation of dopaminergic neurons in the mouse midbrain results in differential degeneration of axons and somas across distinct regions (SNc vs VTA). These findings are important. This mouse model also has the advantage of showing a axon-first degeneration over an experimentally-useful time course (2-4 weeks). 2. The findings that direct excitation of dopaminergic neurons causes differential degeneration sheds light on the mechanisms of dopaminergic neuron selective vulnerability. The evidence that activation of dopaminergic neurons causes degeneration and alters mRNA expression is convincing, as the authors use both vehicle and CNO control groups, but the evidence that chronic dopaminergic activation alters circadian rhythm and motor behavior is incomplete as the authors did not run a CNO-control condition in these experiments.

      Strengths:

      This is an exciting and important paper.

      The paper compares mouse transcriptomics with human patient data.

      It shows that selective degeneration can occur across the midbrain dopaminergic neurons even in the absence of a genetic, prion, or toxin neurodegeneration mechanism.

      We thank the reviewer for these insightful comments.

      Weaknesses:

      Major concerns:

      (1) The lack of a CNO-positive, DREADD-negative control group in the behavioral experiments is the main limitation in interpreting the behavioral data. Without knowing whether CNO on its own has an impact on circadian rhythm or motor activity, the certainty that dopaminergic hyperactivity is causing these effects is lacking.

      This is an important point. Although we show that CNO does not produce degeneration of DA neuron terminals, we do not exclude a contribution to the behavioral changes. We agree that this behavioral control is necessary, and will address it in revision with a CNO-only running wheel cohort.

      (2) One of the most exciting things about this paper is that the SNc degenerates more strongly than the VTA when both regions are, in theory, excited to the same extent. However, it is not perfectly clear that both regions respond to CNO to the same extent. The electrophysiological data showing CNO responsiveness is only conducted in the SNc. If the VTA response is significantly reduced vs the SNc response, then the selectivity of the SNc degeneration could just be because the SNc was more hyperactive than the VTA. Electrophysiology experiments comparing the VTA and SNc response to CNO could support the idea that the SNc has substantial intrinsic vulnerability factors compared to the VTA.

      We agree that additional electrophysiology conducted in the VTA dopamine neurons would meaningfully add to our understanding of the selective vulnerability in this model, and will complete these experiments in revision.

      (3) The mice have access to a running wheel for the circadian rhythm experiments. Running has been shown to alter the dopaminergic system (Bastioli et al., 2022) and so the authors should clarify whether the histology, electrophysiology, fiber photometry, and transcriptomics data are conducted on mice that have been running or sedentary.

      We will explicitly clarify which mice had access to a running wheel in our revision. Briefly, mice for histology, electrophysiology, and transcriptomics all had access to a running wheel during their treatment. The mice used for photometry underwent about 7 days of running wheel access approximately 3 weeks prior to the beginning of the experiment. The photometry headcaps sterically prevented mice from having access to a running wheel in their home cage.

      Reviewer #3 (Public Review):

      Summary:

      In this manuscript, Rademacher and colleagues examined the effect on the integrity of the dopamine system in mice of chronically stimulating dopamine neurons using a chemogenetic approach. They find that one to two weeks of constant exposure to the chemogenetic activator CNO leads to a decrease in the density of tyrosine hydroxylase staining in striatal brain sections and to a small reduction of the global population of tyrosine hydroxylase positive neurons in the ventral midbrain. They also report alterations in gene expression in both regions using a spatial transcriptomics approach. Globally, the work is well done and valuable and some of the conclusions are interesting. However, the conceptual advance is perhaps a bit limited in the sense that there is extensive previous work in the literature showing that excessive depolarization of multiple types of neurons associated with intracellular calcium elevations promotes neuronal degeneration. The present work adds to this by showing evidence of a similar phenomenon in dopamine neurons.

      We thank the reviewer for the careful and thoughtful review of our manuscript.

      While extensive depolarization and associated intracellular calcium elevations promotes degeneration generally, we emphasize that the process we describe is novel. Indeed, prior studies delivering chronic DREADDs to vulnerable neurons in models of Alzheimer’s disease did not report an increase in neurodegeneration, despite seeing changes in protein aggregation (e.g. Yuan and Grutzendler, J Neurosci 2016, PMID: 26758850; Hussaini et al., PLOS Bio 2020, PMID: 32822389). Further, a critical finding from our study is that in our paradigm, this stressor does not impact all dopamine neurons equally, as the SNc DA neurons are more vulnerable than the VTA, mirroring selective vulnerability characteristic of Parkinson’s disease. This is consistent with a large body of literature that SNc dopamine neurons are less capable of handling large energetic and calcium loads compared to neighboring VTA neurons, and the finding that chronically altered activity is sufficient to drive this preferential loss is novel.

      In addition, we are not aware of prior studies that have chronically activated DREADDs to produce neurodegeneration. Other studies have shown that acute excitotoxic stressors can produce neuronal degeneration, but the chronic increase in activity is central to our approach.

      In terms of the mechanisms explaining the neuronal loss observed after 2 to 4 weeks of chemogenetic activation, it would be important to consider that dopamine neurons are known from a lot of previous literature to undergo a decrease in firing through a depolarization-block mechanism when chronically depolarized. Is it possible that such a phenomenon explains much of the results observed in the present study? It would be important to consider this in the manuscript.

      As discussed in greater detail in the results section below, our data suggests this may not be a prominent feature in our model. However, we cannot rule out a contribution of depolarization block, and will expand on the discussion of this possibility in the revised manuscript.

      The relevance to Parkinson's disease (PD) is also not totally clear because there is not a lot of previous solid evidence showing that the firing of dopamine neurons is increased in PD, either in human subjects or in mouse models of the disease. As such, it is not clear if the present work is really modelling something that could happen in PD in humans.

      We completely agree that evidence of increased dopamine neuron activity from human PD patients is lacking and the existing data are difficult to interpret without human controls. However, as we outline in the manuscript, multiple lines of evidence suggest that the activity level of dopamine neurons almost certainly does change in PD. Therefore, it is very important that we understand how changes in the level of neural activity influence the degeneration of DA neurons. In this paper we examine the impact of increased activity. Increased activity may be compensatory after initial dopamine neuron loss, or may be an initial driver of death (Rademacher & Nakamura, Exp Neurol 2024, PMID: 38092187). Beyond what is already discussed in the manuscript, additional support for increased activity in PD models include:

      - Elevated firing rates in asymptomatic MitoPark mice (Good et al., FASEB J 2011, PMID: 21233488)

      - Increased frequency of spontaneous firing in patient-derived iPSC dopamine neurons and primary mouse dopamine neurons that overexpress synuclein (Lin et al., Acta Neuropath Comm 2021, PMID: 34099060)

      - Increased spontaneous firing in dopamine neurons of rats injected with synuclein preformed fibrils compared to sham (Tozzi et al., Brain 2021, PMID: 34297092)

      We will include and further discuss these important examples in our revision.

      Similarly, in future studies, it will also be important to study the impact of decreasing DA neuron activity. There will be additional levels of complexity to accurately model changes in PD, which may differ between subtypes of the disease, the disease stage, and the subtype of dopamine neuron. Our study models the possibility of chronically increased pacemaking, and interpretation of our results will be informed as we learn more about how the activity of DA neurons changes in humans in PD. We will discuss and elaborate on these important points in the revision.

      Comments on the introduction:

      The introduction cites a 1990 paper from the lab of Anthony Grace as support of the fact that DA neurons increase their firing rate in PD models. However, in this 1990 paper, the authors stated that: "With respect to DA cell activity, depletions of up to 96% of striatal DA did not result in substantial alterations in the proportion of DA neurons active, their mean firing rate, or their firing pattern. Increases in these parameters only occurred when striatal DA depletions exceeded 96%." Such results argue that an increase in firing rate is most likely to be a consequence of the almost complete loss of dopamine neurons rather than an initial driver of neuronal loss. The present introduction would thus benefit from being revised to clarify the overriding hypothesis and rationale in relation to PD and better represent the findings of the paper by Hollerman and Grace.

      We agree that the findings of Hollerman and Grace support compensatory changes in dopamine neuron activity in response to loss of dopamine neurons, rather than informing whether dopamine neuron loss can also be an initial driver of activity. We will clarify this point in our revision. In addition, the results of other studies on this point are mixed: a 50% reduction in dopamine neurons didn’t alter firing rate or bursting (Harden and Grace, J Neurosci 1995, PMID: 7666198; Bilbao et al, Brain Res 2006, PMID: 16574080), while a 40% loss was found to increase firing rate and bursting (Chen et al, Brain Res 2009. PMID: 19545547) and larger reductions alter burst firing (Hollerman & Grace, Brain Res 1990, PMID: 2126975; Stachowiak et al, J Neurosci 1987, PMID: 3110381). Importantly, even if compensatory, such late-stage increases in dopamine neuron activity may contribute to disease progression and drive a vicious cycle of degeneration in surviving neurons. In addition, we also don’t know how the threshold of dopamine neuron loss and altered activity may differ between mice and humans, and PD patients do not present with clinical symptoms until ~30-60% of nigral neurons are lost (Burke & O’Malley, Exp Neurol 2013, PMID: 22285449; Shulman et al, Annu Rev Pathol 2011, PMID: 21034221).

      Other lines of evidence support the potential role of hyperactivity in disease initiation, including increased activity before dopamine neuron loss in MitoPark mice (Good et al., FASEB J 2011, PMID: 21233488), increased spontaneous firing in patient-derived iPSC dopamine neurons (Lin et al., Acta Neuropath Comm 2021, PMID: 34099060), and increased activity observed in genetic models of PD (Bishop et al., J Neurophysiol 2010, PMID: 20926611; Regoni et al., Cell Death Dis 2020,  PMID: 33173027).

      It would be good that the introduction refers to some of the literature on the links between excessive neuronal activity, calcium, and neurodegeneration. There is a large literature on this and referring to it would help frame the work and its novelty in a broader context.

      We agree that a discussion of hyperactivity, calcium, and neurodegeneration would benefit the introduction. While we briefly discuss calcium and neurodegeneration in the discussion, we will expand on this literature in both the introduction and discussion sections. We will carefully review and contextualize our work within existing frameworks of calcium and neurodegeneration (e.g. Surmeier & Schumacker, J Biol Chem 2013, PMID: 23086948; Verma et al., Transl Neurodegener 2022, PMID: 35078537). We believe that the novelty of our study lies in 1) a chronic chemogenetic activation paradigm via drinking water, 2) demonstrating selective vulnerability of dopamine neurons as a result of altering their activity/excitability alone, and 3) comparing mouse and human spatial transcriptomics.

      Comments on the results section:

      The running wheel results of Figure 1 suggest that the CNO treatment caused a brief increase in running on the first day after which there was a strong decrease during the subsequent days in the active phase. This observation is also in line with the appearance of a depolarization block.

      The authors examined many basic electrophysiological parameters of recorded dopamine neurons in acute brain slices. However, it is surprising that they did not report the resting membrane potential, or the input resistance. It would be important that this be added because these two parameters provide key information on the basal excitability of the recorded neurons. They would also allow us to obtain insight into the possibility that the neurons are chronically depolarized and thus in depolarization block.

      We do report the input resistance in Supplemental Figure 1C, which was unchanged in CNO-treated animals compared to controls. We did not report the resting membrane potential because many of the DA neurons were spontaneously firing. However, we will report the initial membrane potential on first breaking into the cell for the whole cell recordings in the revision, which did not vary between groups. This is still influenced by action potential activity, but is the timepoint in the recording least impacted by dialyzing of the neuron by the internal solution. We observed increased spontaneous action potential activity ex vivo in slices from CNO-treated mice (Figure 1D), thus at least under these conditions these dopamine neurons are not in depolarization block. We also did not see strong evidence of changes in other intrinsic properties of the neurons with whole cell recordings (e.g. Figure S1C). Overall, our electrophysiology experiments are not consistent with the depolarization block model, at least not due to changes in the intrinsic properties of the neurons. Although our ex vivo findings cannot exclude a contribution of depolarization block in vivo, we do show that CNO-treated mice removed from their cages for open field testing continue to have a strong trend for increased activity for approximately 10 days (S1E).  This finding is also consistent with increased activity of the DA neurons. We will add discussion of these important considerations in the revision.

      It is great that the authors quantified not only TH levels but also the levels of mCherry, co-expressed with the chemogenetic receptor. This could in principle help to distinguish between TH downregulation and true loss of dopamine neuron cell bodies. However, the approach used here has a major caveat in that the number of mCherry-positive dopamine neurons depends on the proportion of dopamine neurons that were infected and expressed the DREADD and this could very well vary between different mice. It is very unlikely that the virus injection allowed to infect 100% of the neurons in the VTA and SNc. This could for example explain in part the mismatch between the number of VTA dopamine neurons counted in panel 2G when comparing TH and mCherry counts. Also, I see that the mCherry counts were not provided at the 2-week time point. If the mCherry had been expressed genetically by crossing the DAT-Cre mice with a floxed fluorescent reported mice, the interpretation would have been simpler. In this context, I am not convinced of the benefit of the mCherry quantifications. The authors should consider either removing these results from the final manuscript or discussing this important limitation.

      We thank the reviewer for this insightful comment, and we agree that this is a caveat of our mCherry quantification. Quantitation of the number of mCherry+ DA neurons specifically informs the impact on transduced DA neurons, and mCherry appears to be less susceptible to downregulation versus TH. As the reviewer points out, it carries the caveat that there is some variability between injections. Nonetheless, we believe that it conveys useful complementary data. As suggested, we will discuss this caveat in our revision. Note that mCherry was not quantified at the two-week timepoint because there is no loss of TH+ cells at that time.

      Although the authors conclude that there is a global decrease in the number of dopamine neurons after 4 weeks of CNO treatment, the post-hoc tests failed to confirm that the decrease in dopamine number was significant in the SNc, the region most relevant to Parkinson's. This could be due to the fact that only a small number of mice were tested. A "n" of just 4 or 5 mice is very small for a stereological counting experiment. As such, this experiment was clearly underpowered at the statistical level. Also, the choice of the image used to illustrate this in panel 2G should be reconsidered: the image suggests that a very large loss of dopamine neurons occurred in the SNc and this is not what the numbers show. A more representative image should be used.

      We agree that the stereology experiments were performed on relatively small numbers of animals. Combined with the small effect size, this may have contributed to the post-hoc tests showing a trend of p=0.1 for both the TH and mCherry dopamine cell counts in the SN at 4 weeks. As part of the planned experiments for our revision, we will perform an additional stereologic analysis to further assess the loss of SNc dopamine neurons. We will also review and ensure the images are representative.

      In Figure 3, the authors attempt to compare intracellular calcium levels in dopamine neurons using GCaMP6 fluorescence. Because this calcium indicator is not quantitative (unlike ratiometric sensors such as Fura2), it is usually used to quantify relative changes in intracellular calcium. The present use of this probe to compare absolute values is unusual and the validity of this approach is unclear. This limitation needs to be discussed. The authors also need to refer in the text to the difference between panels D and E of this figure. It is surprising that the fluctuations in calcium levels were not quantified. I guess the hypothesis was that there should be more or larger fluctuations in the mice treated with CNO if the CNO treatment led to increased firing. This needs to be clarified.

      We thank the reviewer for this comment. We understand that this method of comparing absolute values is unconventional. However, these animals were tested concurrently on the same system, and a clear effect on the absolute baseline was observed. We will include a caveat of this in our discussion. Panel D of this figure shows the raw, uncorrected photometry traces, whereas panel E shows the isosbestic corrected traces for the same recording. In panel E, the traces follow time in ascending order. We will also include frequency and amplitude data for these recordings.   

      Although the spatial transcriptomic results are intriguing and certainly a great way to start thinking about how the CNO treatment could lead to the loss of dopamine neurons, the presented results, the focusing of some broad classes of differentially expressed genes and on some specific examples, do not really suggest any clear mechanism of neurodegeneration. It would perhaps be useful for the authors to use the obtained data to validate that a state of chronic depolarization was indeed induced by the chronic CNO treatment. Were genes classically linked to increased activity like cfos or bdnf elevated in the SNc or VTA dopamine neurons? In the striatum, the authors report that the levels of DARP32, a gene whose levels are linked to dopamine levels, are unchanged. Does this mean that there were no major changes in dopamine levels in the striatum of these mice?

      We will review the expression of activity-related genes in our dataset, although we must keep in mind that these genes may behave differently in the context of chronic activation as opposed to acutely increased activity. We will also include experiments assessing striatal dopamine levels by HPLC in the revision.

      The usefulness of comparing the transcriptome of human PD SNc or VTA sections to that of the present mouse model should be better explained. In the human tissues, the transcriptome reflects the state of the tissue many years after extensive loss of dopamine neurons. It is expected that there will be few if any SNc neurons left in such sections. In comparison, the mice after 7 days of CNO treatment do not appear to have lost any dopamine neurons. As such, how can the two extremely different conditions be reasonably compared?

      Our mouse model and human PD progress over distinct timescales, as is the case with essentially all mouse models of neurodegenerative diseases. Nonetheless, in our view there is still great value in comparing gene expression changes in mouse models with those in human disease. It seems very likely that the same pathologic processes that drive degeneration early in the disease continue to drive degeneration later in the disease. Note that we have tried to address the discrepancy in time scales in part by comparing to early PD samples when there is more limited SNc DA neuron loss. Please note the numbers of DA neurons within the areas we have selected for sampling (Figure at right). Therefore, we can indeed use spatial transcriptomics to compare dopamine neurons from mice with initial degeneration and patients where degeneration is ongoing during their disease.

      Author response image 1.

      Violin plot of DA neuron proportions sampled within the vulnerable SNV (deconvoluted RCTD method used in unmasked tissue sections of the SNV). Control and early PD subjects.

      Comments on the discussion:

      In the discussion, the authors state that their calcium photometry results support a central role of calcium in activity-induced neurodegeneration. This conclusion, although plausible because of the very broad pre-existing literature linking calcium elevation (such as in excitotoxicity) to neuronal loss, should be toned down a bit as no causal relationship was established in the experiments that were carried out in the present study.

      Our model utilizes hM3Dq-DREADDs that function by increasing intracellular calcium to increase neuronal excitability, and our results show increased Ca2+ by fiber photometry and changes to Ca2+-related genes, strongly suggesting a causal relation and crucial role of calcium in the mechanism of degeneration. However, we agree that we have not experimentally proven this point, as we acknowledged in the text. Additionally, we have planned revision experiments involving chronic isradipine treatment to further test the role of calcium in the mechanism of degeneration in this model.

      In the discussion, the authors discuss some of the parallel changes in gene expression detected in the mouse model and in the human tissues. Because few if any dopamine neurons are expected to remain in the SNc of the human tissues used, this sort of comparison has important conceptual limitations and these need to be clearly addressed.

      As discussed, we can sample SN DA neurons in early PD (see figure above), and in our view there is great value for such comparisons. We agree that discussion of appropriate caveats is warranted and this will be clearly addressed in the revision.

      A major limitation of the present discussion is that it does not discuss the possibility that the observed phenotypes are caused by the induction of a chronic state of depolarization block by the chronic CNO treatment. I encourage the authors to consider and discuss this hypothesis.

      As discussed above, our analyses of DA neuron firing in slices and open field testing to date do not support a prominent contribution of depolarization block with chronic CNO treatment. However, we cannot rule out this hypothesis, therefore we will include additional electrophysiology experiments and add discussion of this important consideration.  

      Also, the authors need to discuss the fact that previous work was only able to detect an increase in the firing rate of dopamine neurons after more than 95% loss of dopamine neurons. As such, the authors need to clearly discuss the relevance of the present model to PD. Are changes in firing rate a driver of neuronal loss in PD, as the authors try to make the case here, or are such changes only a secondary consequence of extensive neuronal loss (for example because a major loss of dopamine would lead to reduced D2 autoreceptor activation in the remaining neurons, and to reduced autoreceptor-mediated negative feedback on firing). This needs to be discussed.

      As discussed above, while increases in dopamine neuron activity may be compensatory after loss of neurons, the precise percentage required to induce such compensatory changes is not defined in mice and varies between paradigms, and the threshold level is not known in humans. We also reiterate that a compensatory increase in activity could still promote the degeneration of critical surviving DA neurons, whose loss underlies the substantial decline in motor function that typically occurs over the course of PD. Moreover, there are also multiple lines of evidence to suggest that changes in activity can initiate and drive dopamine neuron degeneration (Rademacher & Nakamura, Exp Neurol 2024). For example, overexpression of synuclein can increase firing in cultured dopamine neurons (Dagra et al., NPJ Parkinsons Dis 2021, PMID: 34408150) while mice expressing mutant Parkin have higher mean firing rates (Regoni et al., Cell Death Dis 2020,  PMID: 33173027). Similarly, an increased firing rate has been reported in the MitoPark mouse model of PD at a time preceding DA neuron degeneration (Good et al., FASEB J 2011, PMID: 21233488). We also acknowledge that alterations to dopamine neuron activity are likely complex in PD, and that dopamine neuron health and function can be impacted not just by simple increases in activity, but also by changes in activity patterns and regularity. We will amend our discussion to include the important caveat of changes in activity occurring as compensation, as well as further evidence of changes in activity preceding dopamine neuron death.

      There is a very large, multi-decade literature on calcium elevation and its effects on neuronal loss in many different types of neurons. The authors should discuss their findings in this context and refer to some of this previous work. In a nutshell, the observations of the present manuscript could be summarized by stating that the chronic membrane depolarization induced by the CNO treatment is likely to induce a chronic elevation of intracellular calcium and this is then likely to activate some of the well-known calcium-dependent cell death mechanisms. Whether such cell death is linked in any way to PD is not really demonstrated by the present results. The authors are encouraged to perform a thorough revision of the discussion to address all of these issues, discuss the major limitations of the present model, and refer to the broad pre-existing literature linking membrane depolarization, calcium, and neuronal loss in many neuronal cell types.

      While our model demonstrates classic excitotoxic cell death pathways, we would like to emphasize both the chronic nature of our manipulation and the progressive changes observed, with increasing degeneration seen at 1, 2, and 4 weeks of hyperactivity in an axon-first manner. This is a unique aspect of our study, in contrast to much of the previous literature which has focused on shorter timescales. Thus, while we will revise the discussion to more comprehensively acknowledge previous studies of calcium-dependent neuron cell death, we believe we have made several new contributions that are not predicted by existing literature. We have shown that this chronic manipulation is specifically toxic to nigral dopamine neurons, and the data that VTA dopamine neurons continue to be resilient even at 4 weeks is interesting and disease-relevant. We therefore do not want to use findings from other neuron types to draw assumptions about DA neurons, which are a unique and very diverse population. We acknowledge that as with all preclinical models of PD, we cannot draw definitive conclusions about PD with this data. However, we reiterate that we strongly believe that drawing connections to human disease is important, as dopamine neuron activity is very likely altered in PD and a clearer understanding of how dopamine neuron survival is impacted by activity will provide insight into the mechanisms of PD.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      In this study, the authors engineer the endogenous left boundary of the Drosophila eve TAD, replacing the endogenous Nhomie boundary by either a neutral DNA, a wildtype Nhomie boundary, an inverted Nhomie boundary, or a second copy of the Homie boundary. They perform Micro-C on young embryos and conclude that endogenous Nhomie and Homie boundaries flanking eve pair with head-to-tail directionality to form a chromosomal stem loop. Abrogating the Nhomie boundary leads to ectopic activation of genes in the former neighboring TAD by eve embryonic stripe enhancers. Replacing Nhomie by an inverted version or by Homie (which pairs with itself head-to-head) transformed the stem loop into a circle loop. An important finding was that stem and circle loops differentially impact endogenous gene regulation both within the eve TAD and in the TADs bracketing eve. Intriguingly, an eve TAD with a circle loop configuration leads to ectopic activation of flanking genes by eve enhancers - indicating compromised regulatory boundary activity despite the presence of an eve TAD with intact left and right boundaries.

      Strengths:

      Overall, the results obtained are of high-quality and are meticulously discussed. This work advances our fundamental understanding of how 3D genome topologies affect enhancer-promoter communication.

      Weaknesses:

      Though convincingly demonstrated at eve, the generalizability of TAD formation by directional boundary pairing remains unclear, though the authors propose this mechanism could underly the formation of all TADs in Drosophila and possibly even in mammals. Strong and ample evidence has been obtained to date that cohesin-mediated chromosomal loop extrusion explains the formation of a large fraction of TADs in mammals. 

      (1.1) The difficultly with most all of the studies on mammal TADs, cohesin and CTCF roadblocks is that the sequencing depth is not sufficient, and large bin sizes (>1 kb) are needed to visualize chromosome architecture.  The resulting contact profiles show TAD neighborhoods, not actual TADs.

      The problem with these studies is illustrated by comparing the contact profiles of mammalian MicroC data sets at different bin sizes in Author response image 1.  In this figure, the darkness of the “pixels” in panels E, F, G and H was enhanced by reducing brightness in photoshop.

      Author response image 1.

      Mammalian MicroC profiles different bun sizes

      Panels A and C show “TADs” using bin sizes typical of most mammalian studies (see Krietenstein et al. (2023) (Krietenstein et al. 2020)).  At this level of resolution, TADs, the “trees” that are the building blocks of chromosomes, are not visible.  Instead, what is seen are TAD neighborhoods or “forests”.  Each neighborhood consists of several dozen individual TADs.  The large bins in these panels also artificially accentuated TAD:TAD interactions, generating a series of “stripes” and “dots” that correspond to TADs bumping into each other and sequences getting crosslinked.  For example, in panel A there is prominent stripe on the edge of a “TAD” (blue arrow).  In panel C, this stripe resolves into a series of dots arranged as parallel, but interrupted “stripes” (green and blue arrows).  At the next level of resolution, it can be seen that the stripe marked by the blue arrow and magenta asterisk is generated by contacts between the left boundary of the TAD indicated by the magenta bar with sequences in a TAD (blue bar) ~180 kb way.  While dots and stripes are prominent features in contact profiles visualized with larger bin sizes (A and C), the actual TADs that are observed with a bin size of 200 bp (examples are underlined by black bars in panel G) are not bordered by stripes, nor are they topped by obvious dots.  The one possible exception is the dot that appears at the top of the volcano triangle underlined with magenta.

      The chromosome 1 DNA segment from the MicroC data of Hseih et al. (2023) (Hsieh et al. 2020) shows a putative volcano triangle with a plume (indicated by a V in Author response image 1 panels D, F and H).  Sequences in the V TAD don’t crosslink with their immediate neighbors, and this gives a “plume” above the volcano triangle, as indicate by the light blue asterisk in panels D, F and H.  Interestingly the V TAD does contact two distant TADs, U on the left and W on the right. The U TAD is ~550 kb from V, and the region of contact is indicated by the black arrow.  The W TAD is ~585 kb from V, and the region of contact is indicated by the magenta arrow.  While the plume still seems to be visible with a bin size of 400 bp (light blue asterisk), it is hard to discern when the bin size is 200 bp, as there are not enough reads.

      The evidence demonstrating that cohesin is required for TAD formation/maintenance is based on low resolution Hi-C data, and the effects that are observed are on TAD neighborhoods (forests) and not TADs (trees).  In fact, there is published evidence that cohesin is not required in mammals for TAD formation/maintenance.  In an experiment from Goel et al. 2023 the authors depleted the cohesin component Rad21 and then visualized the effects on TAD organization using the high resolution region capture MicroC (RCMC) protocol.  The MicroC contact map in this figure visualizes a ~250 kb DNA segment around the Ppm1pg locus at 250 bp resolution.  On the right side of the diagonal is the untreated control, while the left side shows the MicroC profile of the same region after Rad21 depletion.  The authors indicated that there was a 97% depletion of Rad21 in their experiment.  However, as is evident from a comparison of the experimental and control, loss of Rad21 has no apparent effect on the TAD organization of this mammalian DNA segment.

      Several other features are worth noting.  First, unlike the MicroC experiments shown in Author response image 1, there are dots at the apex of the TADs in this chromosomal segment.  In the MicroC protocol, fixed chromatin is digested to mononucleosomes by extensive MNase digestion.  The resulting DNA fragments are then ligated, and dinucleosome-length fragments are isolated and sequenced. 

      DNA sequences that are nucleosome free in chromatin (which would be promoters, enhancers, silencers and boundary elements) are typically digested to oligonucleotides in this procedure and won’t be recovered. This means that the dots shown here must correspond to mononucleosome-length elements that are MNase resistant.  This is also true for the dots in the MicroC contact profiles of the Drosophila Abd-B regulatory domain (see Fig. 2B in the paper).  Second, the TADs are connected to each other by 45o stripes (see blue and green arrowheads).  While it is not clear from this experiment whether the stipes are generated by an active mechanism (enzyme) or by some “passive” mechanism (e.g., sliding), the stripes in this chromosomal segment are not generated by cohesin, as they are unperturbed by Rad21 depletion.  Third, there are no volcano triangles with plumes in this chromosomal DNA segment.  Instead, the contact patterns (purple and green asterisks) between neighboring TADs closely resemble those seen for the Abd-B regulatory domains (compare Goel et al. 2023 with Fig. 2B in the paper).  This similarity suggests that the TADs in and around Ppm1g may be circle-loops, not stem-loops.  As volcano triangles with plumes also seem to be rare in the MicroC data sets of Krietenstein et al. (Krietenstein et al. 2020) and Hesih et al. (Hsieh et al. 2020) (with the caveat that these data sets are low resolution: see Author response image 1), it is possible that much of the mammalian genome is assembled into circle-loop TADs, a topology that can’t be generated by the cohesin loop extrusion (bolo tie clip) /CTCF roadblock model.

      While Rad21 depletion has no apparent effect on TADs, it does appear to impact TAD neighborhoods.  This is in a supplemental figure in Goel et al. (Goel et al. 2023).  In this figure, TADs in the Ppm1g region of chromosome 5 are visualized with bin sizes of 5 kb and 1 kb.  A 1.2 Mb DNA segment is shown for the 5 kb bin size, while an 800 kb DNA segment is shown for the 1 kb bin size.  As can be seen from comparing the MicroC profiles in Author response image 2 with that in Goel et al. 2023, individual TADs are not visible.  Instead, the individual TADs are binned into large TAD “neighborhoods” that consist of several dozen or more TADs.

      Unlike the individual TADs shown in Goel et al. 2023, the TAD neighborhoods in Author response image 2 are sensitive to Rad21 depletion.  The effects of Rad21 depletion can be seen by comparing the relative pixel density inside the blue lines before (above the diagonal) and after (below the diagonal) auxin-induced Rad21 degradation.  The reduction in pixel density is greatest for more distant TAD:TAD contacts (farthest from the diagonal).  By contrast, the TADs themselves are unaffected (Goel et al. 2023), as are contacts between individual TADs and their immediate neighbors.  In addition, contacts between partially overlapping TAD neighborhoods are also lost.  At this point it isn’t clear why contacts between distant TADs in the same neighborhood are lost when Rad21 is depleted; however, a plausible speculation is that it is related to the functioning of cohesin in holding newly replicated DNAs together until mitosis and whatever other role it might have in chromosome condensation.

      Author response image 2.

      Ppm1g full locus chr5

      Moreover, given the unique specificity with which Nhomie and Homie are known to pair (and exhibit "homing" activity), it is conceivable that formation of the eve TAD by boundary pairing represents a phenomenon observed at exceptional loci rather than a universal rule of TAD formation. Indeed, characteristic Micro-C features of the eve TAD are only observed at a restricted number of loci in the fly genome…..

      (1.2) The available evidence does not support the claim that nhomie and homie are “exceptional.”  To begin with, nhomie and homie rely on precisely the same set of factors that have been implicated in the functioning of other boundaries in the fly genome.  For example, homie requires (among other factors) the generic boundary protein Su(Hw) for insulation and long-distance interactions (Fujioka et al. 2024).  (This is also true of nhomie: unpublished data.)  The Su(Hw) protein (like other fly polydactyl zinc finger proteins) can engage in distant interactions.  This was first shown by Sigrist and Pirrotta (Sigrist and Pirrotta 1997), who found that the su(Hw) element from the gypsy transposon can mediate long-distance regulatory interactions (PRE dependent silencing) between transgenes inserted at different sites on homologous chromosomes (trans interactions) and at sites on different chromosomes.

      The ability to mediate long-distance interactions is not unique to the su(Hw) element, or homie and nhomie.  Muller et al. (Muller et al. 1999) found that the Mcp boundary from the Drosophila BX-C is also able to engage in long-distance regulatory interactions—both PRE-dependent silencing of mini-white and enhancer activation of mini-white and yellow.  The functioning of the Mcp boundary depends upon two other generic insulator proteins, Pita and the fly CTCF homolog (Kyrchanova et al. 2017).  Like Su(Hw) both are polydactyl zinc finger proteins, and they resemble the mammalian CTCF protein in that their N-terminal domain mediates multimerization (Bonchuk et al. 2020; Zolotarev et al. 2016).  Figure 6 from Muller et el. 1999 shows PRE-dependent “pairing sensitive silencing” interactions between transgenes carrying a mini-white reporter, the Mcp and scs’ (Beaf dependent)(Hart et al. 1997) boundary elements, and a PRE closely linked to Mcp.  In this experiment flies homozygous for different transgene inserts were mated and the eye color was examined in their transheterozygous progeny.  As indicated in the figure, the strongest trans-silencing interactions were observed for inserts on the same chromosomal arm; however, transgenes inserted on the left arm of chromosome 3 can interact across the centromere with transgenes inserted on the right arm of chromosome 3. 

      Figure 5C (left) from Muller et el. 1999 shows a trans-silencing interaction between w#11.102 at 84D and w#11.16 approximately 5.8 Mb away, at 87D.  Figure 5C (right) shows a trans-silencing interaction across the centromere between w#14.29 on the left arm of chromosome 3 at 78F and w#11.102 on the right arm of chromosome 3 at 84D. The eye color phenotype of mini-white-containing transgenes is usually additive: homozygyous inserts have twice as dark eye color as the corresponding hemizygous inserts.  Likewise, in flies trans-_heterozygous for _mini-white transgenes inserted at different sites, the eye color is equivalent to the sum of the two transgenes.  This is not true when mini-white transgenes are silenced by PREs.  In the combination shown in panel A, the t_rans-_heterozygous fly has a lighter eye color than either of the parents.  In the combination in panel B, the _trans-_heterozygous fly is slightly lighter than either parent.

      As evident from the diagram in Figure 6 from Muller et el. 1999, all of the transgenes inserted on the 3rd chromosome that were tested were able to participate in long distance (>Mbs) regulatory interactions.  On the other hand, not all possible pairwise interactions are observed.  This would suggest that potential interactions depend upon the large scale (Mb) 3D folding of the 3rd chromosome.

      When the scs boundary (Zw5 dependent) (Gaszner et al. 1999) was added to the transgene to give sMws’, it further enhanced the ability of distant transgenes to find each other and pair.  All eight of the sMws’ inserts that were tested were able to interact with at least one other sMws’ insert on a different chromosome and silence mini-white.  Vazquez et al. () subsequently tagged the sMws’ transgene with LacO sequences (ps0Mws’) and visualized pairing interactions in imaginal discs.  Trans-heterozygous combinations on the same chromosome were found paired in 94-99% of the disc nuclei, while a trans-heterozygous combination on different chromosomes was found paired in 96% of the nuclei (Table 3 from Vazquez et al. 2006).  Vazquez et al. also examined a combination of four transgenes inserted on the same chromosome (two at the same insertion site, and two at different insertion sites).  In this case, all four transgenes were clustered together in 94% of the nuclei (Table 3 from Vazquez et al. 2006).  Their studies also suggest that the distant transgenes remain paired for at least several hours.  A similar experiment was done by Li et al. (Li et al. 2011), except that the transgene contained only a single boundary, Mcp or Fab-7.  While pairing was still observed in trans-heterozygotes, the frequency was reduced without scs and scs’.

      It is worth pointing out that there is no plausible mechanism in which cohesin could extrude a loop through hundreds of intervening TADs, across the centromere (ff#13.101_ßà_w#11.102: Figure 6 from Muller et el. 1999; w#14.29_ßà_w#11.02: Figure 6 from Muller et el. 1999 and 5) and come to a halt when it “encounters” Mcp containing transgenes on different homologs.  The same is true for Mcp-dependent pairing interactions in cis (Fig. 7 in Muller et al. (Muller et al. 1999)) or Mcp-dependent pairing interactions between transgenes inserted on different chromosomes (Fig. 8 in Muller et al. (Muller et al. 1999); Line 8 in Table 3 from Vazquez et al. 2006). 

      These are not the only boundaries that can engage in long-distance pairing.  Mohana et al. (Mohana et al. 2023) identified nearly 60 meta-loops, many of which appear to be formed by the pairing of TAD boundary elements.  Two examples (at 200 bp resolution from 12-16 hr embryos) are shown in Author response image 3.

      Author response image 3.

      Metaloops on the 2nd and 3rd chromosomes: circle-loops and multiple stem-loops

      One of these meta-loops (panel A) is generated by the pairing of two TAD boundaries on the 2nd chromosome.  The first boundary, blue, (indicated by blue arrow) is located at ~2,006, 500 bp between a small TAD containing the Nplp4 and CG15353 genes and a larger TAD containing 3 genes, CG33543, Obp22a and Npc2aNplp4 encodes a neuropeptide.  The functions of CG15354 and CG33543 are unknown.  Obp22a encodes an odorant binding protein, while Npc2a encodes the Niemann-Pick type C-2a protein which is involved sterol homeostasis.  The other boundary (purple: indicated by purple arrow) is located between two TADs 2.8 Mb away at 4,794,250 bp.  The upstream TAD contains the fipi gene (CG15630) which has neuronal functions in male courtship, while the downstream TAD contains CG3294, which is thought to be a spliceosome component, and schlaff (slf) which encodes a chitin binding protein.  As illustrated in the accompanying diagram, the blue boundary pairs with the purple boundary in a head-to-head orientation, generating a ~2.8 Mb loop with a circle-loop topology.  As a result of this pairing, the multi-gene (CG33543, Obp22a and Npc2a) TAD upstream of the blue boundary interacts with the CG15630 TAD upstream of the purple boundary.  Conversely the small Nplp4:CG15353 TAD downstream of the blue boundary interacts with the CG3294:slf TAD downstream of the purple boundary.  Even if one imagined that the cohesin bolo tie clip was somehow able to extrude 2.8 Mb of chromatin and then know to stop when it encountered the blue and purple boundaries, it would’ve generated a stemloop, not a circle-loop.

      The second meta-loop (panel B) is more complicated as it is generated by pairing interactions between four boundary elements.  The blue boundary (blue arrow) located ~4,801,800 bp (3L) separates a large TAD containing the RhoGEF64C gene from a small TAD containing CG7509, which encodes a predicted subunit of an extracellular carboxypeptidase.  As can be seen in the MicroC contact profile and the accompanying diagram, the blue boundary pairs with the purple boundary (purple arrow) which is located at ~7,013, 500 (3L) just upstream of the 2nd internal promoter (indicated by black arrowhead) of the Mp (Multiplexin) gene.  This pairing interaction is head-to-tail and generates a large stem-loop that spans ~2.2 Mb.  The stem-loop brings sequences upstream of the blue boundary and downstream of the purple boundary into contact (the strings below a bolo tie clip), just as was observed in the boundary bypass experiments of Muravyova et al. (Muravyova et al. 2001) and Kyrchanova et al. (Kyrchanova et al. 2008).  The physical interactions result in a box of contacts (right top) between sequences in the large RhoGEF64C TAD and sequences in a large TAD that contains an internal Mp promoter.  The second pairing interaction is between the brown boundary (brown arrow) and the green boundary (green arrow).  The brown boundary is located at ~4 805,600 bp (3L) and separates the TAD containing CG7590 from a large TAD containing CG1808 (predicted to encode an oxidoreductase) and the Dhc64C (Dynein heavy chain 64C) gene.  The green boundary is located at ~6,995,500 bp (3L), and it separates a TAD containing CG32388 and the biniou (bin) transcription factor from a TAD that contains the most distal promoter of the Mp (Multiplexin) gene (blue arrowhead).  As indicated in the diagram, the brown and green boundaries pair with each other head-to-tail, and this generates a small internal loop (and the final configuration would resemble a bolo tie with two tie clips).  This small internal loop brings the CG7590 TAD into contact with the TAD that extends from the distal Mp promoter to the 2nd internal Mp promoter.  The resulting contact profile is a rectangular box with diagonal endpoints corresponding to the paired blue:purple and brown:green boundaries.  The pairing of the brown:green boundaries also brings the TADs immediately downstream of the brown boundary and upstream of the green boundary into contact with each other, and this gives a rectangular box of interactions between the Dhc64C TAD, and sequences in the bin/CG3238 TAD.  This box is located on the lower left side of the contact map.

      Since the bin and Mp meta-loops in Author response image 3B are stem-loops, they could have been generated by “sequential” cohesin loop extrusion events.  Besides the fact that cohesin extrusion of 2 Mb of chromatin and breaking through multiple intervening TAD boundaries challenges the imagination, there is no mechanism in the cohesion loop extrusion/CTCF roadblock model to explain why cohesion complex 1 would come to a halt at the purple boundary on one side and the blue boundary on the other, while cohesin complex 2 would instead stop when it hits the brown and green boundaries.  This highlights another problem with the cohesin loop extrusion/CTCF roadblock model, namely that the roadblocks are functionally autonomous: they have an intrinsic ability to block cohesin that is entirely independent of the intrinsic ability of other roadblocks in the neighborhood.  As a result, there is no mechanism for generating specificity in loop formation.  By contrast, boundary pairing interactions are by definition non-autonomous and depend on the ability of individual boundaries to pair with other boundaries: specificity is built into the model. The mechanism for pairing, and accordingly the basis for partner preferences/specificity, are reasonably well understood.  Probably the most common mechanism in flies is based on shared binding sites for architectural proteins that can form dimers or multimers (Bonchuk et al. 2021; Fedotova et al. 2017).  Flies have a large family of polydactyl zinc finger DNA binding proteins, and as noted above, many of these form dimers or multimers and also function as TAD boundary proteins.  This pairing principle was first discovered by Kyrchanova et al. (Kyrchanova et al. 2008).  This paper also showed that orientation-dependent pairing interactions is a common feature of endogenous fly boundaries.  Another mechanism for pairing is specific protein:protein interactions between different DNA binding factors (Blanton et al. 2003).  Yet a third mechanism would be proteins that bridge different DNA binding proteins together.  The boundaries that use these different mechanisms (BX-C boundaries, scs, scs’) depend upon the same sorts of proteins that are used by homie and nhomie.  Likewise, these same set of factors reappear in one combination or another in most other TAD boundaries.  As for the orientation of pairing interactions, this is most likely determined by the order of binding sites for chromosome architectural proteins in the partner boundaries.

      …and many TADs lack focal 3D interactions between their boundaries.

      (1.3) The idea that flies differ from mammals in that they “lack” focal 3D interactions is simply mistaken.  One of the problems with drawing this distinction is that most all of the “focal 3D interactions” seen mammalian Hi-C experiments are a consequence of binning large DNA segments in low resolution restriction enzyme-dependent experiments.  This is even true in the two “high” resolution MicroC experiments that have been published (Hsieh et al. 2020; Krietenstein et al. 2020).  As illustrated above in Author response image 1, most of the “focal 3D interactions” (the dots at the apex of TAD triangles) seen with large bin sizes (1 kb and greater) disappear when the bin size is 200 bp and TADs rather than TAD neighborhoods are being visualized.

      As described in point #1.1, in the MicroC protocol, fixed chromatin is first digested to mononucloesomes by extensive MNase digestion, processed/biotinylated, and ligated to give dinucleosome-length fragments, which are then sequenced.  Regions of chromatin that are nucleosome free (promoters, enhancers, silencers, boundary elements) will typically be reduced to oligonucleotides in this procedure and will not be recovered when dinucleosome-length fragments are sequenced.  The loss of sequences from typical paired boundary elements is illustrated by the lar meta-loop shown in Author response image 4 (at 200 bp resolution).  Panels A and B show the contact profiles generated when the blue boundary (which separates two TADs that span  the Lar (Leukocyteantigen-related-like) transcription unit interacts with the purple boundary (which separates two TADs in a gene poor region ~620 kb away).  The blue and purple boundaries pair with each other head-to-head, and this pairing orientation generates yet another circle-loop.  In the circle-loop topology, sequences in the TADs upstream of both boundaries come into contact with each other, and this gives the small dark rectangular box to the upper left of the paired boundaries (Author response image 4A).  (Note that this small box corresponds to the two small TADs upstream of the blue and purple boundaries, respectively. See panel B.)  Sequences in the TADs downstream of the two boundaries also come into contact with each other, and this gives the large box to the lower right of the paired boundaries.  While this meta-loop is clearly generated by pairing interactions between the blue and purple boundaries, the interacting sequences are degraded in the MicroC protocol, and sequences corresponding to the blue and purple boundaries aren’t recovered.  This can be seen in panel B (red arrow and red arrowheads).  When a different Hi-C procedure is used (dHS-C) that captures nucleosome-free regions of chromatin that are physically linked to each other (Author response image 4C & D), the sequences in the interacting blue and purple boundaries are recovered and generate a prominent “dot” at their physical intersection (blue arrow in panel D).

      Author response image 4.

      Lar metaloop. Panels A & bB: MicroC. Panels C & D: dHS-C

      While sequences corresponding to the blue and purple boundaries are lost in the MicroC procedure, there is at least one class of elements that engage in physical pairing interactions whose sequences are (comparatively) resistant to MNase digestion.  This class of elements includes many PREs ((Kyrchanova et al. 2018); unpublished data), the boundary bypass elements in the Abd-B region of BX-C (Kyrchanova et al. 2023; Kyrchanova et al. 2019a; Kyrchanova et al. 2019b; Postika et al. 2018), and “tethering” elements (Batut et al. 2022; Li et al. 2023).  In all of the cases tested, these elements are bound in nuclear extracts by a large (>1000 kD) GAGA factor-containing multiprotein complex called LBC.  LBC also binds to the hsp70 and eve promoters (unpublished data).  Indirect end-labeling experiments (Galloni et al. 1993; Samal et al. 1981; Udvardy and Schedl 1984) indicate that the LBC protects a ~120-180 bp DNA segment from MNase digestion.  It is likely that this is the reason why LBC-bound sequences can be recovered in MicroC experiments as dots when they are physically linked to each other.  One such example (based on the ChIP signatures of the paired elements) is indicated by the green arrow in panel B and D of Author response image 4.  Note that there are no dots corresponding to these two LBC elements within either of the TADs immediately downstream of the blue and purple boundaries.  Instead the sequences corresponding to the two LBC elements are only recovered when the two elements pair with each other over a distance of ~620 kb.  The fact that these two elements pair with each other is consistent with other findings which indicate that, like classical boundaries, LBC elements exhibit partner preferences.  In fact, LBC elements can sometimes function as TAD boundaries.  For example, the Fab-7 boundary has two LBC elements, and full Fab-7 boundary function can be reconstituted with just these two elements (Kyrchanova et al. 2018).

      Reviewer #2 (Public Review):

      "Chromatin Structure II: Stem-loops and circle-loops" by Ke*, Fujioka*, Schedl, and Jaynes reports a set of experiments and subsequent analyses focusing on the role of Drosophila boundary elements in shaping 3D genome structure and regulating gene expression. The authors primarily focus on the region of the fly genome containing the even skipped (eve) gene; eve is expressed in a canonical spatial pattern in fly embryos and its locus is flanked by the well-characterized neighbor of homie (nhomie) and homie boundary elements. The main focus of investigation is the orientation dependence of these boundary elements, which had been observed previously using reporter assays. In this study, the authors use Crispr/Cas9 editing followed by recombination-mediated cassette exchange to create a series of recombinant fly lines in which the nhomie boundary element is either replaced with exongenous sequence from phage 𝝀, an inversion of nhomie, or a copy of homie that has the same orientation as the endogenous homie sequence. The nhomie sequence is also regenerated in its native orientation to control for effects introduced by the transgenesis process.

      The authors then perform high-resolution Micro-C to analyze 3D structure and couple this with fluorescent and colorimetric RNA in situ hybridization experiments to measure the expression of eve and nearby genes during different stages of fly development. The major findings of these experiments are that total loss of boundary sequence (replacement with 𝝀 DNA) results in major 3D structure changes and the most prominent observed gene changes, while inversion of the nhomie boundary or replacement with homie resulted in more modest effects in terms of 3D structure and gene expression changes and a distinct pattern of gene expression change from the 𝝀 DNA replacement. As the samples in which the nhomie boundary is inverted or replaced with homie have similar Micro-C profiles at the eve locus and show similar patterns of a spurious gene activation relative to the control, the observed effects appear to be driven by the relative orientation of the nhomie and homie boundary elements to one another.

      Collectively, the findings reported in the manuscript are of broad interest to the 3D genome field. Although extensive work has gone into characterizing the patterns of 3D genome organization in a whole host of species, the underlying mechanisms that structure genomes and their functional consequences are still poorly understood. The perhaps best understood system, mechanistically, is the coordinated action of CTCF with the cohesin complex, which in vertebrates appears to shape 3D contact maps through a loop extrusion-pausing mechanism that relies on orientation-dependent sequence elements found at the boundaries of interacting chromatin loops.

      (2.1) The notion that mammalian genome is shaped in 3D by the coordinate action of cohesin and CTCF has achieved the status of dogma in the field of chromosome structure in vertebrates.  However, as we have pointed out in #1.1, the evidence supporting this dogma is far from convincing.  To begin with, it is based on low resolution Hi-C experiments that rely on large bin sizes to visualize so-called “TADs.”  In fact, the notion that cohesin/CTCF are responsible on their own for shaping the mammalian 3D genome appears to be a result of mistaking a series of forests for the actual trees that populate each of the forests.

      As illustrated in Author response image 1 above, the “TADs” that are visualized in these low resolution data sets are not TADs at all, but rather TAD neighborhoods consisting of several dozen or more individual TADs.  Moreover, the “interesting” features that are evident at low resolution (>1 kb)—the dots and stripes—largely disappear at resolutions appropriate for visualizing individual TADs (~200 bp).

      In Goel et al. 2023, we presented data from one of the key experiments in Goel et al. (Goel et al. 2023).  In this experiment,  the authors used RCMC to generate high resolution (~250 bp) MicroC contact maps before and after Rad21 depletion.  Contrary to dogma, Rad21 depletion has absolutely no effect on TADs in a ~250 kb DNA segment—and these TADs look very much like the TADs we observe in the Drosophila genome, in particular in the Abd-B region of BX-C that is thought to be assembled into a series of circle-loops (see Fig. 2B).

      While Goel et al. (Goel et al. 2023) observed no effect of Rad21 depletion on TADs, they found that loss of Rad21 disturbs long-distance (but not short-distance) contacts in large TAD neighborhoods when their RCMC data set is visualized using bin sizes of 5 kb and I kb.  This is shown in Author response image 2.  The significance of this finding is, however, uncertain.  It could mean that the 3D organization of large TAD neighborhoods have a special requirement for cohesin activity.  On the other hand, since cohesin functions to hold sister chromosomes together after replication until they separate during mitosis (and might also participate in mitotic condensation), it is also possible that the loss of long-range contacts in large TAD neighborhoods when Rad21 is depleted is simply a reflection of this particular activity.  Further studies will be required to address these possibilities.

      As for CTCF: a careful inspection of the ChIP data in Goel et al. 2023 indicates that CTCF is not found at each and every TAD boundary.  In fact, the notion that CTCF is the be-all and end-all of TAD boundaries in mammals is truly hard to fathom.  For one, the demands for specificity in TAD formation (and in regulatory interactions) are likely much greater than those in flies, and specificity can’t be generated by a single DNA binding protein.  For another, several dozen chromosomal architectural proteins have already been identified in flies.  This means that (unlike what is thought to be true in mammals) it is possible to use a combinatorial mechanism to generate specificity in, for example, the long distance interactions in RFig 6 and 7.  As noted in #2.1 above, many of the known chromosomal architectural proteins in flies are polydactyl zinc finger proteins (just like CTCF).  There are some 200 different polydactyl zinc finger proteins in flies, and the function of only a hand full of these is known at present.  However, it seems likely that a reasonable fraction of this class of DNA binding proteins will ultimately turn out to have an architectural function of some type (Bonchuk et al. 2021; Fedotova et al. 2017).  The number of different polydactyl zinc finger protein genes in mammals is nearly 3 times that of flies.  It is really possible that of these, only CTCF is involved in shaping the 3D structure of the mammalian genome?

      Despite having a CTCF paralog and cohesin, the Drosophila genome does not appear to be structure by loop extrusion-pausing. The identification of orientation-dependent elements with pronounced structural effects on genome folding thus may shed light on alternative mechanisms used to regulated genome structure, which in turn may yield insights into the significance of particular folding patterns.

      (2.2) Here we would like to draw the reviewer’s and reader’s attention to Author response image 3, which shows that orientation-dependent pairing interactions have a significant impact on physical interactions between different sequences.  We would also refer the reader to two other publications.  One of these is Kyrchanova et al. (Kyrchanova et al. 2008), which was the first to demonstrate that orientation of pairing interactions matters.  The second is Fujioka et al. (Fujioka et al. 2016), which describes experiments indicating that nhomie and homie pair with each other head-to-tail and with themselves head-to-head.

      On the whole, this study is comprehensive and represents a useful contribution to the 3D genome field. The transgenic lines and Micro-C datasets generated in the course of the work will be valuable resources for the research community. Moreover, the manuscript, while dense in places, is generally clearly written and comprehensive in its description of the work. However, I have a number of comments and critiques of the manuscript, mainly centering on the framing of the experiments and presentation of the Micro-C results and on manner in which the data are analyzed and reported. They are as follows:

      Major Points:

      (1) The authors motivate much of the introduction and results with hypothetical "stem loop" and "circle loop" models of chromosome confirmation, which they argue are reflected in the Micro-C data and help to explain the observed ISH patterns. While such structures may possibly form, the support for these specific models vs. the many alternatives is not in any way justified. For instance, no consideration is given to important biophysical properties such as persistence length, packing/scaling, and conformational entropy. As the biophysical properties of chromatin are a very trafficked topic both in terms of experimentation and computational modeling and generally considered in the analysis of chromosome conformation data, the study would be strengthened by acknowledgement of this body of work and more direct integration of its findings.

      (2.3) The reviewer is not correct in claiming that “stem-loops” and “circle-loops” are “hypothetical.”  There is ample evidence that both types of loops are present in eukaryotic genomes, and that loop conformation has significant readouts in terms of not only the physical properties of TADs but also their functional properties.  Here we would draw the reviewer’s attention to Author response image 3 and Author response image 4 for examples of loops formed by the orientation-dependent pairing of yet other TAD boundary elements.  As evident from the MicroC data in these figures, circle-loops and stem-loops have readily distinguishable contact patterns.  The experiments in Fujioka et al. (Fujioka et al. 2016) demonstrate that homie and nhomie pair with each other head-to-tail, while they pair with themselves head-to-head.  The accompany paper (Bing et al. 2024) also provides evidence that loop topology is reflected both in the pattern of activation of reporters and in the MicroC contact profiles.  We would also mention again Kyrchanova et al. (Kyrchanova et al. 2008), who were the first to report orientation-dependent pairing of endogenous fly boundaries.

      At this juncture it would premature to try to incorporate computational modeling of chromosome conformation in our studies.  The reason is that the experimental foundations that would be essential for building accurate models are lacking.  As should be evident from RFigs. 1-3 above, studies on mammalian chromosomes are simply not of high enough resolution to draw firm conclusions about chromosome conformation: in most studies only the forests are visible.  While the situation is better in flies, there are still too many unknown.  As just one example, it would be important to know the orientation of the boundary pairing interactions that generate each TAD.  While it is possible to infer loop topology from how TADs interact with their neighbors (a plume versus clouds), a conclusive identification of stem- and circle-loops will require a method to unambiguously determine whether a TAD boundary pairs with its neighbor head-to-head or headto-tail.

      (2) Similar to Point 1, while there is a fair amount of discussion of how the observed results are or are not consistent with loop extrusion, there is no discussion of the biophysical forces that are thought to underly compartmentalization such as block-polymer co-segregation and their potential influence. I found this absence surprising, as it is generally accepted that A/B compartmentalization essentially can explain the contact maps observed in Drosophila and other non-vertebrate eukaryotes (Rowley, ..., Corces 2017; PMID 28826674). The manuscript would be strengthened by consideration of this phenomenon.

      (2.4) Compartments in mammals have typically been identified and characterized using lowresolution data sets, and these studies have relied on visualizing compartments using quite large bin sizes (>>1 kb).  Our experiments have nothing to do with the large-scale compartments seen in these Hi-C experiments.  Instead, we are studying the properties of individual TADs: how TADs are formed, the relationship between TAD topology and boundary:boundary pairing, and the impact of TAD topology on interactions between TADs in the immediate neighborhood.  There is no evidence to date that these large compartments or “block polymer co-segregation” have a) any impact on the properties of individual boundary elements, b) have a role in determining which boundary elements actually come together to form a given TAD, c) impact the orientation of the interactions between boundaries that generate the TAD or d) determine how TADs tend to interact with their immediate neighbors.  

      In more recent publications (c.f., Harris et al. 2023) compartments have shrunk in size and instead of being units of several hundred kb, the median length of the “compartmental” unit in mammalian cells is about12 kb. This is not too much different from the size of fly TADs.  However, the available evidence does not support the idea that block polymer co-segregation/co-repulsion drive the TAD:TAD interactions seen in MicroC experiments.  For example, according to this “micro-compartment” model, the specific patterns of interaction between TADs in the CG3294 meta-loop in Author response image 3 would be driven by block polymer co-segregation and co-repulsion. In this model, the TAD upstream of the blue boundary (which contains CG33543, the odorant binding protein gene Obp22a and the Npc2a gene which encodes a protein involved in sterol homeostasis) would share the same chromatin state/biophysical properties as the TAD upstream of the purple boundary, which has the fipi gene. While it is true that CG33543, Obp22a and also the fipi gene are not expressed in embryos, Npc2a is expressed at high levels during embryogenesis, yet it is part of the TAD that interacts with the fipi TAD.  The TAD downstream of the blue boundary contains CG15353 and Nplp4 and it interacts with the TAD downstream of the purple boundary which contains CG3294 and slfCG15353 and Nplp4 are not expressed in the embryo and as such should share a compartment with a TAD that is also silent. However, slf is expressed at a high level in 1216 hr embryos, while CG3294 is expressed at a low level.  In neither case would one conclude that the TADs upstream and downstream of the blue and purple boundaries, respectively, interact because of shared chromatin/biophysical states that drive block polymer co-segregation corepulsion. 

      One might also consider several gedanken experiments involving the long-range interactions that generate the CG3294 meta-loop in Author response image 3.    According to the micro-compartment model the patchwork pattern of crosslinking evident in the CG3294 meta-loop arises because the interacting  TADs share the same biochemical/biophysical properties, and this drives block polymer cosegregation and co-repulsion.  If this model is correct, then this patchwork pattern of TAD:TAD interactions would remain unchanged if we were to delete the blue or the purple boundary.  However, given what we know about how boundaries can find and pair with distant boundaries (c.f., Figure 6 from Muller et el. 1999 and the discussion in #1.2), the result of these gedanken experiments seem clear: the patchwork pattern shown in Author response image 3A will disappear.  What would happen if we inverted the blue or the purple boundary? Would the TAD containing CG33543, Obp22a and Npc2a still interact with fipi as would be expected from the compartment model?  Or would the pattern of interactions flip so that the CG33543, Obp22a and Npc2a TAD interacts with the TAD containing CG3294 and slf?  Again we can anticipate the results based on previous studies: the interacting TADs will switch when the CG3294 meta-loop is converted into a stem-loop.  If this happened, the only explanation possible in the compartment model is that the chromatin states change when the boundary is inverted so that TAD upstream of blue boundary now shares the same chromatin state as the TAD downstream of the purple boundary, while the TAD downstream of the blue boundary shares same state as the TAD upstream of the purple boundary.  However, there is no evidence that boundary orientation per se can induce a complete switch in “chromatin states” as would be required in the compartment model. 

      While we have not done these experimental manipulations with the CG3294 meta-loop, an equivalent experiment was done in Bing et al. (Bing et al. 2024).  However, instead of deleting a boundary element, we inserted a homie boundary element together with two reporters (gfp and LacZ) 142 kb away from the eve TAD.  The result of this gedanken “reverse boundary deletion” experiment is shown in Author response image 5.  Panel A shows the MicroC contact profile in the region spanning the transgene insertion site and the eve TAD in wild type (read “deletion”) NC14 embryos.  Panel B shows the MicroC contact profile from 12-16 hr embryos carrying the homie dual reporter transgene inserted at -142 kb.  Prior to the “deletion”, the homie element in the transgene pairs with nhomie and homie in the eve TAD and this generates a “mini-metaloop.”  In this particular insert, the homie boundary in the transgene (red arrow) is “pointing” in the opposite orientation from the homie boundary in the eve TAD (red arrow).  In this orientation, the pairing of the transgene homie with eve nhomie/homie brings the LacZ reporter into contact with sequences in the eve TAD.  Since a mini-metaloop is formed by homie_à _nhomie/homie pairing, sequences in TADs upstream and downstream of the transgene insert interact with sequences in TADs close to the eve TAD (Author response image 5B).  Taken together these interactions correspond to the interaction patchwork that is typically seen in “compartments” (see boxed region and inset).  If this patchwork is driven as per the model, by block polymer co-segregation and co-repulsion, then it should still be present when the transgene is deleted.  However, panel A shows that the interactions linking the transgene and the sequences in TADs next to the transgene to eve and TADs next to eve disappear when the homie boundary (plus transgene) is “deleted” in wild type flies.

      Author response image 5.

      Boundary deletion and compartments

      A second experiment would be to invert the homie boundary so that instead of pointing away from eve it points towards eve.  Again, if the compartmental patchwork is driven by block polymer co-segregation and co-repulsion, inverting the homie boundary in the transgene should have no effect on the compartmental contact profile.  Inspection of Fig. 7 in Bing et al. (Bing et al. 2024) will show that this prediction doesn’t hold either.  When homie is inverted, sequences in the eve TAD interact with the gfp reporter not the LacZ reporter.  In addition, there are corresponding changes in how sequences in TADs to either side of eve interact with sequences to either side of the transgene insert.  

      Yet another “test” of compartments generated by block polymer co-segregation/co-repulsion is provided by the plume above the eve volcano triangle.  According to the compartment model, sequences in TADs flanking the eve locus form the plume above the eve volcano triangle because their chromatin shares properties that drive block polymer co-segregation.  These same properties result in repulsive interactions with chromatin in the eve TAD, and this would explain why the eve TAD doesn’t crosslink with its neighbors.  If the distinctive chromatin properties of eve and the neighboring TADs drive block polymer co-segregation and co-repulsion, then inverting the nhomie boundary or introducing homie in the forward orientation should have absolutely no effect on the physical interactions between chromatin in the eve TAD and chromatin in the neighboring TADs.  However, Figures 4 and 6 in this paper indicate that boundary pairing orientation, not block polymer co-segregation/co-repulsion, is responsible for forming the plume above the eve TAD. Other findings also appear to be inconsistent with the compartment model. (A) The plume topping the eve volcano triangle is present in NC14 embryos when eve is broadly expressed (and potentially active throughout the embryo).  It is also present in 12-16 hr embryos when eve is only expressed in a very small subset of cells and is subject to PcG silencing everywhere else in the embryo.  B) According to the compartment model the precise patchwork pattern of physical interactions should depend upon the transcriptional program/chromatin state that is characteristic of a particular developmental stage or cell type.  As cell fate decisions are just being made during NC14 one might expect that most nuclei will share similar chromatin states throughout much of the genome.  This would not be true for 12-16 hr embryos.  At this stage the compartmental patchwork would be generated by a complex mixture of interactions in cells that have quite different transcriptional programs and chromatin states.  In this case, the patchwork pattern would be expected to become fuzzy as a given chromosomal segment would be in compartment A in one group of cells and in compartment B in another.   Unlike 12-16 hr embryos,  larval wing discs would be much more homogeneous and likely give a distinct and relatively well resolved compartmental pattern. We’ve examined the compartment patchwork of the same chromosomal segments in NC14 embryos, 12-16 hr embryos and larval wing disc cells.  While there are some differences (e.g., changes in some of the BX-C TADs in the wing disc sample) the compartmental patchwork patterns are surprisingly similar in all three cases. Nor is there any “fuzziness” in the compartmental patterns evident in 12-16 hr embryos, despite the fact that there are many different cell types at this stage of development.  C) TAD interactions with their neighbors and compartmental patchworks are substantially suppressed in salivary gland polytene chromosomes.  This would suggest that features of chromosome structure might be the driving force behind many of the “compartmental” interactions as opposed to distinct biochemical/biophysical of properties of small chromosomal segments that drive polymer co- segregation/co-repulsion.  

      (3) The contact maps presented in the study represent many cells and distinct cell types. It is clear from single-cell Hi-C and multiplexed FISH experiments that chromosome conformation is highly variable even within populations of the same cell, let alone between cell types, with structures such as TADs being entirely absent at the single cell level and only appearing upon pseudobulking. It is difficult to square these observations with the models of relatively static structures depicted here. The authors should provide commentary on this point.

      (2.5) As should be evident from Author response image 1, single-cell Hi-C experiments would not provide useful information about the physical organization of individual TADs, TAD boundaries or how individual TADs interact with their immediate neighbors.  In addition, since they capture only a very small fraction of the possible contacts within and between TADs, we suspect that these single-cell studies aren’t likely to be useful for making solid conclusions about TAD neighborhoods like those shown in Author response image 1 panels A, B, C and D, or Author response image 2.  While it might be possible to discern relatively stable contacts between pairs of insulators in single cells with the right experimental protocol, the stabilities/dynamics of these interactions may be better judged by the length of time that physical interactions are seen to persist in live imaging studies such as Chen et al. (2018), Vazquez et al. (2006) and Li et al. (2011).

      The in situ FISH data we’ve seen also seems problematic in that probe hybridization results in a significant decondensation of chromatin.  For two probe sets complementary to adjacent ~1.2 kb DNA sequences, the measured center-to-center distance that we’ve seen was ~110 nM.  This is about 1/3rd the length that is expected for a 1.2 kb naked DNA fragment, and about 1.7 times larger than that expected for a beads-on-a-string nucleosome array (~60 nM).  However, chromatin is thought to be compacted into a 30 nM fiber, which is estimated to reduce the length of DNA by at least another ~6 fold.  If this estimate is correct, FISH hybridization would appear to result in a ~10 fold decompaction of chromatin.  A decompaction of this magnitude would necessarily be followed by a significant distortion in the actual conformation of chromatin loops.

      (4) The analysis of the Micro-C data appears to be largely qualitative. Key information about the number of reads sequenced, reaps mapped, and data quality are not presented. No quantitative framework for identifying features such as the "plumes" is described. The study and its findings would be strengthened by a more rigorous analysis of these rich datasets, including the use of systematic thresholds for calling patterns of organization in the data.

      Additional information on the number of reads and data quality have been included in the methods section. 

      (5) Related to Point 4, the lack of quantitative details about the Micro-C data make it difficult to evaluate if the changes observed are due to biological or technical factors. It is essential that the authors provide quantitative means of controlling for factors like sampling depth, normalization, and data quality between the samples.

      In our view the changes in the MicroC contact patterns for the eve locus and its neighbors when the nhomie boundary is manipulated are not only clear cut and unambiguous but are also readily evident in the Figs that are presented in the manuscript.  If the reviewer believes that there aren’t significant differences between the MicroC contact patterns for the four different nhomie replacements, it seems certain that they would also remain unconvinced by a quantitative analysis.

      The reviewer also suggests that biological and/or technical differences between the four samples could account for the observed changes in the MicroC patterns for the eve TAD and its neighbors.  If this were the case, then similar changes in MicroC patterns should be observed elsewhere in the genome.  Since much of the genome is analyzed in these MicroC experiments there is an abundance of internal controls for each experimental manipulation of the nhomie boundary.  For two of the nhomie replacements, nhomie reverse and homie forward, the plume above the eve volcano triangle is replaced by clouds surrounding the eve volcano triangle.  If these changes in the eve MicroC contact patterns are due to significant technical (or biological) factors, we should observe precisely the same sorts of changes in TADs elsewhere in the genome that are volcano triangles with plumes.   Author response image 6 shows the MicroC contact pattern for several genes in the Antennapedia complex.  The deformed gene is included in a TAD which, like eve, is a volcano triangle topped by a plume.  A comparison of the deformed MicroC contact patterns for nhomie forward (panel B) with the MicroC patterns for nhomie reverse (panel C) and homie forward (panel D) indicates that while there are clearly technical differences between the samples, these differences do not result in the conversion of the deformed plume into clouds as is observed for the eve TAD.  The MicroC patterns elsewhere in Antennapedia complex are also very similar in all four samples.  Likewise, comparisons of regions elsewhere in the fly genome indicate that the basic contact patterns are similar in all four samples.   So while there are technical differences which are reflected in the relative pixel density in the TAD triangles and the LDC domains, these differences do not result in converting plumes into clouds nor do the alter the basic patterns of TAD triangles and LDC domains.  As for biological differences— the embryos in each sample are at roughly the same developmental stage and were collected and processed using the same procedures. Thus, the biological factors that could reasonably be expected to impact the organization of specific TADs (e.g., cell type specific differences) are not going to impact the patterns we see in our experiments. 

      Author response image 6.

      (6) The ISH effects reported are modest, especially in the case of the HCR. The details provided for how the imaging data were acquired and analyzed are minimal, which makes evaluating them challenging. It would strengthen the study to provide much more detail about the acquisition and analysis and to include depiction of intermediates in the analysis process, e.g. the showing segmentation of stripes.

      The imaging analysis is presented in Fig. 5 is just standard confocal microscopy.  Individual embryos were visualized and scored.  An embryo in which stripes could be readily detected was scored as ‘positive’ while an embryo in which stripes couldn’t be detected was scored as ‘negative.’   

      Recommendations for the authors:

      Editor comments:

      It was noted that the Jaynes lab previously published extensive genetic evidence to support the stem loop and circle loop models of Homie-Nhomie interactions (Fujioka 2016 Plos Genetics) that were more convincing than the Micro-C data presented here in proof of their prior model. Maybe the authors could more clearly summarize their prior genetic results to further try to convince the reader about the validity of their model.

      Reviewer #1 (Recommendations For The Authors):

      Below, I list specific comments to further improve the manuscript for publication. Most importantly, I recommend the authors tone down their proposal that boundary pairing is a universal TAD forming mechanism.

      (1) The title is cryptic.

      (2) The second sentence in the abstract is an overstatement: "In flies, TADs are formed by physical interactions between neighboring boundaries". Hi-C and Micro-C studies have not provided evidence that most TADs in Drosophila show focal interactions between their bracketing boundaries. The authors rely too strongly on prior studies that used artificial reporter transgenes to show that multimerized insulator protein binding sites or some endogenous fly boundaries can mediate boundary bypass, as evidence that endogenous boundaries pair.

      Please see responses #1.1 and #1.3 and figures Author response image 1 and Author response image 3.  Note that using dHS-C, most TADs that we’ve looked at so far are topped by a “dot” at their apex.

      (3) Line 64: the references do not cite the stated "studies dating back to the '90's'".

      The papers cited for that sentence are reviews which discussed the earlier findings.  The relevant publications are cited at the appropriate places in the same paragraph.  

      (4) Line 93: "On the other hand, while boundaries have partner preferences, they are also promiscuous in their ability to establish functional interactions with other boundaries." It was unclear what is meant here.

      Boundaries that a) share binding sites for proteins that multimerized, b) have binding sites for proteins that interact with each other, or c) have binding sites for proteins that can be bridged by a third protein can potentially pair with each other.  However, while these mechanisms enable promiscuous pairing interactions, they will also generate partner preferences (through a greater number of a, b and/or c).

      (5) It could be interesting to discuss the fact that it remains unclear whether Nhomie and Homie pair in cis or in trans, given that homologous chromosomes are paired in Drosophila.

      The studies in Fujioka et al. (Fujioka et al. 2016) show that nhomie and homie can pair both in cis and in trans.  Given the results described in #1.2, we imagine that they are paired in both cis and trans in our experiments.

      (6) Line 321: Could the authors further explain why they think that "the nhomie reverse circle-loop also differs from the nhomie deletion (λ DNA) in that there is not such an obvious preference for which eve enhancers activate expression"?

      The likely explanation is that the topology/folding of the altered TADs impacts the probability of interactions between the various eve enhancers and the promoters of the flanking genes.  

      (7) The manuscript would benefit from shortening the long Discussion by avoiding repeating points described previously in the Results.

      (8) Line 495: "If, as seems likely, a significant fraction of the TADs genome-wide are circle loops, this would effectively exclude cohesin-based loop extrusion as a general mechanism for TAD formation in flies". The evidence provided in this manuscript appears insufficient to discard ample evidence from multiple laboratories that TADs form by compartmentalization or loop extrusion. Multiple laboratories have, for example, demonstrated that cohesin depletion disrupts a large fraction of mammalian TADs. 

      Points made here and in #9 have been responded to in #1.1, #2.1 and #2.4 above.  We would suggest that the evidence for loop extrusion falls short of compelling (as it is based on the analysis of TAD neighborhoods, not TADs—that is forests, not trees) and given the results reported in Goel et al. (in particular Fig. 4 and Sup Fig. 8) is clearly suspect. This is not to mention the fact that cohesin loop-extrusion can’t generate circle-loops TADs, yet circle-loops clearly exist.  Likewise, as discussed in #2.4, it is not clear to us that the shared chromatin states, polymer co-segregation and co-repulsion account for the compartmental patchwork patterns of TAD;TAD interactions. The results from the  experimental manipulations in this paper and the accompanying paper, together with studies by others (e.g., Kyrchanova et al. (Kyrchanova et al. 2008), Mohana et al. (Mohana et al. 2023) would also seem to be at odds with the model for compartments as currently formulated.  

      The unique properties of Nhomie and Homie, namely the remarkable specificity with which they physically pair over large distances (Fujioka et al. 2016) may rather suggest that boundary pairing is a phenomenon restricted to special loci. Moreover, it has not yet been demonstrated that Nhomie or Homie are also able to pair with the TAD boundaries on their left or right, respectively.

      Points made here were discussed in detail in #1.2.  As described in detail in #1.2, It is not the case that nhomie and homie are in “unique” or “special.”  Other fly boundaries can do the same things.  As for whether nhomie and homie pair with their neighbors:  We haven’t done transgene experiments (e.g., testing by transvection or boundary bypass).  Likewise, in MicroC experiments there are no obvious dots at the apex of the neighboring TADs that would correspond to nhomie pairing with the neighboring boundary to the left and homie pairing with the neighboring boundary to the right. However, this is to be expected. As we discussed in in #1.3 above, only MNase resistant elements will generate dots in standard MicroC experiments.  On the other hand, when boundary:boundary interactions are analyzed by dHS-C (c.f., Author response image 4), there are dots at the apex of both neighboring TADs.  This would be direct evidence that nhomie pairs with the neighboring boundary to the left and homie pairs with the neighboring boundary to the right.

      (9) The comment in point 8 also applies to the concluding 2 sentences (lines 519-524) of the Discussion.

      See response to 8 above. Otherwise, the concluding sentences are completely accurate. Validation of the cohesin loop extrusion/CTCF roadblock model will required demonstrating a) that all TADs are either stem-loops or unanchored loops and b) that TAD endpoints are always marked by CTCF. 

      The likely presence of circle-loops and evidence that TAD boundaries that don’t have CTCF (c.f.,Goel et al. 2023) already suggests that this model can’t (either fully or not all) account for TAD formation in mammals. 

      (10) Figs. 3 and 6: It would be helpful to add the WT screenshot in the same figure, for direct comparison.

      It is easy enough to scroll between Figs-especially since nhomie forward looks just like WT.

      (11) Fig. 6: It would be helpful to show a cartoon view of a circle loop to the right of the Micro-C screenshot, as was done in Fig. 3.

      Good idea.   Added to the Fig.

      (12) Fig. 5: It would be helpful to standardize the labelling of the different genotypes throughout the figures and panels ("inverted" versus "reverse" versus an arrow indicating the direction).

      Fixed.

      Reviewer #2 (Recommendations For The Authors):

      Minor Points:

      (1) The Micro-C data does not appear to be deposited in an appropriate repository. It would be beneficial to the community to make these data available in this way.

      This has been done.

      (2) Readers not familiar with Drosophila development would benefit from a gentle introduction to the stages analyzed and some brief discussion on how the phenomenon of somatic homolog pairing might influence the study, if at all.

      We included a rough description the stages that were analyzed for both the in situs and MicroC. We thought that an actual description of what is going on at each of the stages wasn’t necessary as the process of development is not a focus of this manuscript.  In other studies, we’ve found that there are only minor differences in MicroC patterns between the blastoderm stage and stage 12-16 embryos.  While these minor differences are clearly interesting, we didn’t discuss them in the text.   In all of experiments chromosomes are likely to be paired.  In NC14 embryos (the stage for visualizing eve stripes and the MicroC contact profiles in Fig. 2) replication of euchromatic sequences is thought to be quite rapid.  While homolog pairing is incomplete at this stage, sister chromosomes are paired.  In stage 12-16 embryos, homologs will be paired and if the cells are arrested in G2, then sister chromosome will also be paired.  So in all of experiments, chromosomes (sisters and/or homologs) are paired. However, since we don’t have examples of unpaired chromosomes, our experiments don’t provide any info on how chromosome pairing might impact MicroC/expression patterns.

      (3) "P > 0.01" appears several times. I believe the authors mean to report "P < 0.01".

      Fixed.  

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    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      In the manuscript titled "Vangl2 suppresses NF-κB signaling and ameliorates sepsis by targeting p65 for NDP52-mediated autophagic degradation" by Lu et al, the authors show that Vangl2, a planner cell polarity component, plays a direct role in autophagic degradation of NFkB-p65 by facilitating its ubiquitination via PDLIM2 and subsequent recognition and autophagic targeting via the autophagy adaptor protein NDP52. Conceptually it is a wonderful study with excellent execution of experiments and controls. The concerns with the manuscript are mainly on two counts - First issue is the kinetics of p65 regulation reported here, which does not fit into the kinetics of the mechanism proposed here, i.e., Vangl2-mediated ubiquitination followed by autophagic degradation of p65. The second issue is more technical- an absolute lack of quantitative analyses. The authors rely mostly on visual qualitative interpretation to assess an increase or decrease in associations between partner molecules throughout the study. While the overall mechanism is interesting, the authors should address these concerns as highlighted below:

      Major points:

      (1) Kinetics of p65 regulation by Vangl2: As mentioned above, authors report that LPS stimulation leads to higher IKK and p65 activation in the absence of Vangl2. The mechanism of action authors subsequently work out is that- Vangl2 helps recruit E3 ligase PDLIM to p65, which causes K63 ubiquitination, which is recognised by NDP52 for autophagic targeting. Curiously, peak p65 activation is achieved within 30 minutes of LPS stimulation. The time scale of all other assays is way longer. It is not clear that in WT cells, p65 could be targeted to autophagic degradation in Vangl2 dependent manner within 30 minutes. The HA-Myc-Flag-based overexpression and Co-IP studies do confirm the interactions as proposed. However, they do not prove that this mechanism was responsible for the Vangl2-mediated modulation of p65 activation upon LPS stimulation. Moreover, the Vangl2 KO line also shows increased IKK activation. The authors do not show the cause behind increased IKK activation, which in itself can trigger increased p65 phosphorylation.

      We thank the reviewer for this valuable suggestion.

      Indeed, we agreed with the reviewer that peak p65 activation is achieved within 30 minutes of LPS stimulation in vitro, and p65 could not be targeted to autophagic degradation in a Vangl2 dependent manner within 30 minutes. Given that the protein and mRNA levels of Vangl2 were elevated at 3-6 h of LPS stimulation (Fig. S1 C-E), we extended the stimulation time scale in the revised manuscript. The data (Fig. 2A-D in the revised manuscript) demonstrated that IKK phosphorylation was enhanced in Vangl2 KO myeloid cells during the early phase (within 3 h) of LPS stimulation, but not for the prolonged period of LPS stimulation. The underlying mechanism may be complex. Only p65 phosphorylation was continuously enhanced after long-term LPS stimulation in Vangl2 KO cells, compared to WT cells. Furthermore, the overexpression of Vangl2 in A549 cells also demonstrated a reduction of phosphorylation and total endogenous p65 (Fig. 2 I, J in the revised manuscript). These findings were corroborated by overexpression and Co-IP experiments, which collectively indicated that Vangl2 regulates the stability of p65 by promoting its interaction with NDP52 and autophagic degradation. (Page 7; Line 183-185).  

      (2) The other major concern is regarding the lack of quantitative assessments. For Co-IP experiments, I can understand it is qualitative observation. However, when the authors infer that there is an increase or decrease in the association through co-IP immunoblots, it should also be quantified, especially since the differences are quite marginal and could be easily misinterpreted.

      We are grateful to the reviewer for this suggestion. The quantitative analysis has been updated in the revised version.

      (3) Figure 4E and F: It is evident that inhibiting Autolysosome (CQ or BafA1) or autophagy (3MA) led to the recovery of p65 levels and inducing autophagy by Rapamycin led to faster decay in p65 levels. Did the authors also note/explore the possibility that Vangl2 itself may be degraded via the autophagy pathway? IB of WCL upon CQ/BAF/3MA or upon Rapa treatment does indicate the same. If true, how would that impact the dynamics of p65 activation?

      We thank the reviewer for this question. Previous studies have shown that Vangl2 is primarily degraded by the proteasome pathway, rather than by the autolysosomal pathway (doi: 10.1126/sciadv.abg2099; doi: 10.1038/s41598-019-39642-z). In our experiments, Vangl2 recruits E3 ligase PDLIM2 to enhance K63-linked ubiquitination on p65, which serves as a recognition signal for cargo receptor NDP52-mediated selective autophagic degradation. Vangl2 facilitated the interaction between p65 and NDP52, yet itself did not undergo significant autophagic degradation.

      (4) Autophagic targeting of p65 should also be shown through alternate evidence, like microscopy etc., in the LPS-stimulated WT cells.

      We thank the reviewer for this suggestion. We have added the data (co-localization of p65 and LC3 was detected by immunofluorescence) in the revised version (Fig. S4 H in the revised manuscript). (Page 9, lines 267-268)

      Reviewer #2 (Public Review):

      Vangl2, a core planar cell polarity protein involved in Wnt/PCP signaling, mediates cell proliferation, differentiation, homeostasis, and cell migration. Vangl2 malfunctioning has been linked to various human ailments, including autoimmune and neoplastic disorders. Interestingly, Vangl2 was shown to interact with the autophagy regulator p62, and indeed, autophagic degradation limits the activity of inflammatory mediators such as p65/NF-κB. However, if Vangl2, per se, contributes to restraining aberrant p65/NF-kB activity remains unclear.

      In this manuscript, Lu et al. describe that Vangl2 expression is upregulated in human sepsis-associated PBMCs and that Vangl2 mitigates experimental sepsis in mice by negatively regulating p65/NF-κB signaling in myeloid cells. Vangl2 recruits the E3 ubiquitin ligase PDLIM2 to promote K63-linked poly-ubiquitination of p65. Vangl2 also facilitates the recognition of ubiquitinated p65 by the cargo receptor NDP52. These molecular processes cause selective autophagic degradation of p65. Indeed, abrogation of PDLIM2 or NDP52 functions rescued p65 from autophagic degradation, leading to extended p65/NF-κB activity.

      As such, the manuscript presents a substantial body of interesting work and a novel mechanism of NF-κB control. If found true, the proposed mechanism may expand therapeutic opportunities for inflammatory diseases. However, the current draft has significant weaknesses that need to be addressed.

      We appreciate the reviewer’s comments on our manuscript, and we have further improved the manuscript as suggested.

      Specific comments

      (1) Vangl2 deficiency did not cause a discernible increase in the cellular level of total endogenous p65 (Fig 2A and Fig 2B) but accumulated also phosphorylated IKK.

      Even Fig 4D reveals that Vangl2 exerts a rather modest effect on the total p65 level and the figure does not provide any standard error for the quantified data. Therefore, these results do not fully support the proposed model (Figure 7) - this is a significant draw back. Instead, these data provoke an alternate hypothesis that Vangl2 could be specifically mediating autophagic removal of phosphorylated IKK and phosphorylated IKK, leading to exacerbated inflammatory NF-κB response in Vangl2-deficient cells. One may need to use phosphorylation-defective mutants of p65, at least in the over-expression experiments, to dissect between these possibilities.

      We appreciate the reviewer’s comments on our manuscript, and we have further improved the manuscript as suggested.

      (1) Indeed, we agreed with the reviewer that Vangl2 deficiency did not cause a discernible increase in the cellular level of total p65 after a short time of LPS stimulation in vitro, and p65 could not be targeted to autophagic degradation in a Vangl2 dependent manner within 30 minutes. Given that the protein and mRNA levels of Vangl2 were elevated at 3-6 h of LPS stimulation (Fig. S1 C-E), we extended the stimulation time scale in the revised manuscript. The data (Fig. 2A-D in the revised manuscript) demonstrated that IKK phosphorylation was enhanced in Vangl2 KO myeloid cells during the early phase (within 3 h) of LPS stimulation, but not for the prolonged period of LPS stimulation. The underlying mechanism may be complex. Only phosphorylation of p65 and total endogenous p65 was continuously enhanced after long-term LPS stimulation in Vangl2 KO cells, compared to WT cells. Furthermore, the overexpression of Vangl2 in A549 cells also demonstrated a reduction of phosphorylation and total endogenous p65 (Fig. 2 I, J in the revised manuscript). These findings were corroborated by overexpression and Co-IP experiments, which collectively indicated that Vangl2 regulates the stability of p65 by promoting its interaction with NDP52 and autophagic degradation. (Page 7; Line 183-185).  

      (2) Similarly, the stimulation time scale in Fig 4D was extended, and it was demonstrated that p65 was more stable in Vangl2-deficient cells.

      3) Moreover, we constructed phosphorylation-defective mutants of p65 (S536A), and found that Vangl2 could also promote the degradation of the p65 phosphorylation mutants (Fig. S4 A, B in the revised manuscript). Thus, Vangl2 promote the degradation of the basal/unphosphorylated p65. (Page 8, lines 237-240)

      (2) Fig 1A: The data indicates the presence of two subgroups within the sepsis cohort - one with high Vangl2 expressions and the other with relatively normal Vangl2 expression. Was there any difference with respect to NF-κB target inflammatory gene expressions between these subgroups?

      As suggested, we conducted an analysis of NF-kB target inflammatory gene expressions between the high and relatively low Vangl2 expression groups in sepsis patients. The results showed that the serum of the high Vangl2 expression group exhibited lower levels of IL-6, WBC, and CRP than the low Vangl2 expression group, which suggested an inverse correlation between Vangl2 and the inflammatory response (Fig. S1 A in the revised manuscript) (Page 5, lines 126-128).

      (3) The effect of Vangl2 deficiency was rather modest in the neutrophil. Could it be that Vangl2 mediates its effect mostly in macrophages?

      As showed in Fig. S1C-E, the induction of Vangl2 by LPS stimulation is more rapid in macrophages than in neutrophils. This may contribute to its dominant effect in macrophages. Consequently, we primarily focused our investigation on the role of Vangl2 in macrophages.

      (4) Fig 1D and Figure 1E: Data for unstimulated Vangl2 cells should be provided. Also, the source of the IL-1β primary antibody has not been mentioned.

      Thank you for the suggestion. We have updated the data for unstimulated cells in the revised manuscript (Fig. 1 D, E in the revised manuscript). Also, IL-1β primary antibody was purchased from Cell Signaling Technology and the information has been included in the Materials and Methods section (Table S1).

      (5) The relevance and the requirement of RNA-seq analysis are not clear in the present draft. Figure 1E already reveals upregulation of the signature NF-κB target inflammatory genes upon Vangl2 deficiency.

      We agreed with the reviewer that the data presented in Figure 1E demonstrated the upregulation of the signature NF-kB target inflammatory genes upon Vangl2 deficiency in a murine model of LPS induced sepsis. Subsequently, we proceeded to investigate the mechanism by which Vangl2 regulates NF-kB target inflammatory genes at the cellular level in Figure 2. To this end, we performed RNA-seq analysis to screen signal pathways involved in LPS-induced septic shock by comparing LPS-stimulated BMDMs from Vangl2ΔM and WT mice, and identified that TNF signaling pathway and cytokine-cytokine receptor interaction were found to be significantly enriched in Vangl2ΔM BMDMs upon LPS stimulation. This analysis provides further evidence that Vangl2 plays a role in regulating NF-kB signaling pathways and the release of related inflammatory cytokines.

      (6) Fig 2A reveals an increased accumulation of phosphorylated p65 and IKK in Vangl2-deficient macrophages upon LPS stimulation within 30 minutes. However, Vangl2 accumulates at around 60 minutes post-stimulation in WT cells. Similar results were obtained for neutrophils (Fig 2B). There appears to be a temporal disconnect between Vangl2 and phosphorylated p65 accumulation - this must be clarified.

      This concern has been addressed above (see response to questions 1 from reviewer #2). 

      (7) Figure 2E and 2F do not have untreated controls. Presentations in Fig 2E may be improved to more clearly depict IL6 and TNF data, preferably with separate Y-axes.

      Thank you for the suggestion. We have added untreated controls and separated Y-axes for IL-6 and TNF data in the revised manuscript (Fig. 2 E, F in the revised manuscript).

      (8) Line 219: "strongly with IKKα, p65 and MyD88, and weak" - should be revised.

      We have improved the manuscript as suggested in the revised manuscript (Page 7; Line 203).

      (9) It is not clear why IKKβ was excluded from interaction studies in Fig S3G.

      We added the Co-IP experiment and showed that HA-tagged Vangl2 only interacted with Flag-tagged p65, but not with Flag-tagged IKKb in 293T cells (Fig S3H). Furthermore, endogenous co-IP immunoblot analyses showed that Vangl2 did not associate with IKKb (Fig. S3I)

      (10) Fig 3F- In the text, authors mentioned that Vangl2 strongly associates with p65 upon LPS stimulation in BMDM. However, no controls, including input or another p65-interacting protein, were used.

      As reviewer suggested, we have added input and positive control (IkBa) in this experiment (Fig. 3F in the revised manuscript). The results demonstrated that the interaction between p65 and IkBa was attenuated, although the total IkBa did not undergo significant degradation over long-term course of LPS stimulation.

      (11) Figure 4D - Authors claim that Vangl2-deficient BMDMs stabilized the expression of endogenous p65 after LPS treatment. However, p65 levels were particularly constitutively elevated in knockout cells, and LPS signaling did not cause any further upregulation. This again indicates the role of Vangl2 in the basal state. The authors need to explain this and revise the test accordingly.

      Thank you for the reviewer's comments. We repeated the experiment to ascertain whether Vangl2 could stabilize the expression of endogenous p65 before and after LPS treatment. It was found that, due to the extremely low expression of Vangl2 in WT cells in the absence of stimulation, there was no observable difference on the basal level of p65 between WT and Vangl2DM cells. However, upon prolonged LPS stimulation, Vangl2 expression was induced, resulting in p65 degradation in WT cells. In contrast, p65 protein was more stable in Vangl2 deficient cells after LPS stimulation (Fig. 4D in the revised manuscript).

      Reviewer #3 (Public Review):

      Lu et al. describe Vangl2 as a negative regulator of inflammation in myeloid cells. The primary mechanism appears to be through binding p65 and promoting its degradation, albeit in an unusual autolysosome/autophagy dependent manner. Overall, the findings are novel and the crosstalk of PCP pathway protein Vangl2 with NF-kappaB is of interest. …….Regardless, Vangl2 as a negative regulator of NF-kappaB is an important finding. There are, however, some concerns about methodology and statistics that need to be addressed.

      Thank you for your comments on our manuscript, and we have further improved the manuscript as suggested.

      (1) Whether PCP is anyway relevant or if this is a PCP-independent function of Vangl2 is not directly explored (the later appears more likely from the manuscript/discussion). PCP pathways intersect often with developmentally important pathways such as WNT, HH/GLI, Fat-Dachsous and even mechanical tension. It might be of importance to investigate whether Vangl2-dependent NF-kappaB is influenced by developmental pathways.

      Thank you for the reviewer's insightful comments. Our study revealed that Vangl2 recruits the E3 ubiquitin ligase PDLIM2 to facilitate K63-linked ubiquitination of p65, which is subsequently recognized by autophagy receptor NDP52 and then promotes the autophagic degradation of p65. Our findings by using autophagy inhibitors and autophagic-deficient cells indicate that Vangl2 regulates NF-kB signaling through a selective autophagic pathway, rather than affecting the PCP pathway, WNT, HH/GLI, Fat-Dachsous or even mechanical tension. Moreover, a discussion section has been added to the revised version. (Page 12, lines 377-393)

      (2) Are Vangl2 phosphorylations (S5, S82 and S84) in anyway necessary for the observed effects on NF-kappaB or would a phospho-mutant (alanine substitution mutant) Vangl2 phenocopy WT Vangl2 for regulation of NF-kappaB?

      As suggested, we generated phospho-mutants of Vangl2 (S82/84A) and observed that Vangl2 (S82/84A) could still facilitate the degradation of p65 (Fig. S4 B in the revised manuscript), suggesting that Vangl2 regulates the NF-kB pathway independently of its phosphorylation.

      (3) Another area to strengthen might be with regards to specificity of cell types where this phenomenon may be observed. LPS treatment in mice resulted in Vangl2 upregulation in spleen and lymph nodes, but not in lung and liver. What explains the specificity of organ/cell-type Vangl2 upregulation and its consequences observed here? Why is NF-kappaB signaling not more broadly or even ubiquitously affected in all cell types in a Vangl2-dependent manner, rather than being restricted to macrophages, neutrophils and peritoneal macrophages, or, for that matter, in spleen and LN and not liver and lung? After all, one may think that the PCP proteins, as well as NF-kappaB, are ubiquitous.

      Thank you for the reviewer's comments.

      (1) LPS is an important mediator to trigger sepsis with excessive immune activation. As is well known, the spleen and lymph nodes are important peripheral immune organs, where immune cells (e.g., macrophages) are abundant and respond sensitively to LPS stimulation. Nevertheless, immune cells represent a minor fraction of the lungs and liver. Consequently, Vangl2 represents a pivotal regulator of immune function, exhibiting a more pronounced increase in the immune organs and cells.

      2) Induction of Vangl2 expression by LPS stimulation is cell specific. Given that different cells exhibit varying protein abundances, the molecular events involved may also differ. Moreover, we observed high Vangl2 expression in the liver at the basal state (Author response image 1), whereas it was not induced after 12 h of LPS stimulation. Therefore, the functional role of Vangl2 exhibits significant phenotype in macrophages and neutrophils/spleen and LN, rather than in liver or lung cells.

      Author response image 1.

      Vangl2 showed no significant changes in the liver after LPS treatment. Mice (n≥3) were treated with LPS (30 mg/kg, i.p.). Livers were collected at 12 h after LPS treatment. Immunoblot analysis of Vangl2.

      Recommendations For The Authors:

      Reviewer #1 (Recommendations For The Authors):

      General points:

      Figure 4G- panels appear mislabeled. Pl correct.

      We have corrected this mislabeling as you suggested.

      The dynamics of Vangl2 interaction with p65 and autophagy adaptors is not clear/apparent. For example, Vangl2 expression destabilises p65 levels (as in Fig. 4), but in Fig. 5, it seems there is no decline in the p65 protein level, and a large fraction of it coprecipitates with NDP52.

      We appreciate the reviewer’s comments. In the co-IP assay, we used the lysosomal inhibitor CQ to inhibit p65 degradation to observe the interaction between p65 and NDP52 or Vangl2.

      Fig 5E- I would expect p65 levels to be lower in WT cells than Vangl2 KO cells. But as such, there is no difference between the two.

      We appreciate the reviewer’s comments. We repeated the experiments and updated the data. Firstly, Vangl2 was not induced in WT cells in the absence of LPS stimulation, thus there was no difference in p65 expression between the two groups at the basal level. Secondly, we used CQ/Baf-A1 to inhibit the degradation of Vangl2 in the co-IP assay to observe the interaction between p65 and other molecule.

      Reviewer #2 (Recommendations For The Authors):

      A few points that can be looked at and revised.

      (1) Quantification of the presented data is needed for Fig 4D and Fig 4E.

      We added the quantification analysis as suggested.  

      (2) The labeling of Fig 4G should be scrutinized.

      We have corrected this mislabeling as you suggested.

      (3) Fig 6B and Fig 6C should be explained in the result section more elaborately.

      We thank the reviewer for the suggestion, and we have rephrased this sentence to better describe the results. (Page 10, lines 306-313)

      (4) Line 85: "Vangl2 mediated downstream of Toll-like or interleukin (IL)-1" - unclear.

      We appreciate the reviewer’s comments on our manuscript, and we have further improved the manuscript as suggested in the revised manuscript. (Page 3, lines 68)

      (5) Line 181: "mice. Differentially expression analysis" - this should be revised.

      We appreciate the reviewer’s comments on our manuscript, and we have further improved the manuscript as suggested in the revised manuscript. (Page 11, lines 323)

      (6) Line 261-264- CHX-chase assay showed the degradation rate of p65 in Vangl2-deficient BMDM was slower compared with WT cells. However, Vangl2 is not induced in WT BMDMs upon CHX treatment (Fig. S4B).

      We appreciate the reviewer’s comments on our manuscript, and we have further improved the manuscript as suggested in the revised manuscript (Fig. S4D).

      (7) Finally, some editing to provide data only critical for the conclusions could improve the ease of reading.

      We have further improved the manuscript as suggested in the revised manuscript.

      Reviewer #3 (Recommendations For The Authors):

      Comments (general, please address at least in Discussion. Some experimental data, for example the role, if any, of Vangl2 phosphorylations will be very useful):

      (1) It might be interesting to explore whether there are any potential effects of developmental pathways on the observed effect mediated by Vangl2 or if the effects are entirely a PCP-independent function of Vangl2. Please see above public review.

      Thank you for the reviewer's insightful comments. Our study revealed that Vangl2 recruits the E3 ubiquitin ligase PDLIM2 to facilitate K63-linked ubiquitination of p65, which is subsequently recognized by autophagy receptor NDP52 and then promotes the autophagic degradation of p65. Our findings by using autophagy inhibitors and autophagic-deficient cells indicate that Vangl2 regulates NF-kB signaling through a selective autophagic pathway, rather than affecting the PCP pathway, WNT, HH/GLI, Fat-Dachsous or even mechanical tension. Furthermore, we generated phospho-mutants of Vangl2 (S82/84A) and observed that Vangl2 (S82/84A) could still facilitate the degradation of p65 (Fig. S4 B), suggesting that Vangl2 regulates the NF-kB pathway independently of its phosphorylation. In addition, a discussion section has been added to the revised version. (Page 12, lines 377-393)

      (2) What explains the specificity of organ/cell-type Vangl2 upregulation and its consequences observed here? Why is NF-kappaB signaling not more broadly or even ubiquitously affected in all cell types in a Vangl2-dependent manner, rather than being restricted to macrophages, neutrophils and peritoneal macrophages, or, for that matter, in spleen and LN and not liver and lung? Afterall, one may think that the PCP proteins, as well as NF-kappaB, are ubiquitous.

      Thank you for the reviewer's comments. A similar question has been addressed above (refer to the response to question 3 of reviewer 3).

      (3) Another specificity-related question that comes to mind is whether the Vangl2 function in autolysomal/autophagic degradation is restricted to p65 as the exclusive substrate? The cytosolic targeting of p65 as opposed to the more well-known nuclear-targeting is interesting.

      Our previous finding demonstrated that Vangl2 inhibits antiviral IFN-I signaling by targeting TBK1 for autophagic degradation (doi: 10.1126/sciadv.adg2339), thereby indicating that p65 is not the sole substrate for Vangl2. However, in the NF-kB pathway, p65 is a specific substrate for Vangl2. Moreover, our findings indicate that the interaction between Vangl2 and p65 occurs predominantly in the cytoplasm, rather than in the nucleus (Fig. S4 C).

      (4) Pharmacological approach is used to tease apart autolysosome versus proteasome pathway. What is the physiological importance of autophagic degradation? It is interesting to note that Vangl2 was already previously implicated in degrading LAMP-2A and increasing chaperon-mediated autophagy (CMA)-lysosome numbers (PMID: 34214490).

      Previous literature has domonstrated that Vangl2 can inhibit CMA degradation (PMID: 34214490). However, in our study, we found that Vangl2 can promote the selective autophagic degradation of p65. It is important to note that CMA degradation and selective autophagic degradation are two distinct degradation modes, which is not contradictory.

      (5) Are these phenotypes discernable in heterozygotes or only when ablated in homozygosity? Any phenotypes recapitulated in the looptail heterozygote mice?

      We found that these phenotypes discernable only in homozygosity.

      (6) What is the conservation of the Vangl2 p65-interaction site between Vangl2 and Vangl1? PDLIM2 recruitment between Vangl2 and Vangl1?

      We appreciate the reviewer’s comments on our manuscript. Previous studies have shown that human Vangl1 and Vangl2 exhibit only 72% identity and exhibit distinct functional properties (doi: 10.1530/ERC-14-0141).Thus, the interaction of Vangl2 with p65 and PDLIM2 recruitment may not necessarily occur in Vangl1.

      Comments (specific to experiments and data analyses. Please address the following):

      (7) The patient population used in Fig 1 is not described in the Methods. This is a critical omission. Were age, sex etc. controlled for between healthy and disease? How was the diagnosis made? What times during sepsis were the samples collected? As presented, this data is impossible to evaluate and interpret.

      We appreciate the reviewer’s comments on our manuscript, and we have further improved the manuscript as suggested in the revised supplement materials. (Supplementary information, Page 12, lines 146-147)

      (8) In general, the statistical method should be described for each experiment presented in the figures. Comparisons should not be made only at the time point with maximal difference (such as in Fig 1F or Fig 2C, but at all time points using appropriate statistical methods). The sample size should also be included to allow determination appropriateness of parametric or non-parametric tests.

      We appreciate the reviewer’s comments on our manuscript, and we have further improved the manuscript as suggested in the revised manuscript (Figures 1F and 2C).

      (9) PCP pathways can activate p62/SQSTM1 or JNK via RhoA. JNK activation should be tested experimentally.

      According to the reviewer's comments, we further examined the effect of Vangl2 on the JNK pathway. The results showed that Vangl2 did not affect the JNK pathway (Author response image 2). This suggests that Vangl2 functions independently of the PCP pathway.

      Author response image 2.

      Vangl2 did not affect the JNK pathway. WT and Vangl2-deficient (n≥3) BMDMs were stimulated with LPS (100 ng/ml) for the indicated times. Immunoblot analysis of total and phosphorylated JNK.

      (10) Why are different cells such as A549, HEK293, CHO, 293T, THP-1 used during the studies for different experiments? Consistency would improve rigor. At least, logical explanation driving the cell type of choice for each experiment should be included in the manuscript. Nonetheless, one aspect of using a panel of cell lines indicate that the effect of Vangl2 on NF-kappa B is pleiotropic.

      We are grateful to the reviewer for their comments on our manuscript. A549, HEK293, CHO, and 293T cells are commonly utilized in protein-protein interaction studies. The selection of cell lines for overexpression (exogenous) experiment is dependent on their transfection efficiency and the ability to express TLR4 (the receptor for LPS). Additionally, we conducted endogenous experiments by using THP-1 and BMDMs, which are human macrophage cell lines and murine primary macrophages, respectively. Moreover, we generated Vangl2f/f lyz-cre mice by specifically knocking out Vangl2 in myeloid cells, and investigated the effect of Vangl2 on NF-kB signaling in vivo.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      The manuscript examines the contribution of the dorsal and intermediate hippocampus to goal-directed navigation in a wide virtual environment where visual cues are provided by the scenery on the periphery of a wide arena. Among a choice of 2 reward zones located near the arena periphery, rats learn to navigate from the center of the arena to the reward zone associated with the highest reward. Navigation performance is largely assessed from the rats' body orientation when they leave the arena center and when they reach the periphery, as well as the angular mismatch between the reward zone and the site rats reach the periphery. Muscimol inactivation of the dorsal and intermediate hippocampus alters rat navigation to the reward zone, but the effect was more pronounced for the inactivation of the intermediate hippocampus, with some rat trajectories ending in the zone associated with the lowest reward. Based on these results, the authors suggest that the intermediate hippocampus is critical, especially for navigating to the highest reward zone.

      Strengths:

      -The authors developed an effective approach to study goal-directed navigation in a virtual environment where visual cues are provided by the peripheral scenery.

      - In general, the text is clearly written and the figures are well-designed and relatively straightforward to interpret, even without reading the legends.

      - An intriguing result, which would deserve to be better investigated and/or discussed, was that rats tended to rotate always in the counterclockwise direction. Could this be because of a hardware bias making it easier to turn left, some aspect of the peripheral landscape, or a natural preference of rats to turn left that is observable (or reported) in a real environment?

      Thank you for the insightful question. As the reviewer mentioned, the counterclockwise rotation behavior was intriguing and unexpected. To answer the reviewer’s question properly, we examined whether such stereotypical turning behavior appeared before the rats acquired the task rule and reward zones in the pre-surgical training phase of the task. Data from the last day of shaping and the first day of the pre-surgical main task day showed no significant difference in the number of trials in which the first body-turn was either clockwise or counterclockwise, suggesting that the rats did not have a bias toward a specific side (p=0.46 for Shaping; p=0.76 for the Main task, Wilcoxon signed-rank test). These results excluded the possibility that there was something in the apparatus's hardware that made the rats turn only to the left. Also, since we used the same peripheral landscape for the shaping and main task, we could assume that the peripheral landscape did not cause movement bias.

      Author response image 1.

      Although it remains inconclusive, we have noticed that some prior studies alluded to a phenomenon similar to this issue, framed as the topic of lateralization or spatial preference by comparing left and right biases. For example, Wishaw et al. (1992) suggested that there was natural lateralization in rats (“Most of the rats displayed either a strong right limb bias or a strong left limb bias.”) but no dominance to a specific side. Andrade et al. (2001) also claimed that “83% of Wistar rats spontaneously showed a clear preference for left or right arms in the T-maze.” However, to the best of our knowledge, there has been no direct evidence that rats have a dominant natural preference only to one side.

      Therefore, while the left-turning behavior remains an intriguing topic for further investigation, we find it difficult to pinpoint the reason behind the behavior in the current study. However, we would like to emphasize that this behavior did not interrupt testing our hypothesis. Nonetheless, we agree with the reviewer’s point that the counterclockwise rotation needs to be discussed more, so we revised the manuscript as follows:

      “To rule out the potential effect of hardware bias or any particular aspect of peripheral landscape to make rats turn only to one side, we measured the direction of the first body-turn in each trial on the last day of shaping and the first day of the main task (i.e., before rats learned the reward zones). There was no significant difference between the clockwise and counterclockwise turns (p=0.46 for shaping, p=0.76 for main task; Wilcoxon signed-rank test), indicating that the stereotypical pattern of counterclockwise body-turn appeared only after the rats learned the reward locations.” (p.6)

      - Another interesting observation, which would also deserve to be addressed in the discussion, is the fact that dHP/iHP inactivations produced to some extent consistent shifts in departing and peripheral crossing directions. This is visible from the distributions in Figures 6 and 7, which still show a peak under muscimol inactivation, but this peak is shifted to earlier angles than the correct ones. Such change is not straightforward to interpret, unlike the shortening of the mean vector length.

      Maybe rats under muscimol could navigate simply by using the association of reward zone with some visual cues in the peripheral scene, in brain areas other than the hippocampus, and therefore stopped their rotation as soon as they saw the cues, a bit before the correct angle. While with their hippocampus is intact, rats could estimate precisely the spatial relationship between the reward zone and visual cues.

      We agree with the possibility suggested by the reviewer. However, although not described in the original manuscript, we performed several different control experiments in a few rats using various visual stimulus manipulations to test how their behaviors change as a result. One of the experiments was the landmark omission test, where one of the landmarks was omitted. The landmark to be made disappear was pseudorandomly manipulated on a trial-by-trial basis. We observed that the omission of one landmark, regardless of its identity, did not cause a specific behavioral change in finding the reward zones, suggesting that the rats were not relying on a single visual landmark when finding the reward zone.

      Author response image 2.

      Therefore, it is unlikely that rats used the spatial relationship between the reward zone and a specific visual cue to solve the task in our study. However, the result was based on an insufficient sample size (n=3), not permitting any meaningful statistical testing. Thus, we have now updated this information in the manuscript as an anecdotal result as follows:

      “Additionally, to investigate whether the rats used a certain landmark as a beacon to find the reward zones, we conducted the landmark omission test as a part of control experiments. Here, one of the landmarks was omitted, and the landmark to be made disappear was pseudorandomly manipulated on a trial-by-trial basis. The omission of one landmark, regardless of its identity, did not cause a specific behavioral change in finding the reward zones, suggesting that the rats were not relying on a single visual landmark when finding the reward zones. The result can be reported anecdotally only because of an insufficient sample size (n=3), not permitting any meaningful statistical testing.” (p.9)

      Weaknesses:

      -I am not sure that the differential role of dHP and iHP for navigation to high/low reward locations is supported by the data. The current results could be compatible with iHP inactivation producing a stronger impairment on spatial orientation than dHP inactivation, generating more erratic trajectories that crossed by chance the second reward zone.

      To make the point that iHP inactivation affects the disambiguation of high and low reward locations, the authors should show that the fraction of trajectories aiming at the low reward zone is higher than expected by chance. Somehow we would expect to see a significant peak pointing toward the low reward zone in the distribution of Figures 6-7.

      We thank the reviewer for the valuable comments. We agree that it is difficult to rigorously distinguish the loss of value representation from spatial disorientation in our experiment. Since the trial ended once the rat touched either reward zone, it was difficult to specify whether they intended to arrive at the location or just moved randomly and arrived there by chance. Moreover, it is possible that the drug infusion did not completely inactivate the iHP but only partially did so.

      To investigate this issue further, we checked whether the distribution of the departure direction (DD) differed between the trials in which rats initially headed north (NW, N, NE) and south (SE, S, SW) at the start. In the manuscript, we demonstrated that DD aligned with the high-value zone, indicating that the rat remembered the scenes associated with the high-value zone (p.8). Based on the rats’ characteristic counterclockwise rotation, the reward zone rats would face first upon starting while heading north would be the high-value zone. On the other hand, the rat would face the low-value reward zone when starting while heading south. In this case, normal rats would inhibit leaving the start zone and rotate further until they face the high-value zone before finally departing the start location. If the iHP inactivation caused a more severe impairment in spatial orientation but not in value representation, it is likely that the iHP-inactivated rats in both north- and south-starting trials would behave similarly with the dHP-inactivated rats, but producing a larger deviation from the high-value zone. However, if the iHP inactivation affected the disambiguation of high and low reward locations, north and south-starting trials would show different DD distributions.

      The circular plots shown below are the DD distributions of dMUS and iMUS. We could see that when they started facing north, iHP-inactivated rats still aligned themselves towards the high-value zone and thus remained spatially oriented, similar to the dHP inactivation session. However, in the south-starting trials, the DD distribution was completely different from the north-starting trials; the rats failed in body alignment towards the high-value zone. Instead, they departed the start point while heading south in most trials. This pattern was not seen in dMUS sessions, even in their south-starting trials, illustrating the distinct deficit caused by iHP inactivation. Additionally, most of the rats with iHP inactivation visited the low-value zone more in south-headed starting trials than in the north-headed trials, except for one rat.

      Author response image 3.

      Furthermore, we would like to clarify that we do not limit the effect of iHP inactivation to the impairment in distinguishing the high and low reward zones. It is possible that iHP inactivation resulted in the loss of a global value-representing map, leading to the impairment in distinguishing both reward zones from other non-rewarded areas in the environment. Figures 6 and 7 implicated this possibility by showing that the peaks are not restricted only to the reward zones. Unfortunately, we cannot rigorously address this in the current study because of the limitations of our experimental design mentioned above.

      Nonetheless, we agree with the reviewer that this limitation needs to be addressed, so we now added how the current study needs further investigation to clarify what causes the behavioral change after the iHP inactivation in the Limitations section (p.21).

      Reviewer #2 (Public Review):

      Summary:

      The aim of this paper was to elucidate the role of the dorsal HP and intermediate HP (dHP and iHP) in value-based spatial navigation through behavioral and pharmacological experiments using a newly developed VR apparatus. The authors inactivated dHP and iHP by muscimol injection and analyzed the differences in behavior. The results showed that dHP was important for spatial navigation, while iHP was critical for both value judgments and spatial navigation. The present study developed a new sophisticated behavioral experimental apparatus and proposed a behavioral paradigm that is useful for studying value-dependent spatial navigation. In addition, the present study provides important results that support previous findings of differential function along the dorsoventral axis of the hippocampus.

      Strengths:

      The authors developed a VR-based value-based spatial navigation task that allowed separate evaluation of "high-value target selection" and "spatial navigation to the target." They were also able to quantify behavioral parameters, allowing detailed analysis of the rats' behavioral patterns before and after learning or pharmacological inactivation.

      Weaknesses:

      Although differences in function along the dorsoventral axis of the hippocampus is an important topic that has received considerable attention, differences in value coding have been shown in previous studies, including the work of the authors; the present paper is an important study that supports previous studies, but the novelty of the findings is not that high, as the results are from pharmacological and behavioral experiments only.

      We appreciate the reviewer's insightful comments. In response, we would like to emphasize that a very limited number of studies investigated the function of the intermediate hippocampus, especially in spatial memory tasks. We tested the differential functions of the dorsal and intermediate hippocampus using a within-animal design and used reversible inactivation manipulation (i.e., muscimol injection) to prevent potential compensation by other brain regions when using irreversible manipulation techniques (i.e., lesion). Also, very few studies have analyzed the navigation trajectories of animals as closely as in the current study. We emphasize the novelty of our study by comparing it with prior studies, as shown below in Table 1.

      Author response table 1.

      Comparison of our study with those from prior studies

      Moreover, to the best of our knowledge, the current manuscript is the first to investigate the hippocampal subregions along the long axis in a VR environment using a hippocampal-dependent spatial memory task. Nonetheless, we agree that the current study has a limitation as a behavior-only experiment. We now have added a comment on how other techniques, such as electrophysiology, would develop our findings in the Limitation section (p.21).

      Reviewer #3 (Public Review):

      Summary:

      The authors established a new virtual reality place preference task. On the task, rats, which were body-restrained on top of a moveable Styrofoam ball and could move through a circular virtual environment by moving the Styrofoam ball, learned to navigate reliably to a high-reward location over a low-reward location, using allocentric visual cues arranged around the virtual environment.

      The authors also showed that functional inhibition by bilateral microinfusion of the GABA-A receptor agonist muscimol, which targeted the dorsal or intermediate hippocampus, disrupted task performance. The impact of functional inhibition targeting the intermediate hippocampus was more pronounced than that of functional inhibition targeting the dorsal hippocampus.

      Moreover, the authors demonstrated that the same manipulations did not significantly disrupt rats' performance on a virtual reality task that required them to navigate to a spherical landmark to obtain reward, although there were numerical impairments in the main performance measure and the absence of statistically significant impairments may partly reflect a small sample size (see comments below).

      Overall, the study established a new virtual-reality place preference task for rats and established that performance on this task requires the dorsal to intermediate hippocampus. They also established that task performance is more sensitive to the same muscimol infusion (presumably - doses and volumes used were not clearly defined in the manuscript, see comments below) when the infusion was applied to the intermediate hippocampus, compared to the dorsal hippocampus, although this does not offer strong support for the authors claim that dorsal hippocampus is responsible for accurate spatial navigation and intermediate hippocampus for place-value associations (see comments below).

      Strengths:

      (1) The authors established a new place preference task for body-restrained rats in a virtual environment and, using temporary pharmacological inhibition by intra-cerebral microinfusion of the GABA-A receptor agonist muscimol, showed that task performance requires dorsal to intermediate hippocampus.

      (2) These findings extend our knowledge about place learning tasks that require dorsal to intermediate hippocampus and add to previous evidence that, for some place memory tasks, the intermediate hippocampus may be more important than other parts of the hippocampus, including the dorsal hippocampus, for goal-directed navigation based on allocentric place memory.

      (3) The hippocampus-dependent task may be useful for future recording studies examining how hippocampal neurons support behavioral performance based on place information.

      Weaknesses:

      (1) The new findings do not strongly support the authors' suggestion that the dorsal hippocampus is responsible for accurate spatial navigation and the intermediate hippocampus for place-value associations.

      The authors base this claim on the differential effects of the dorsal and intermediate hippocampal muscimol infusions on different performance measures. More specifically, dorsal hippocampal muscimol infusion significantly increased perimeter crossings and perimeter crossing deviations, whereas dorsal infusion did not significantly change other measures of task performance, including departure direction and visits to the high-value location. However, these statistical outcomes offer only limited evidence that dorsal hippocampal infusion specifically affected the perimeter crossing, without affecting the other measures. Numerically the pattern of infusion effects is quite similar across these various measures: intermediate hippocampal infusions markedly impaired these performance measures compared to vehicle infusions, and the values of these measures after dorsal hippocampal muscimol infusion were between the values in the intermediate hippocampal muscimol and the vehicle condition (Figures 5-7). Moreover, I am not so sure that the perimeter crossing measures really reflect distinct aspects of navigational performance compared to departure direction and hit rate, and, even if they did, which aspects this would be. For example, in line 316, the authors suggest that 'departure direction and PCD [perimeter crossing deviation] [are] indices of the effectiveness and accuracy of navigation, respectively'. However, what do the authors mean by 'effectiveness' and 'accuracy'? Accuracy typically refers to whether or not the navigation is 'correct', i.e. how much it deviates from the goal location, which would be indexed by all performance measures.

      So, overall, I would recommend toning down the claim that the findings suggest that the dorsal hippocampus is responsible for accurate spatial navigation and the intermediate hippocampus for place-value associations.

      The reviewer mentioned that the statistical outcomes offer limited evidence as the dHP inactivation results were always positioned between the results of the iHP inactivation and controls. However, we would like to emphasize that, projecting to each other, the two subregions are not completely segregated anatomically. It is highly likely this is also true functionally and there should be some overlap in their roles. Considering such relationships between the dHP and iHP, it could be natural to see an intermediate effect after inactivating the dHP, and that is why we focused on the “magnitude” of behavioral changes after inactivation instead of complete dissociation between the two subregions in our manuscript. Unfortunately, because of the nature of the drug infusion study, further dissociation would be difficult, requiring further investigation with different experimental techniques, such as physiological examinations of the neural firing patterns between the two regions. We mentioned this caveat of the current study in the Limitations as follows:

      “However, our study includes only behavioral results and further mechanistic explanations as to the processes underlying the behavioral deficits require physiological investigations at the cellular level. Neurophysiological recordings during VR task performance could answer, for example, the questions such as whether the value-associated map in the iHP is built upon the map inherited from the dHP or it is independently developed in the iHP.” (p.21)

      Regarding the reviewer’s comment on the meaning of measuring the perimeter crossing directions, we would like to draw the reviewer’s attention to the individual trajectories during the iMUS sessions described in Figure 5. Particularly when they were not confident with the location of the higher reward, rats changed their heading directions during the navigation, which resulted in a less efficient route to the goal location. Rats showing this type of behavior tended to hit the perimeter of the arena first before correcting their routes toward the goal zone. In contrast, rats showing effective navigation hardly bumped into the wall or perimeter before hitting the goal zone. Thus, their PCDs matched DDs almost always. When considered together with DD, our PCD measure could tell whether rats not hitting the goal zone directly after departure were impaired in either maintaining the correct heading direction to the goal zone at the start location or orienting themselves to the target zone accurately from the start. Our results suggest that the latter is the case. We included the relevant explanation in the Discussion section as follows:

      “Particularly, rats changed their heading directions during the navigation when they were not confident with the location of the higher reward, resulting in a less efficient route to the goal location. Rats showing this type of behavior tended to hit the perimeter of the arena first before correcting their routes. Therefore, when considered together with DD, our PCD measure could tell that the rats not hitting the goal zone directly after departure were impaired in orienting themselves to the target zone accurately from the start, not in maintaining the correct heading direction to the goal zone at the start location.” (p.19)

      Nonetheless, we agree with the reviewer that the term ‘accuracy’ might be confusing with performance accuracy, so we replaced the term with ‘precision’ throughout the manuscript, referring to the precise targeting of the reward zones.

      (2) The claim that the different effects of intermediate and dorsal hippocampal muscimol infusions reflect different functions of intermediate and dorsal hippocampus rests on the assumption that both manipulations inhibit similar volumes of hippocampal tissue to a similar extent, but at different levels along the dorso-ventral axis of the hippocampus. However, this is not a foregone conclusion (e.g., drug spread may differ depending on the infusion site or drug effects may differ due to differential expression of GABA-A receptors in the dorsal and intermediate hippocampus), and the authors do not provide direct evidence for this assumption. Therefore, a possible alternative account of the weaker effects of dorsal compared to intermediate hippocampal muscimol infusions on place-preference performance is that the dorsal infusions affect less hippocampal volume or less markedly inhibit neurons within the affected volume than the intermediate infusions. I would recommend that the authors briefly consider this issue in the discussion. Moreover, from the Methods, it is not clear which infusion volume and muscimol concentration were used for the different infusions (see below, 4.a.), and this must be clarified.

      We appreciate these insightful comments from the reviewer and agree that we do not provide direct evidence for the point raised by the reviewer. To the best of our knowledge, most of the behavioral studies on the long axis of the hippocampus did not particularly address the differential expression of GABA-A receptors along the axis. We could not find any literature that specifically introduced and compared the levels of expression of GABA-A receptors or the diffusion range of muscimol in the intermediate hippocampus to the other subregions. However, we found that Sotiriou et al. (2005) made such comparisons with respect to the expression of different GABA-A receptors. They concluded that the dorsal and ventral hippocampi have different levels of the GABA-A receptor subtypes. The a1/b2/g2 subtype was dominant in the dorsal hippocampus, while the a2/b1/g2 subtype was prevalent in the ventral hippocampus. Sotiriou and colleagues also mentioned the lower affinity of GABA-A receptor binding in the ventral hippocampus, and this result is consistent with the Papatheodoropoulos et al. (2002) study that showed a weaker synaptic inhibition in the ventral hippocampus compared to the dorsal hippocampus. Papatheodoropoulos et al. speculated differences in GABA receptors as one of the potential causes underlying the differential synaptic inhibition between the dorsal and ventral hippocampal regions. Based on these findings, the same volume of muscimol is more likely to cause a more severe effect on the ventral hippocampus than the dorsal hippocampus. Therefore, we do not believe that the less significant changes after the dorsal hippocampal inactivation were induced by the expression level of GABA-A receptors. Additionally, we have demonstrated in our previous study that muscimol injections in the dorsal hippocampus impair performance to the chance level in scene-based behavioral tasks (Lee et al., 2014; Kim et al., 2012).

      Nonetheless, we mentioned the possibility of differential muscimol expressions between the two target regions. Following the suggestion of the reviewer, we now included this information in the Discussion as follows:

      “Although there is still a possibility that the levels of expression of GABA-A receptors might be different along the longitudinal axis of the hippocampus, …” (p.20)

      Regarding the drug infusion volume and concentration, we included these details in the Methods. Please see our detailed response to 4.a. below.

      (3) It is good that the authors included a comparison/control study using a spherical beacon-guided navigation task, to examine the specific psychological mechanisms disrupted by the hippocampal manipulations. However, as outlined below (4.b.), the sample size for the comparison study was lower than for the main study, and the data in Figure 8 suggest that the comparison task may be affected by the hippocampal manipulations similarly to the place-preference task, albeit less markedly. This would raise the question as to which mechanisms that are common to the two tasks may be affected by hippocampal functional inhibition, which should be considered in the discussion.

      The sample size for the object-guided navigation task was smaller because we initially did not plan the experiment, but later in the study decided to conduct the control test. Therefore, the object-guided navigation task was added to the study design after finishing the first three rats, resulting in a smaller sample size than the place preference task. We included this detail in the manuscript, as follows:

      “Note the smaller sample size in the object-guided navigation task. This was because the task was later added to the study design.” (p.24)

      Regarding the mechanism behind the two different tasks, we did not perform the same heading direction analysis here as in the place preference task because the two tasks have different characteristics such as task complexity. The object-guided navigation task is somewhat similar to the visually guided (or cued) version of the water maze task, which is widely known as hippocampal-independent (Morris et al., 1986; Packard et al., 1989; also see our descriptions on p.15). Therefore, we would argue that the two tasks (i.e., place preference task and object-guided navigation task) used in the current manuscript do not share neural mechanisms in common. Additionally, we confirmed that several behavioral measurements related to motor capacity, such as travel distance and latency, along with the direct hit proportion provided in Figure 8, did not show any statistically significant changes across drug conditions.

      4. Several important methodological details require clarification:

      a. Drug infusions (from line 673):

      - '0.3 to 0.5 μl of either phosphate-buffered saline (PBS) or muscimol (MUS) was infused into each hemisphere'; the authors need to clarify when which infusion volume was used and why different infusion volumes were used.

      We thank the reviewer for carefully reading our manuscript. We were cautious about side effects, such as suppressed locomotion or overly aggressive behavior, since the iHP injection site was close to the ventricle. We were keenly aware that the intermediate to ventral hippocampal regions are sensitive to the drug dosage from our previous experiments. Thus, we observed the rat’s behavior for 20 minutes after drug injection in a clean cage. We started from 0.5 μl, based on our previous study, but if the injected rat showed any sign of side effects in the cage, we stopped the experiment for the day and tried with a lower dosage (i.e., 0.4 μl first, then 0.3 μl, etc.) until we found the right dosage under which the rat did not show any side effect. This procedure is necessary because cannula tip positions are slightly different from rat to rat. When undergoing this procedure, five out of eight rats received 0.4 μl, two received 0.3 μl, and one received 0.5 μl. Still, there was no significant difference in performance, including the high-value visit percentage, departing and perimeter crossing directions, across all dosages. This information is now added in the Methods section as follows:

      “If the rat showed any side effect, particularly sluggishness or aggression, we reduced the drug injection amount in the rat by 0.1 ml until we found the dosage with which there was no visible side effect. As a result, five of the rats received 0.4 ml, two received 0.3 ml, and one received 0.5 ml.” (p.25)

      - I could not find the concentration of the muscimol solution that was used. The authors must clarify this and also should include a justification of the doses used, e.g. based on previous studies.

      Thank you for the suggestion. We used the drug concentration of 1mg/ml, which was adapted from our previous muscimol study (Lee et al., 2014; Kim et al., 2012). The manuscript is now updated, as follows:

      “…or muscimol (MUS; 1mg/ml, dissolved in saline) was infused into each hemisphere via a 33-gauge injection cannula at an injection speed of 0.167 ml/min, based on our previous study (Lee et al., 2014; Kim et al., 2012).” (p.25)

      -  Please also clarify if the injectors and dummies were flush with the guides or by which distance they protruded from the guides.

      The injection and dummy cannula both protruded from the guide cannula by 1 mm, and this information is now added to the Methods section, as follows:

      “The injection cannula and dummy cannula extended 1 mm below the tip of the guide cannula.” (p.25)

      b. Sample sizes: The authors should include sample size justifications, e.g. based on considerations of statistical power, previous studies, practical considerations, or a combination of these factors. Importantly, the smaller sample size in the control study using the spherical beacon-guided navigation task (n=5 rats) limits comparability with the main study using the place-preference task (n=8). Numerically, the findings on the control task (Figure 8) look quite similar to the findings on the place-preference task, with intermediate hippocampal muscimol infusions causing the most pronounced impairment and dorsal hippocampal muscimol infusions causing a weaker impairment. These effects may have reached statistical significance if the same sample size had been used in the place-preference study.

      We set the current sample size for several reasons. First, based on our previous studies, we assumed that eight, or more than six, would be enough to achieve statistical power in a “within-animal design” study. Also, considering the ethical commitments, we tried to keep the number of animals used in the study to the least. Last, our paradigm required very long training periods (3 months on average per animal), so we could not increase the sample size for practical reasons. Regarding the reasons for the smaller sample size for the object-guided navigation task, please see the previous response to 3 above. The manuscript is now revised as follows:

      “Based on our prior studies (Park et al., 2017; Yoo and Lee, 2017; Lee et al., 2014), the sample size of our study was set to the least number to achieve the necessary statistical power in the current within-subject study design for ethical commitments and practical considerations (i.e., relatively long training periods).” (p.22)

      c. Statistical analyses: Why were the data of the intermediate and dorsal hippocampal PBS infusion conditions averaged for some of the analyses (Figure 5; Figure 6B and C; Figure 7B and C; Figure 8B) but not for others (Figure 6A and Figure 7A)?

      The reviewer is correct that we only illustrated the separate dPBS and iPBS data for Figures 6A and 7A. Since the directional analysis is the main focus of the current manuscript, we tried to provide better visualization and more detailed examples of how the drug infusion changed the behavioral patterns between the PBS and MUS conditions in each region. Except for the visualization of DD and PCD, we averaged the PBS sessions to increase statistical power, as described in p.9. We added a detailed description of the reasons for illustrating dPBS and iPBS data separately in the manuscript, as follows:

      “Note that dPBS and iPBS sessions were separately illustrated here for better visualization of changes in the behavioral pattern for each subregion.” (p.12)

      Reviewing Editor (Recommendations For The Authors):

      The strength of evidence rating in the assessment is currently noted as "incomplete." This can be improved following revisions if you amend your conclusions in the paper, including in the title and abstract, such that the paper's major conclusions more closely match what is shown in the Results.

      Following the suggestions of the reviewing editor, we have mentioned the caveats of our study in the Limitations section of our revised manuscript (p.21). In addition, the manuscript has been revised so that the conclusions in the paper match more closely to the experimental results as can been seen in some of the relevant sentences in the abstract and main text as follows:

      “Inactivation of both dHP and iHP with muscimol altered efficiency and precision of wayfinding behavior, but iHP inactivation induced more severe damage, including impaired place preference. Our findings suggest that the iHP is more critical for value-dependent navigation toward higher-value goal locations.” (Abstract; p.2)

      “Whereas inactivation of the dHP mainly affected the precision of wayfinding, iHP inactivation impaired value-dependent navigation more severely by affecting place preference.” (p.5)

      “The iHP causes more damage to value-dependent spatial navigation than the dHP, which is important for navigational precision” (p.12)

      However, we haven’t changed the title of the manuscript as it carries what we’d like to deliver in this study accurately.

      Reviewer #1 (Recommendations For The Authors):

      - What were the dimensions of the environment? What distance did rats typically run to reach the reward zone? A scale bar would be helpful in Figure 1.

      We used the same circular arena from the shaping session, which was 1.6 meters in diameter (p.23), and the shortest path between the start location and either reward zone was 0.62 meters. We revised the manuscript for clarification as follows:

      “For the pre-training session, rats were required to find hidden reward zones…, on the same circular arena from the shaping session.” (p.23)

      “Therefore, the shortest path length between the start position and the reward zone was 0.62 meters.” (p.23)

      We also added a scale bar in Figure 1C for a better understanding.

      - Line 169: "The scene rotation plot covers the period from the start of the trial to when the rat leaves the starting point at the center and the departure circle (Figure 2B)."

      The sentence is unclear. Maybe it should be "... from the start of the trial to when the rat leaves the departure circle”.

      The sentence has been revised following the reviewer's suggestion. (p.7)

      - Line 147: "First, they learned to rotate the spherical treadmill counterclockwise to move around in the virtual environment (presumably to perform energy-efficient navigation)."

      It is not clear from this sentence if rats naturally preferred the counterclockwise direction or if the counterclockwise direction was a task requirement.

      We now clarified in our revised manuscript that it was not a task requirement to turn counterclockwise, as follows:

      “First, although it was not required in the task, they learned to rotate the spherical treadmill counterclockwise…” (p.6)

      - Line 149: "Second, once a trial started, but before leaving the starting point at the center, the animal rotated the treadmill to turn the virtual environment immediately to align its starting direction with the visual scene associated with the high-value reward zone."

      The sentence is unclear. Maybe "Second, once a trial started, the animal rotated the treadmill immediately to align its starting direction with the visual scene associated with the high-value reward zone.”

      We have updated the description following the suggestion. (p.6)

      Reviewer #2 (Recommendations For The Authors):

      - There are some misleading descriptions of the conclusion of the results in this paper. In this study, the functions of (a) selection of high-value target and (b) spatial navigation to the target were assessed in the behavioral experiments. The results of the pharmacological experiments showed that dHP inactivation impaired (b) and iHP inactivation impaired both (a) and (b) (Figures 5 B & D). However, the last sentence of the abstract states that dHP is important for the functions of (a) and iHP for (b). There are several other similar statements in the main text. Since the separation of (a) and (b) is an important and original aspect of this study, the description should clearly show the conclusion that dHP is important for (a) and iHP is important for both (a) and (b).

      Related to the above, the paragraph title in the Discussion "The iHP may contain a value-associated cognitive map with reasonable spatial resolution for goal-directed navigation (536-537)" is also somewhat misleading: "with reasonable resolution for goal-directed behavior" seems to reflect the results of an object-guided navigation task (Figure 8). However, the term "goal-directed behavior" is also used for value-dependent spatial navigation (i.e., the main task), which causes confusion. I would like to suggest clarifying the wording on this point.

      First, we need to correct the reviewer’s statement regarding our descriptions of the results. As the reviewer mentioned, our results indicated that the dHP inactivation impaired (b) but not (a), while the iHP inactivation impaired both (a) and (b). Regarding the iHP inactivation result, we focused on the impairment of (a) since our aim was to investigate spatial-value association in the hippocampus. Also, it was more likely that (a) affected (b), but not the other way, because (a) remained intact when (b) was impaired after dHP inactivation. We emphasized this difference between dHP and iHP inactivation, which was (a). Therefore, we mentioned in the last sentence of the abstract that the dHP is important for (b), which is the precision of spatial navigation to the target location, and the iHP is critical for (a).

      Moreover, we would like to clarify that we were not referring to the object-guided navigation task in Figure 8 in the phrase ‘with a reasonable spatial resolution for goal-directed navigation.’ Please note that the object-guided navigation task did not require fine spatial resolution to find the reward. The phrase instead referred to the dHP inactivation result (Figure 5 and 6), where the rats could find the high-value zone even with dHP inactivation, although the navigational precision decreased. Nonetheless, we agree with the reviewer for the confusion that the title might cause, so now have updated the title as follows:

      “The iHP may contain a value-associated cognitive map with reasonable spatial resolution for value-based navigation” (p.19)

      - As an earlier study focusing on the physiology of iHP, Maurer et al, Hippocampus 15:841 (2005) is also a pioneering and important study, and I suggest citing it.

      Thank you for the suggestion. We included the Maurer et al. (2005) study in the Introduction section as follows:

      “…Specifically, there is physiological evidence that the size of a place field becomes larger as recordings of place cells move from the dHP to the vHP (Jung et al., 1994; Maurer et al., 2005; Kjelstrup et al., 2008; Royer et al., 2010).” (p.4)

      - One of the strengths of this paper is that we have developed a new control system for the VR navigation task device, but I cannot get a very detailed description of this system in the Methods section. Also, no information about the system control has been uploaded to GitHub. I would suggest adding a description of the manufacturer, model number, and size of components, such as a rotary encoder and ball, and information about the software of the control system, with enough detail to allow the reader to reconstruct the system.

      We have now added detailed descriptions of the VR system in the Methods section (see “2D VR system). (p.22)

      Reviewer #3 (Recommendations For The Authors):

      (1) Some comments on specific passages of text:

      Lines 87 to 89: 'Surprisingly, beyond the recognition of anatomical divisions, little is known about the functional differentiation of subregions along the dorsoventral axis of the hippocampus. Moreover, the available literature on the subject is somewhat inconsistent.'

      I would recommend to rephrase these statements. Regarding the first statement, there is substantial evidence for functional differentiation along the dorso-ventral axis of the hippocampus (e.g., see reviews by Moser and Moser, 1998, Hippocampus; Bannerman et al., 2004, Neurosci Biobehav Rev; Bast, 2007, Rev Neurosci; Bast, 2011, Curr Opin Neurobiol; Fanselow and Dong, 2010, Neuron; Strange et al., 2014, Nature Rev Neurosci). Regarding the second statement, the authors may consider being more specific, as the inconsistencies demonstrated seem to relate mainly to the hippocampal representation of value information, instead of functional differentiation along the dorso-ventral hippocampal axis in general.

      We agree with the reviewer that the abovementioned statements need further clarification. The manuscript is now revised as follows:

      “Surprisingly, beyond the recognition of anatomical divisions, the available literature on the functional differentiation of subregions along the dorsoventral axis of the hippocampus, particularly in the context of value representation, is somewhat inconsistent.” (p.4)

      Lines 92 to 93: 'Thus, it has been thought that the dHP is more specialized for precise spatial representation than the iHP and vHP.'

      I think 'fine-grained' may be the more appropriate term here. Also, check throughout the manuscript when referring to the differences of spatial representations along the hippocampal dorso-ventral axis.

      Thank you for the insightful suggestion. We changed the term to ‘fine-grained’ throughout the manuscript, as follows:

      “Thus, it has been thought that the dHP is more specialized for fine-grained spatial representation than the iHP and vHP.” (p.4)

      “Consequently, the fine-grained spatial map present in the dHP…” (p.20)

      Line 217: well-'trained' rats?

      We initially used the term ‘well-learned’ to focus on the effect of learning, not training. Please note that the rats were already adapted to moving freely in the VR environment during the Shaping sessions, but the immediate counterclockwise body alignment only appeared after they acquired the reward locations for the main task. Nonetheless, we agree that the term might cause confusion, so we revised the manuscript as the reviewer suggested, as follows:

      “This implies that well-trained rats aligned their bodies more efficiently…” (p.8)

      Lines 309 to 311: 'Taken together, these results indicate that iHP inactivation severely damages normal goal-directed navigational patterns in our place preference task.'

      Consider to mention that dHP inactivation also causes impairments, albeit weaker ones.

      We thank the reviewer for the suggestion. We revised the manuscript by mentioning dHP inactivation as follows:

      “Taken together, these results indicate that iHP inactivation more severely damages normal goal-directed navigational patterns than dHP inactivation in our place-preference task.” (p.11-12)

      Lines 550 to 552: 'The involvement of the iHP in spatial value association has been reported in several studies. For example, Bast and colleagues reported that rapid place learning is disrupted by removing the iHP and vHP, even when the dHP remains undamaged (Bast et al., 2009).'

      Bast et al. (2009) did not directly show the role of iHP in 'spatial value associations'. They suggested that the importance of iHP for behavioral performance based on rapid, one-trial, place learning may reflect neuroanatomical features of the intermediate region, especially the combination of afferents that could convey the required fine-grained visuo-spatial information with relevant afferent and efferent connections that may be important to translate hippocampal place memory into appropriate behavioral performance (this may include afferents conveying value information). More recent theoretical and empirical research suggests that projections to the (ventral) striatum may be relevant (see Tessereau et al., 2021, BNA and Bauer et al., 2021, BNA).

      We appreciate the reviewer for this insightful comment. We agree with the reviewer that Bast et al. (2009) did not directly mention spatial value association; however, learning a new platform location needs an update of value information in the spatial environment. Therefore, we thought the study, though indirectly, suggested how the iHP contributes to spatial value associations. Nonetheless, to avoid confusion, we revised the manuscript, as follows:

      “The involvement of the iHP in spatial value association has been reported or implicated in several studies” (p.20)

      (2) Figures and legends:

      Figure 2B: What do the numbers after novice and expert indicate?

      The numbers indicate the rat ID, followed by the session number. We added the details to the Figure legend, as follows:

      “The numbers after ‘Novice’ and ‘Expert’ indicate the rat and session number of the example.” (p.34)

      Figure 2C: Please indicate units of the travel distance and latency measurements.

      The units are now described in the Figure legends, as follows:

      “Mean travel distance in meters and latency in seconds are shown below the VR arena trajectory.” (p.34)

      Figure 3Aii: Here and in other figures - do the vector lengths have a unit (degree?)?

      No, the mean vector length is an averaged value of the resultant vectors, thus having no specific unit.

      Figure 5A: Please explain what the numbers on top of the individual sample trajectories indicate.

      The numbers are IDs for rats, sessions, and trials of specific examples. We added the explanation to the Figure legends, as follows:

      “Numbers above each trajectory indicate the identification numbers for rat, session, and trial.” (p.35)

      (3) Additional comments on some methodological details:

      a. Why was the non-parametric Wilcoxon signed-rank test used for the planned comparison between intermediate and dorsal hippocampal PBS infusions, whereas parametric ANOVA and post-hoc comparisons were used for other analyses? This probably doesn't make a big difference for the interpretation of the present data (as a parametric pairwise comparison would also not have revealed any significant difference between intermediate and dorsal hippocampal PBS infusions), but it would nevertheless be good to clarify the rationale for this.

      We used the non-parametric statistics since our sample size was rather small (n=8) to use the parametric statistics, although we used the parametric ANOVA for some of the results because it is the most commonly known and widely used statistical test in such comparisons. However, we also checked the statistics with the alternatives (i.e., non-parametric Wilcoxon signed-rank test to parametric paired t-test and parametric One-way RM ANOVA with Bonferroni post hoc test to non-parametric Friedman’s test with Dunn’s post hoc test), and the statistical significance did not change with any of the tests. We now added the explanation in the manuscript, as follows:

      “Although most of our statistics were based on the non-parametric tests for the relatively small sample size (n=8), we used the parametric RM ANOVA for comparing three groups (i.e., PBS, dMUS, and iMUS) because it is the most commonly known and widely used statistical test in such comparison. However, we also performed statistical tests with the alternatives for reference, and the statistical significances were not changed with any of the results.” (p.26)

      b. Single housing of rats:

      Why was this chosen? Based on my experience, this is not necessary for studies involving cannula implants and food restriction. Group housing is generally considered to improve the welfare of rats.

      We chose single housing of rats because our training paradigm required precise restrictions on the food consumption of individual rats, which could be difficult in group housing.

      c. Anesthesia:

      Why was pentobarbital used, alongside isoflurane, to anesthetize rats for surgery (line 663)? The use of gaseous anesthesia alone offers very good control of anesthesia and reduces the risk of death from anesthesia compared to the use of pentobarbital.

      Why was anesthesia used for the drug infusions (line 674)? If rats are well-habituated to handling by the experimenter, manual restraint is sufficient for intra-cerebral infusions. Therefore, anesthesia could be omitted, reducing the risk of adverse effects on the experimental rats.

      I do not think that points b. and c. are relevant for the interpretation of the present findings, but the authors may consider these points for future studies to improve further the welfare of the experimental rats.

      We appreciate the reviewer’s careful suggestions. For both the use of pentobarbital during surgery and anesthesia for the drug infusion, we chose to do so to avoid any risk of rats being awake and becoming anxious and to ensure safety during the procedures. They might not be necessary, but they were helpful for the experimenters to proceed with sufficient time to maintain precision. Nonetheless, we agree with the reviewer’s concern, which was the reason why we monitored the rats’ behavior for 20 minutes in the cage after drug infusion to minimize any potential influence on the task performance. We updated the relevant details in the Methods section, as follows:

      “The rat was kept in a clean cage to recover from anesthesia completely and monitored for side effects for 20 minutes, then was moved to the VR apparatus for behavioral testing.” (p.25)

    1. Author response:

      The following is the authors’ response to the original reviews.

      eLife assessment 

      fMRI was used to address an important aspect of human cognition - the capacity for structured representations and symbolic processing - in a cross-species comparison with non-human primates (macaques); the experimental design probed implicit symbolic processing through reversal of learned stimulus pairs. The authors present solid evidence in humans that helps elucidate the role of brain networks in symbolic processing, however the evidence from macaques was incomplete (e.g., sample size constraints, potential and hard-to-quantify differences in attention allocation, motivation, and lived experience between species).

      Thank you very much for your assessment. We would like to address the potential issues that you raise point-by-point below.

      We agree that for macaque monkey physiology, sample size is always a constraint, due to both financial and ethical reasons. We addressed this concern by combining the results from two different labs, which allowed us to test 4 animals in total, which is twice as much as what is common practice in the field of primate physiology. (We discuss this now on lines 473-478.)

      Interspecies differences in motivation, attention allocation, task strategies etc. could also be limiting factors. Note that we did address the potential lack of attention allocation directly in Experiment 2 using implicit reward association, which was successful as evidenced by the activation of attentional control areas in the prefrontal cortex. We cannot guarantee that the strategies that the two species deploy are identical, but we tentatively suggest that this might be a less important factor in the present study than in other interspecies comparisons that use explicit behavioral reports. In the current study, we directly measured surprise responses in the brain in the absence of any explicit instructions in either species, which allowed us to  measure the spontaneous reversal of learned associations, which is a very basic element of symbolic representation. Our reasoning is that such spontaneous responses should be less dependent on attention allocation and task strategies. (We discuss this now in more detail on lines 478-485.)

      Finally, lived experience could be a major factor. Indeed, obvious differences include a lifetime of open-field experiences and education in our human adult subjects, which was not available to the monkey subjects, and includes a strong bias towards explicit learning of symbolic systems (e.g. words, letters, digits, etc). However, we have previously shown that 5-month-old human infants spontaneously generalize learning to the reversed pairs after a short learning in the lab using EEG (Kabdebon et al, PNAS, 2019). This indicates that also with very limited experience, humans spontaneously reverse learned associations. (We discuss this now in more detail on lines 478-485.) It could be very interesting to investigate whether spontaneous reversal could be present in infant macaque monkeys, as there might be a critical period for this effect. Although neurophysiology in awake infant monkeys is highly challenging, it would be very relevant for future work. (We discuss this in more detail on lines 493-498.)

      Public Reviews: 

      Reviewer #1 (Public Review): 

      Kerkoerle and colleagues present a very interesting comparative fMRI study in humans and monkeys, assessing neural responses to surprise reactions at the reversal of a previously learned association. The implicit nature of this task, assessing how this information is represented without requiring explicit decision-making, is an elegant design. The paper reports that both humans and monkeys show neural responses across a range of areas when presented with incongruous stimulus pairs. Monkeys also show a surprise response when the stimuli are presented in a reversed direction. However, humans show no such surprise response based on this reversal, suggesting that they encode the relationship reversibly and bidirectionally, unlike the monkeys. This has been suggested as a hallmark of symbolic representation, that might be absent in nonhuman animals. 

      I find this experiment and the results quite compelling, and the data do support the hypothesis that humans are somewhat unique in their tendency to form reversible, symbolic associations. I think that an important strength of the results is that the critical finding is the presence of an interaction between congruity and canonicity in macaques, which does not appear in humans. These results go a long way to allay concerns I have about the comparison of many human participants to a very small number of macaques. 

      We thank the reviewer for the positive assessment. We also very much appreciate the point about the interaction effect in macaque monkeys – indeed, we do not report just a negative finding. 

      I understand the impossibility of testing 30+ macaques in an fMRI experiment. However, I think it is important to note that differences necessarily arise in the analysis of such datasets. The authors report that they use '...identical training, stimuli, and whole-brain fMRI measures'. However, the monkeys (in experiment 1) actually required 10 times more training. 

      We agree that this description was imprecise. We have changed it to “identical training stimuli” (line 151), indeed the movies used for training were strictly identical. Furthermore, please note that we do report the fMRI results after the same training duration. In experiment 1, after 3 days of training, the monkeys did not show any significant results, even in the canonical direction. However, in experiment 2, with increased attention and motivation, a significant effect was observed on the first day of scanning after training, as was found in human subjects (see Figure 4 and Table 3).

      More importantly, while the fMRI measures are the same, group analysis over 30+ individuals is inherently different from comparing only 2 macaques (including smoothing and averaging away individual differences that might be more present in the monkeys, due to the much smaller sample size). 

      Thank you for understanding that a limited sampling size is intrinsic to macaque monkey physiology. We also agree that data analysis in humans and monkeys is necessarily different. As suggested by the reviewer, we added an analysis to address this, see the corresponding reply to the ‘Recommendations for the authors’ section below.

      Despite this, the results do appear to show that macaques show the predicted interaction effect (even despite the sample size), while humans do not. I think this is quite convincing, although had the results turned out differently (for example an effect in humans that was absent in macaques), I think this difference in sample size would be considerably more concerning. 

      Thank you for noting this. Indeed, the interaction effect is crucial, and the task design was explicitly made to test this precise prediction, described in our manuscript as the “reversibility hypothesis”. The congruity effect in the learned direction served as a control for learning, while the corresponding congruity effect in the reversed direction tested for spontaneous reversal. The reversibility hypothesis stipulates that in humans there should not be a difference between the learned and the reversed direction, while there should be for monkeys. We already wrote about that in the result section of the original manuscript and now also describe this more explicitly in the introduction and beginning of the result section.

      I would also note that while I agree with the authors' conclusions, it is notable to me that the congruity effect observed in humans (red vs blue lines in Fig. 2B) appears to be far more pronounced than any effect observed in the macaques (Fig. 3C-3). Again, this does not challenge the core finding of this paper but does suggest methodological or possibly motivational/attentional differences between the humans and the monkeys (or, for example, that the monkeys had learned the associations less strongly and clearly than the humans). 

      As also explained in response to the eLife assessment above, we expanded the “limitations” section of the discussion, with a deeper description of the possible methodological differences between the two species (see lines 478-485).

      With the same worry in mind, we did increase the attention and motivation of monkeys in experiment 2, and indeed obtained a greater activation to the canonical pairs and their violation, -notably in the prefrontal cortex – but crucially still without reversibility.

      In the end, we believe that the striking interspecies difference in size and extent of the violation effect, even for purely canonical stimuli, is an important part of our findings and points to a more efficient species-specific learning system, that our experiment tentatively relates to a symbolic competence.

      This is a strong paper with elegant methods and makes a worthwhile contribution to our understanding of the neural systems supporting symbolic representations in humans, as opposed to other animals. 

      We again thank the reviewer for the positive review.

      Reviewer #2 (Public Review): 

      In their article titled "Brain mechanisms of reversible symbolic reference: a potential singularity of the human brain", van Kerkoerle et al address the timely question of whether non-human primates (rhesus macaques) possess the ability for reverse symbolic inference as observed in humans. Through an fMRI experiment in both humans and monkeys, they analyzed the bold signal in both species while observing audio-visual and visual-visual stimuli pairs that had been previously learned in a particular direction. Remarkably, the findings pertaining to humans revealed that a broad brain network exhibited increased activity in response to surprises occurring in both the learned and reverse directions. Conversely, in monkeys, the study uncovered that the brain activity within sensory areas only responded to the learned direction but failed to exhibit any discernible response to the reverse direction. These compelling results indicate that the capacity for reversible symbolic inference may be unique to humans. 

      In general, the manuscript is skillfully crafted and highly accessible to readers. The experimental design exhibits originality, and the analyses are tailored to effectively address the central question at hand.

      Although the first experiment raised a number of methodological inquiries, the subsequent second experiment thoroughly addresses these concerns and effectively replicates the initial findings, thereby significantly strengthening the overall study. Overall, this article is already of high quality and brings new insight into human cognition. 

      We sincerely thank the reviewer for the positive comments. 

      I identified three weaknesses in the manuscript: 

      - One major issue in the study is the absence of significant results in monkeys. Indeed, authors draw conclusions regarding the lack of significant difference in activity related to surprise in the multidemand network (MDN) in the reverse congruent versus reverse incongruent conditions. Although the results are convincing (especially with the significant interaction between congruency and canonicity), the article could be improved by including additional analyses in a priori ROI for the MDN in monkeys (as well as in humans, for comparison). 

      First, we disagree with the statement about “absence of significant results in monkeys”. We do report a significant interaction which, as noted by the referee, is a crucial positive finding.

      Second, we performed the suggested analysis for experiment 2, using the bilateral ROIs of the putative monkey MDN from previous literature (Mitchell, et al. 2016), which are based on the human study by Fedorenko et al. (PNAS, 2013). 

      Author response table 1.

      Congruity effect for monkeys in Experiment 2 within the ROIs of the MDN (n=3). Significance was assessed with one-sided one-sample t-tests.

      As can be seen, none of the regions within the monkey MDN showed an FDR-corrected significant difference or interaction. Although the absence of a canonical congruity effect makes it difficult to draw strong conclusions, it did approach significance at an uncorrected level in the lateral frontal posterior region, similar to  the large prefrontal effect we report in Figures 4 and 5. Furthermore, for the reversed congruity effect there was never even a trend at the uncorrected level, and the crucial interaction of canonicity and congruity again approached significance in the lateral prefrontal cortex.  

      We also performed an ANOVA  in the human participants of the VV experiment on the average betas across the 7 different fronto-parietal ROIs as used by Mitchell et al to define their equivalent to the monkey brain (Fig 1a, right in Mitchell et al. 2016) with congruity, canonicity and hemisphere (except for the anterior cingulate which is a bilateral ROI) as within-subject factors. We confirmed the results presented in the manuscript (Figure 4C) with notably no significant interaction between congruity and canonicity in any of these ROIs (all F-values (except insula) <1). A significant main effect of congruity was observed in the posterior middle frontal gyrus (MFG) and inferior precentral sulcus at the FDR corrected level. Analyses restricted to the canonical trials found a congruity effect in these two regions plus the anterior insula and anterior cingulate/presupplementary motor area, whereas no ROIs were significant at a FDR corrected level for reverse trials. There was a trend in the middle MFG and inferior precentral region for reversed trials. Crucially, there was not even a trend for the interaction between congruity and canonicity at the uncorrected level. The difference in the effect size between the canonical and reversed direction can therefore be explained by the larger statistical power due to the larger number of congruent trials (70%, versus 10% for the other trial conditions), not by a significant effect by the canonical and the reversed direction. 

      Author response table 2.

      Congruity effect for humans in Experiment 2 within the ROIs of the MDN (n=23).

      These results support our contention that the type of learning of the stimulus pairs was very different in the two species. We thank the reviewer for suggesting these relevant additional analyses.

      - While the authors acknowledge in the discussion that the number of monkeys included in the study is considerably lower compared to humans, it would be informative to know the variability of the results among human participants. 

      We agree that this is an interesting question, although it is also very open-ended. For instance, we could report each subjects’ individual whole-brain results, but this would take too much space (and the interested reader will be able to do so from the data that we make available as part of this publication). As a step in this direction, we provide below a figure showing the individual congruity effects, separately for each experiment and for each ROI of table 5, and for each of the 52 participants for whom an fMRI localizer was available:

      Author response image 1.

      Difference in mean betas between congruent and incongruent conditions in a-priori linguistic and mathematical ROIs (see definition and analyses in Table 5) in both experiments (experiment 1 = AV, left panel; experiment 2= VV, right panel). Dots correspond to participants (red: canonical trials, green reversed trials).The boxplot notch is located at the median and the lower and upper box hinges at the 25th and 75th centiles. Whiskers extend to 1.5 inter-quartile ranges on either side of the hinges. ROIs are ranked by the median of the Incongruent-Congruent difference across canonical and reversed order, within a given experiment. For purposes of comparison between the two experiments, we have underlined with colors the top-five common ROIs between the two experiments. N.s.: non-significant congruity effect (p>0.05)

      Several regions show a rather consistent difference across subjects (see, for instance, the posterior STS in experiment 1, left panel). Overall, only 3 of the 52 participants did not show any beta superior to 2 in canonical or reversed in any ROIs. The consistency is quite striking, given the limited number of test trials (in total only 16 incongruent trials per direction per participant), and the fact that these ROIs were selected for their responses to spoken or written  sentences, as part of a subsidiary task quite different from the main task.

      - Some details are missing in the methods.  

      Thank you for these comments, we reply to them point-by-point below.

      Reviewer #3 (Public Review): 

      This study investigates the hypothesis that humans (but not non-human primates) spontaneously learn reversible temporal associations (i.e., learning a B-A association after only being exposed to A-B sequences), which the authors consider to be a foundational property of symbolic cognition. To do so, they expose humans and macaques to 2-item sequences (in a visual-auditory experiment, pairs of images and spoken nonwords, and in a visual-visual experiment, pairs of images and abstract geometric shapes) in a fixed temporal order, then measure the brain response during a test phase to congruent vs. incongruent pairs (relative to the trained associations) in canonical vs. reversed order (relative to the presentation order used in training). The advantage of neuroimaging for this question is that it removes the need for a behavioral test, which non-human primates can fail for reasons unrelated to the cognitive construct being investigated. In humans, the researchers find statistically indistinguishable incongruity effects in both directions (supporting a spontaneous reversible association), whereas in monkeys they only find incongruity effects in the canonical direction (supporting an association but a lack of spontaneous reversal). Although the precise pattern of activation varies by experiment type (visual-auditory vs. visual-visual) in both species, the authors point out that some of the regions involved are also those that are most anatomically different between humans and other primates. The authors interpret their finding to support the hypothesis that reversible associations, and by extension symbolic cognition, is uniquely human. 

      This study is a valuable complement to prior behavioral work on this question. However, I have some concerns about methods and framing. 

      We thank the reviewer for the careful summary of the manuscript, and the positive comments.

      Methods - Design issues: 

      The authors originally planned to use the same training/testing protocol for both species but the monkeys did not learn anything, so they dramatically increased the amount of training and evaluation. By my calculation from the methods section, humans were trained on 96 trials and tested on 176, whereas the monkeys got an additional 3,840 training trials and 1,408 testing trials. The authors are explicit that they continued training the monkeys until they got a congruity effect. On the one hand, it is commendable that they are honest about this in their write-up, given that this detail could easily be framed as deliberate after the fact. On the other hand, it is still a form of p-hacking, given that it's critical for their result that the monkeys learn the canonical association (otherwise, the critical comparison to the non-canonical association is meaningless). 

      Thank you for this comment. 

      Indeed, for experiment 1, the amount of training and testing was not equal for the humans and monkeys, as also mentioned by reviewer 2. We now describe in more detail how many training and imaging days we used for each experiment and each species, as well as the number of blocks per day and the number of trials per block (see lines 572-577). We also added the information on the amount of training receives to all of the legends of the Tables.

      We are sorry for giving the impression that we trained until the monkeys learned this. This was not the case. Based on previous literature, we actually anticipated that the short training would not be sufficient, and therefore planned additional training in advance. Specifically, Meyer & Olson (2011) had observed pair learning in the inferior temporal cortex of macaque monkeys after 816 exposures per pair. This is similar to the additional training we gave, about 80 blocks with 12 trials per pair per block. This is  now explained in more detail (lines 577-580).

      Furthermore, we strongly disagree with the pejorative term p-hacking. The aim of the experiment was not to show a congruency effect in the canonical direction in monkeys, but to track and compare their behavior in the same paradigm as that of humans for the reverse direction. It would have been unwise to stop after human-identical training and only show that humans learn better, which is a given. Instead, we looked at brain activations at both times, at the end of human-identical training and when the monkeys had learned the pairs in the canonical direction. 

      Finally, in experiment 2, monkeys were tested after the same 3 days of training as humans. We wrote: “Using this design, we obtained significant canonical congruity effects in monkeys on the first imaging day after the initial training (24 trials per pair), indicating that the animals had learned the associations” (lines 252-253).

      (2) Between-species comparisons are challenging. In addition to having differences in their DNA, human participants have spent many years living in a very different culture than that of NHPs, including years of formal education. As a result, attributing the observed differences to biology is challenging. One approach that has been adopted in some past studies is to examine either young children or adults from cultures that don't have formal educational structures. This is not the approach the authors take. This major confound needs to minimally be explicitly acknowledged up front. 

      Thank you for raising this important point. We already had a section on “limitations” in the manuscript, which we now extended (line 478-485). Indeed, this study is following a previous study in 5-month-old infants using EEG, in which we already showed that after learning associations between labels and categories, infants spontaneously generalize learning to the reversed pairs after a short learning period in the lab (Kabdebon et al, PNAS, 2019). We also cited preliminary results of the same paradigm as used in the current study but using EEG in 4-month-old infants (Ekramnia and Dehaene-Lambertz, 2019), where we replicated the results obtained by Kabdebon et al. 2019 showing that preverbal infants spontaneously generalize learning to the reversed pairs. 

      Functional MRI in awake infants remains a challenge at this age (but see our own work, DehaeneLambertz et al, Science, 2002), especially because the experimental design means only a few trials in the conditions of interest (10%) and thus a long experimental duration that exceed infants’ quietness and attentional capacities in the noisy MRI environment. (We discuss this on lines 493-496.)

      (3) Humans have big advantages in processing and discriminating spoken stimuli and associating them with visual stimuli (after all, this is what words are in spoken human languages). Experiment 2 ameliorates these concerns to some degree, but still, it is difficult to attribute the failure of NHPs to show reversible associations in Experiment 1 to cognitive differences rather than the relative importance of sound string to meaning associations in the human vs. NHP experiences. 

      As the reviewer wrote, we deliberately performed Experiment 2 with visual shapes to control for various factors that might have explained the monkeys' failure in Experiment 1. 

      (4) More minor: The localizer task (math sentences vs. other sentences) makes sense for math but seems to make less sense for language: why would a language region respond more to sentences that don't describe math vs. ones that do? 

      The referee is correct: our use of the word “reciprocally” was improper (although see Amalric et Dehaene, 2016 for significant differences in both directions when non-mathematical sentences concern specific knowledge). We changed the formulation to clarify this as follows: “In these ROIs, we recovered the subject-specific coordinates of each participant’s 10% best voxels in the following comparisons: sentences vs rest for the 6 language Rois ; reading vs listening for the VWFA ; and numerical vs non-numerical sentences for the 8 mathematical ROIs.” (lines 678-680).

      Methods - Analysis issues: 

      (5) The analyses appear to "double dip" by using the same data to define the clusters and to statistically test the average cluster activation (Kriegeskorte et al., 2009). The resulting effect sizes are therefore likely inflated, and the p-values are anticonservative. 

      It is not clear to us which result the reviewer is referring to. In Tables 1-4, we report the values that we found significant in the whole brain analysis, we do not report additional statistical tests for this data. For Table 5, the subject-specific voxels were identified through a separate localizer experiment, which was designed to pinpoint the precise activation areas for each subject in the domains of oral and written language-processing and math. Subsequently, we compared the activation at these voxel locations across different conditions of the main experiment. Thus, the two datasets were distinct, and there was no double dipping. In both interpretations of the comment, we therefore disagree with the reviewer.

      Framing: 

      (6) The framing ("Brain mechanisms of reversible symbolic reference: A potential singularity of the human brain") is bigger than the finding (monkeys don't spontaneously reverse a temporal association but humans do). The title and discussion are full of buzzy terms ("brain mechanisms", "symbolic", and "singularity") that are only connected to the experiments by a debatable chain of assumptions. 

      First, this study shows relatively little about brain "mechanisms" of reversible symbolic associations, which implies insights into how these associations are learned, recognized, and represented. But we're only given standard fMRI analyses that are quite inconsistent across similar experimental paradigms, with purely suggestive connections between these spatial patterns and prior work on comparative brain anatomy. 

      We agree with the referee that the term “mechanism” is ambiguous and, for systems neuroscientists, may suggest more than we are able to do here with functional MRI. We changed the title to “Brain areas for reversible symbolic reference, a potential singularity of the human brain”. This title better describes our specific contribution: mapping out the areas involved in reversibility in humans, and showing that they do not seem to respond similarly in macaque monkeys.

      Second, it's not clear what the relationship is between symbolic cognition and a propensity to spontaneously reverse a temporal association. Certainly, if there are inter-species differences in learning preferences this is important to know about, but why is this construed as a difference in the presence or absence of symbols? Because the associations aren't used in any downstream computation, there is not even any way for participants to know which is the sign and which is the signified: these are merely labels imposed by the researchers on a sequential task. 

      As explained in the introduction, the reversibility test addressed a very minimal core property of symbolic reference. There cannot be a symbol if its attachment doesn’t operate in both directions. Thus, this property is necessary – but we agree that it is not sufficient. Indeed, more tests are needed to establish whether and how the learned symbols are used in further downstream compositional tasks (as discussed in our recent TICS papers, Dehaene et al. 2022). We added a sentence in the introduction to acknowledge this fact:

      “Such reversibility is a core and necessary property of symbols, although we readily acknowledge that it is not sufficient, since genuine symbols present additional referential and compositional properties that will not be tested in the present work.” (lines 89-92).

      Third, the word "singularity" is both problematically ambiguous and not well supported by the results. "Singularity" is a highly loaded word that the authors are simply using to mean "that which is uniquely human". Rather than picking a term with diverse technical meanings across fields and then trying to restrict the definition, it would be better to use a different term. Furthermore, even under the stated definition, this study performed a single pairwise comparison between humans and one other species (macaques), so it is a stretch to then conclude (or insinuate) that the "singularity" has been found (see also pt. 2 above). 

      We have published an extensive review including a description of our use of the term “singularity” (Dehaene et al., TICS 2022). Here is a short except: “Humans are different even in domains such as drawing and geometry that do not involve communicative language. We refer to this observation using the term “human cognitive singularity”, the word singularity being used here in its standard meaning (the condition of being singular) as well as its mathematical sense (a point of sudden change). Hominization was certainly a singularity in biological evolution, so much so that it opened up a new geological age (the Anthropocene). Even if evolution works by small continuous change (and sometimes it doesn’t [4]), it led to a drastic cognitive change in humans.”

      We find the referee’s use of the pejorative term ”insinuate” quite inappropriate. From the title on, we are quite nuanced and refer only to a “potential singularity”. Furthermore, as noted above, we explicitly mention in the discussion the limitations of our study, and in particular the fact that only a single non-human species was tested (see lines 486-493). We are working hard to get chimpanzee data, but this is remarkably difficult for us, and we hope that our paper will incite other groups to collect more evidence on this point.

      (7) Related to pt. 6, there is circularity in the framing whereby the authors say they are setting out to find out what is uniquely human, hypothesizing that the uniquely human thing is symbols, and then selecting a defining trait of symbols (spontaneous reversible association) *because* it seems to be uniquely human (see e.g., "Several studies previously found behavioral evidence for a uniquely human ability to spontaneously reverse a learned association (Imai et al., 2021; Kojima, 1984; Lipkens et al., 1988; Medam et al., 2016; Sidman et al., 1982), and such reversibility was therefore proposed as a defining feature of symbol representation reference (Deacon, 1998; Kabdebon and DehaeneLambertz, 2019; Nieder, 2009).", line 335). They can't have it both ways. Either "symbol" is an independently motivated construct whose presence can be independently tested in humans and other species, or it is by fiat synonymous with the "singularity". This circularity can be broken by a more modest framing that focuses on the core research question (e.g., "What is uniquely human? One possibility is spontaneous reversal of temporal associations.") and then connects (speculatively) to the bigger conceptual landscape in the discussion ("Spontaneous reversal of temporal associations may be a core ability underlying the acquisition of mental symbols").

      We fail to understand the putative circularity that the referee sees in our introduction. We urge him/her to re-read it, and hope that, with the changes that we introduced, it does boil down to his/her summary, i.e. “What is uniquely human? One possibility is spontaneous reversal of temporal associations."

      Reviewer #1 (Recommendations For The Authors): 

      In general, the manuscript was very clear, easy to read, and compelling. I would recommend the authors carefully check the text for consistency and minor typos. For example: 

      The sample size for the monkeys kept changing throughout the paper. E.g., Experiment 1: n = 2 (line 149); n = 3 (line 205).  

      Thank you for catching this error, we corrected it. The number of animals was indeed 2  for experiment 1, and 3 for experiment 2. (Animals JD and YS participated in experiment 1 and JD, JC and DN in experiment 2. So only JD participated in both experiments.)

      Similarly, the number of stimulus pairs is reported inconsistently (4 on line 149, 5 pairs later in the paper). 

      We’re sorry that this was unclear. We used 5 sets of 4 audio-visual pairs each. We now clarify this, on line 157 and on lines 514-516.

      At least one case of p>0.0001, rather than p < 0.0001 (I assume). 

      Thank you once again, we now corrected this.

      Reviewer #2 (Recommendations For The Authors): 

      One major issue in the study is the absence of significant results in monkeys. Indeed, the authors draw conclusions regarding the lack of significant difference in activity related to surprise in the multidemand network (MDN) in the reverse congruent versus reverse incongruent conditions. Although the results are convincing (especially with the significant interaction between congruency and canonicity), the article could be improved by including additional analyses in a priori ROI for the MDN in monkeys (as well as in humans, for comparison). In other words: what are the statistics for the MDN regarding congruity, canonicity, and interaction in both species? Since the authors have already performed this type of analysis for language and Math ROIs (table 5), it should be relatively easy for them to extend it to the MDN. Demonstrating that results in monkeys are far from significant could further convince the reader. 

      Furthermore, while the authors acknowledge in the discussion that the number of monkeys included in the study is considerably lower compared to humans, it would be informative to know the variability of the results among human participants. Specifically, it would be valuable to describe the proportion of human participants in which the effects of congruency, canonicity, and their interaction are significant. Additionally, stating the variability of the F-values for each effect would provide reassurance to the reader regarding the distinctiveness of humans in comparison to monkeys. Low variability in the results would serve to mitigate concerns that the observed disparity is merely a consequence of testing a unique subset of monkeys, which may differ from the general population. Indeed, this would be a greater support to the notion that the dissimilarity stems from a genuine distinction between the two species. 

      We responded to both of these points above.

      In terms of methods, details are missing: 

      - How many trials of each condition are there exactly? (10% of 44 trials is 4.4) : 

      We wrote: “In both humans and monkeys, each block started with 4 trials in the learned direction (congruent canonical trials), one trial for each of the 4 pairs (2 O-L and 2 L-O pairs). The rest of the block consisted of 40 trials in which 70% of trials were identical to the training; 10% were incongruent pairs but the direction (O-L or L-O) was correct (incongruent canonical trials), thus testing whether the association was learned; 10% were congruent pairs but the direction within the pairs was reversed relative to the learned pairs (congruent reversed trials) and 10% were incongruent pairs in reverse (incongruent reversed trials).”(See lines 596-600.)

      Thus, each block comprised 4 initial trials, 28 canonical congruent trials, 4 canonical incongruent, 4 reverse congruent and 4 reverse incongruent trials, i.e. 4+28+3x4=40 trials.

      - How long is one trial? 

      As written in the method section: “In each trial, the first stimulus (label or object) was presented during 700ms, followed by an inter-stimulus-interval of 100ms then the second stimulus during 700ms. The pairs were separated by a variable inter-trial-interval of 3-5 seconds” i.e. 700+100+700=1500, plus 3 to 4.75 seconds of blank between the trials (see lines 531-533).

      - How are the stimulus presentations jittered? 

      See : “The pairs were separated by a variable inter-trial-interval randomly chosen among eight different durations between 3 and 4.75 seconds (step=250 ms). The series of 8 intervals was randomized again each time it was completed.”(lines 533-535).

      - What is the statistical power achieved for humans? And for monkeys? 

      We know of no standard way to define power for fMRI experiments. Power will depend on so many parameters, including the fMRI signal-to-noise ratio, the attention of the subject, the areas being considered, the type of analysis (whole-brain versus ROIs), etc.

      - Videos are mentioned in the methods, is it the image and sound? It is not clear. 

      We’re sorry that it was unclear. Video’s were only used for the training of the human subjects. We now corrected this in the method section (lines 552-554).

      Reviewer #3 (Recommendations For The Authors): 

      The main recommendations are to adjust the framing (making it less bold and more connected to the empirical evidence) and to ensure independence in the statistical analyses of the fMRI data. 

      See our replies to the reviewer’s comments on “Framing” above. In particular, we changed the title of the paper from “Brain mechanisms of reversible symbolic reference” to “Brain areas for reversible symbolic reference”.

      References cited in this response

      Dehaene, S., Al Roumi, F., Lakretz, Y., Planton, S., & Sablé-Meyer, M. (2022). Symbols and mental programs : A hypothesis about human singularity. Trends in Cognitive Sciences, 26(9), 751‑766. https://doi.org/10.1016/j.tics.2022.06.010.

      Dehaene-Lambertz, Ghislaine, Stanislas Dehaene, et Lucie Hertz-Pannier. Functional Neuroimaging of Speech Perception in Infants. Science 298, no 5600 (2002): 2013-15. https://doi.org/10.1126/science.1077066.

      Ekramnia M, Dehaene-Lambertz G. 2019. Investigating bidirectionality of associations in young infants as an approach to the symbolic system. Presented at the CogSci. p. 3449.

      Fedorenko E, Duncan J, Kanwisher N (2013) Broad domain generality in focal regions of frontal and parietal cortex. Proc Natl Acad Sci U S A 110:16616-16621.

      Kabdebon, Claire, et Ghislaine Dehaene-Lambertz. « Symbolic Labeling in 5-Month-Old Human Infants ». Proceedings of the National Academy of Sciences 116, no 12 (2019): 5805-10. https://doi.org/10.1073/pnas.1809144116.

      Mitchell, D. J., Bell, A. H., Buckley, M. J., Mitchell, A. S., Sallet, J., & Duncan, J. (2016). A Putative Multiple-Demand System in the Macaque Brain. Journal of Neuroscience, 36(33), 8574‑8585. https://doi.org/10.1523/JNEUROSCI.0810-16.2016

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer 1:

      (1) In several instances the paper does not address apparent inconsistencies between the prior literature and the findings. For example, the first main finding is that recalled items have more differentiated lateral temporal cortex representations within lists than not recalled items. This seems to be the opposite of the prediction from temporal context models that are used to motivate the paper-context models would predict that greater contextual similarity within a list should lead to greater memory through enhanced temporal clustering in recall. This is what El-Kalliny et al (2019) found, using a highly similar design (free recall, intracranial recordings from the lateral temporal lobe). The authors never address this contradiction in any depth to reconcile it with the previous literature and with the motivating theoretical model. 

      Figure 2 supports the findings from El-Kalliny and colleagues because it shows the relationship of each list item relative to the first item (El-Kalliny et al. 2019). Items encoded adjacent to SP1 show the highest spectral similarity supporting the idea of overlapping context predicted by the Temporal Context Model. However, our figure characterizes how increasing inter-item distance affects spectral similarity. It shows that two items successfully recalled from temporally distant serial positions show reduced spectral similarity. These findings align with the predictions of the temporal context model because two temporally distant items would lack significant contextual overlap and therefore would have more distinct spectral representations.

      El-Kalliny and colleagues do use a similar experimental set-up however the authors define drift differently. They identified patients with a tendency to temporally cluster, and observed those patients tend to drift less between temporally clustered items however they do not specify drift relative to a constant serial position as we do in our analysis. They define drift as spectral change between two adjacent items which is a more relative measure between any two items rather than in relation to a fixed point like SP1. Finally, our analysis focuses only on gamma activity while El-Kalliny and colleagues identified drift across a much broader set of frequency bands.

      (2) The way that the authors conduct the analysis of medial parietal neural similarity at boundaries leads to results that cannot be conclusively interpreted. The authors report enhanced similarity across lists for the first item in each list, which they interpret as reflecting a qualitatively distinct boundary signal. However, this finding can readily be explained by contextual drift if one assumes that whatever happens at the start of each list is similar or identical across lists (for example, a get ready prompt or reminder of instructions). The authors do not include analyses to rule this out, which undermines one of the main findings. 

      Extensions of the temporal context model (Lohnas et al. 2015) predict context at the beginning of a list will be most similar to the end of the prior list. The theory assumes a single-context state, consisting of a recency-weighted average of prior items, that is updated, even across different encoding periods.

      However, our results show a boundary item representation is most similar to the prior lists first item rather than the last item. Our results conflict with the extension of TCM because the shared similarity of boundary items suggests the context state for the first item in the list is not a recency-weighted average of the items presented immediately prior. The same boundary sensitive signal is not present in other regions, namely the hippocampus and lateral temporal cortex. Those regions do not show similarity between items at the beginning of each list.  

      Our main conclusion from these data was that the medial parietal lobe activity seems to be specifically sensitive to task boundaries, defined by the first event or the get ready prompt, while other regions are not.

      (3) Although several previous studies have linked hippocampal fMRI and electrophysiological activity at event boundaries with memory performance, the authors do not find similar relationships between hippocampal activity, event boundaries, and memory There are potential explanations for why this might be the case, including the distinction between item vs. associative memory, which has been a prominent feature of previous work examining this question. However, the authors do not address these potential explanations (or others) to explain their findings' divergence from prior work -this makes it difficult to interpret and to draw conclusions from the data about the hippocampus' mechanistic role in forming event memories.

      The following text was added and revised in the discussion to discuss hippocampal activity shown in our results and its lack of sensitivity to boundaries.  

      “Spectral activity in the medial parietal lobe aligned closely with boundaries. Drift between item pairs seemed to reset at each boundary, leading to renewed similarity after each boundary. This observation aligns with previous work suggesting boundaries reset temporal context.  In the temporal cortex, our findings extend prior studies which suggest the temporal lobe may play a role in associating adjacently presented items (Yaffe et al. 2014, ElKalliny et al 2019). We found items encoded in distant serial positions, but within the same list, drifted significantly more than items from adjacent serial positions (Figure 2C). Consistent with the predictions of the temporal context model, the reduced similarity between distant items may reflect reduced contextual overlap proportional to the time elapsed between them. However, across task boundaries, our study did not detect a robust change in drift rate in the medial or lateral temporal cortex. This finding contrasts with significant work (Ben-Yakov et al. 2018, Ezzyat et al.  2014; Griffiths et al. 2020) which shows hippocampal sensitivity to event-boundaries. One interpretation would be that boundary representations in the hippocampus are quite sparse and represented by populations of time-sensitive cells whose activity is indexed to task-related boundaries (Umbach et al. 2020). While the sparse representations may not be detectable in gamma activity, perhaps it suggests drift in these regions represents a more abstract set of contextual features accumulated from multiple brain regions.”

      (4) There is a similar absence of interpretation with respect to the previous literature for the data showing enhanced boundary-related similarity in the medial parietal cortex. The authors’ interpretation seems to be that they have identified a boundary-specific signal that reflects a large and abrupt change in context, however, another plausible interpretation is that enhanced similarity in the medial parietal cortex is related to a representation of a schema for the task structure that has been acquired across repeated instances. 

      We agree our results could suggest the MPL creates a generalized situational model or schematic of the task. Unfortunately, our behavioral task does not allow us to differentiate between these ideas and pure boundary representation. However, given boundaries are a component in defining situational models, we chose to interpret our results conservatively as a form of boundary representation.  

      (5) The authors do not directly compare their model to other models that could explain how variability in neural activity predicts memory. One example is the neural fatigue hypothesis, which the authors mention, however there are no analyses or data to suggest that their data is better fit by a boundary/contextual drift mechanism as opposed to neural fatigue. 

      The study by Lohnas and colleagues does find higher HFA was greater for recalled items but does not describe a serial position specific trend (Lohnas et al. 2020). For our study, we stringently controlled for recall success in each of our analyses. Our main finding of boundary similarity compares recalled boundary items to recalled items in each of the other serial positions. We also show the similarity of nonrecalled items in all serial positions to demonstrate the lack of boundary representation in first list items, when neural fatigue is presumably least present.

      In addition, their study demonstrated neural fatigue in the hippocampus. They did not find evidence of fatigue in the DLPFC, suggesting region-specific mechanisms of neural fatigue. Our results are focused on the medial parietal lobe, and we were not able to find a fatigue model of the region for further comparison. While our results do not rule out the possibility of neural fatigue driving a drifting or boundary signal, we focus on the relevance of the signal to memory performance.

      (6) P2. Line 65 cites Polyn et al (2009b) as an example where ‘random’ boundary insertions improve subsequent memory. However, the boundaries in that study always occurred at the same serial position and were therefore completely predictable and not random.

      The citation was removed from the corresponding sentence.

      (7) P2. Line 74 cites Pu et al. (2022) as an example of medial temporal lobe ‘regional activity’ showing sensitivity to event boundaries; however, this paper reported behavioral and computational modeling results and did not include measurement of neural activity. 

      The citation was removed from the corresponding sentence.

      (8) P.3 Line 117, Hseih et al (2014) and Hseih and Ranganath (2015) are cited as evidence that ‘spectral’ relatedness decreases as a function of distance, but neither of these studies examined ‘spectral’ activity (fMRI univariate and multivariate). The manuscript would benefit from a careful review and updating of how the prior literature is cited, which will increase the impact of the findings for readers. 

      The text has been updated to reflect this distinction by modifying the statement to:  “Previous work consistent with temporal context models suggests neural pattern similarity reduces as a function of distance between related memories.”

      (9) Several previous studies have found hippocampal activity at event boundaries correlates with memory performance (Ben-Yakov et al 2011, 2018; Baldassano et al 2017), yet here the authors do not find evidence for hippocampal activity at event boundaries related to memory. Does this difference reflect something important about how the hippocampus vs. medial parietal cortex vs. lateral temporal cortex contribute to memory formation? Currently, there is not much discussion about how to interpret the differences between brain regions. Previous work has suggested that hippocampal pattern similarity at event boundaries specifically supports associative memory across events (Ezzyat & Davachi, 2014; Griffiths & Fuentemilla, 2020; Heusser et al., 2016), which may help explain their findings. In any case the authors could increase the impact of their paper by further situating their findings within the previous literature. 

      We would not suggest there is no boundary-related activity in the hippocampus. Similar to an earlier point made by the reviewer, to clarify our interpretation of regional differences, the following text has been added to the discussion.  

      “However, across task boundaries, our study did not detect a robust change in drift rate in the medial or lateral temporal cortex. This finding contrasts with significant work (Ezzyat and Davachi, 2014; Griffiths and Fuentemilla, 2020) which shows hippocampal sensitivity to event-boundaries. One interpretation would be that boundary representations in the hippocampus are quite sparse and represented by populations of time-sensitive cells whose activity is indexed to task-related boundaries (Umbach et al 2020). While the sparse representations may not be detectable in gamma activity, perhaps it suggests drift in these regions represents a more abstract set of contextual features accumulated from multiple brain regions (Baldassano et al. 2017). “

      (10) The authors mention neural fatigue as an alternative theory to explain the primacy effect (Serruya et al., 2014), however there are no analyses or data to suggest that their data is better fit by a boundary mechanism as opposed to neural fatigue. Previous studies have shown that gamma activity in the hippocampus changes with serial position and with encoding history (Serruya et al 2014; Lohnas et al 2020). Here, the authors could compare the reported pattern similarity results to control analyses that replicate this prior work, which would strengthen their argument that there is unique information at boundaries that is distinct from a neural fatigue signal. 

      The serial position effects described by Serruya and colleagues describe decreasing HFA with increasing serial position in the MTL, lateral temporal cortex and prefrontal cortex (Serruya et al. 2014). Despite their findings, we do not observe a strong boundary effect in those regions (see Supp Fig 3 a,b). The lack of boundary effect in regions where HFA is selectively increased for primacy items suggests the global neural fatigue model does not account for our results.

      Notably, the authors do not characterize HFA trends in the MPL. Nevertheless, their findings do not rule out the possibility of a boundary effect driving the HFA. We demonstrate boundary-relevant HFA only in the MPL but not in other regions. In addition, we show a correlation between SP1 recalls and boundary representation strength, as well as a conserved similarity of multiple boundary-adjacent items.  

      Next, the neural fatigue study by Lohnas and colleagues does find higher HFA was greater for recalled items but does not describe a serial position specific trend (Lohnas et al. 2015). For our study, we stringently controlled for recall success in each of our analyses. Our main finding of boundary similarity compares recalled boundary items to recalled items in each of the other serial positions. We also show the similarity of non-recalled items in all serial positions to demonstrate the lack of boundary representation in the first list items, when neural fatigue is presumably least present.

      In addition, their study demonstrated neural fatigue in the hippocampus. They did not find evidence of fatigue in the DLPFC, suggesting region-specific mechanisms of neural fatigue. Our results are focused on the medial parietal lobe, and we were not able to find a fatigue model of the region for further comparison. While our results do not rule out the possibility of neural fatigue driving a drifting or boundary signal, we focus on the relevance of the signal to memory performance.

      (11) For the analyses that examine cross-list similarity (e.g. the medial parietal analysis in Figure 3), how did the authors choose the number of lists over which similarity was calculated? Was the selection of this free parameter cross-validated to ensure that it is not overfitting the data? Given that there were 25 lists per session, using the three succeeding lists seems arbitrary. Why not use every list across the whole session? 

      Given the volume of data, number of patients, and computational time available at our facility, we extended the analysis as far as we could to characterize the observed trend.

      (12) P4. Line 155 says that Figure 3C shows example subject data, but it looks like it is actually Figure 3D. 

      The text was updated to reference the correct figure.

      (13) The t-tests on P.4 Line 159 have two sets of degrees of freedom but should only have one. 

      The t-tests described by Figure 3B represent the mean parameter estimate of the predictor for boundary proximity contrasted by region for all item pairs. The statistical test in this case was an unpaired t-test between parameter estimates for patients with electrodes in each of the regions. The numbers within parentheses represent the sample size, or number of subjects, contributing electrodes to each region.

      Reviewer 2:

      (1) Because this is not a traditional event boundary study, the data are not ideally positioned to demonstrate boundary specific effects. In a typical study investigating event boundary effects, a series of stimuli are presented and within that series occurs an event boundary – for instance, a change in background color. The power of this design is that all aspects between stimuli are strictly controlled – in particular, the timing – meaning that the only difference between boundary-bridging items is the boundary itself. The current study was not designed in this manner, thus it is not possible to fully control for effects of time or that multiple boundaries occur between study lists (study to distractor, distractor to recall, recall to study). Each list in a free recall study can be considered its own “mini” experiment such that the same mechanisms should theoretically be recruited across any/all lists. There are multiple possible processes engaged at the start of a free recall study list which may not be specific to event boundaries per se. For example, and as cited by the authors, neural fatigue/attentional decline (and concurrent gamma power decline) may account for serial position effects. Thus, SP1 on all lists will be similar by virtue of the fact that attention/gamma decrease across serial position, which may or may not be a boundaryspecific effect. In an extreme example, the analyses currently reported could be performed on an independent dataset with the same design (e.g. 12 word delayed free recall) and such analyses could potentially reveal high similarity between SP1-list1 in the current study and SP1-list1 in the second dataset, effects which could not be specifically attributed to boundaries.

      The neural fatigue study by Lohnas and colleagues does find higher HFA was greater for recalled items but does not describe a serial position specific trend (Lohnas et al. 2020). For our study, we stringently controlled for recall success in each of our analyses. Our main finding of boundary similarity compares recalled boundary items to recalled items in each of the other serial positions. We also show the similarity of non-recalled items in all serial positions to demonstrate the lack of boundary representation in the first list items, when neural fatigue is presumably least present.

      In addition, their study demonstrated neural fatigue in the hippocampus. They did not find evidence of fatigue in the DLPFC, suggesting region-specific mechanisms of neural fatigue. Our results are focused on the medial parietal lobe, and we were not able to find a fatigue model of the region for further comparison. While our results do not rule out the possibility of neural fatigue driving a drifting or boundary signal, we focus on the relevance of the signal to memory performance.

      (2) Comparisons of recalled "pairs" does not account for the lag between those items during study or recall, which based on retrieved context theory and prior findings (e.g. Manning et al., 2011), should modulate similarity between item representations. Although the GLM will capture a linear trend, it will not reveal serial position specific effects. It appears that the betas reported for the SP12 analyses are driven by the fact that similarity with SP12 generally increases across serial position, rather a specific effect of "high similarity to SP12 in adjacent lists" (Page 5, excluding perhaps the comparison with list x+1). It is also unclear how the SP12 similarity analyses support the statement that "end-list items are represented more distinctly, or less similarly, to all succeeding items" (Page 5). It is not clear how the authors account for the fact that the same participants do not contribute equally to all ROIs or if the effects are consistent if only participants who have electrodes in all ROIs are included.

      In our study, all pairs are defined by the lag between a reference and target item. The results in Figure 3 show the similarity between each serial position in relation to SP1; Figure 4 shows lag between each serial position relative to SP2 and 3; and Figure 5 shows lag relative to SP12. Each statistical model accounts for the lag by ordering the data by increased inter-item distance. Further, our definition of lag is significantly more rigorous than that used by Manning and colleagues. Our similarity results for Figures 3-5 characterize the change in similarity relative to a constant reference point, such as SP1, rather than a relative reference point, such as +1 lag, which aggregates similarity between pairs such as SP1 to SP2 with SP4 to SP5, which maybe recalled via different memory mechanisms.  

      In Figure 5, we agree your characterization that ‘similarity with SP12 generally increases across serial position’ is a more accurate description of the trend. The text has been updated to reflect this by changing the interpretation to “later serial positions in adjacent lists shared a gradually increasing similarity to SP12.”  

      Next, we clarify the statement "end-list items are represented more distinctly, or less similarly, to all succeeding items". When recalling SP12, the subsequent items recalled exhibit significantly lower similarity to SP12 (see Figure 5D, pink). Consequently, the spectral representation of successfully recalled end-list items appears more distinct from later items in similar serial positions. This stands in contrast to our observations illustrated in Figures 3 and 4, where successfully recalled start-list items demonstrate greater similarity to later items in similar serial positions.

      (3) The authors use the term "perceptual" boundary which is confusing. First, "perceptual boundary" seems to be a specific subset of the broader term "event boundary," and it is unclear why/how the current study is investigating "perceptual" boundaries specifically. Second and relatedly, the current study does not have a sole "perceptual" boundary (as discussed in point 1 above), it is really a combination of perceptual and conceptual since the task is changing (from recalling the words in the previous list to studying the words in the current list OR studying the words in the current list to solving math problems in the current list) in addition to changes in stimulus presentation. 

      We agree with the statement that ‘perceptual’ as a modifier to the boundaries described here does not add significant information. Therefore, we have removed all reference to perceptual boundaries.

      (4) Although the results show that item-item similarity in the gamma band decreases across serial position, it is unclear how the present findings further describe "how gamma activity facilitates contextual associations" (Page 5). As mentioned in point 1 above, such effects could be driven by attentional declines across serial position -- and a concurrent decline in gamma power -- which may be unrelated to, and actually potentially impair, the formation of contextual associations, given evidence from the literature that increased gamma power facilitates binding processes.

      We agree that our study does not elucidate a mechanistic relationship between gamma power and contextual associations. The referenced sentence has been changed to: “how gamma activity is associated with context”.

      Please see our response to point 1 above. In addition, studies demonstrating decreasing gamma power with increasing serial position focus primarily on the MTL, lateral temporal cortex and prefrontal cortex (Serruya et al. 2012). Despite their findings, we do not observe a strong boundary effect in those regions (see Supp Fig 3 a,b). The lack of boundary effect in regions where HFA is selectively increased for primacy items suggests the global attentional decline or neural fatigue model does not account for our results.

      Notably, HFA trends in the MPL are poorly described. Further, gamma power decline does not rule out the possibility of a boundary effect driving the HFA. We demonstrate boundary-relevant HFA only in the MPL but not in other regions. In addition, we show a correlation between SP1 recalls and boundary representation strength, as well as a conserved similarity of multiple boundary-adjacent items.

      (5) Some of the logic and interpretations are inconsistent with the literature. For example, the authors state that "The temporal context model (TCM) suggests that gradual drift in item similarity provides context information to support recovery of individual items" however, this does not seem like an accurate characterization of TCM. According to TCM, context is a recency-weighted average of previous experience. Context "drifts" insofar as information is added to/removed from context. Context drift thus influences item similarity -- it is not that item similarity itself drifts, but that any change in item-item similarity is due to context drift. 

      The current findings do not appear at odds with the conceptualization of drift and context in current version of the context maintenance and retrieval model. Furthermore, the context representation is posited to include information beyond basic item representations. Two items, regardless of their temporal distance, can be associated with similar contexts if related information is included in both context representations, as predicted and shown for multiple forms of relatedness including semantic relatedness (Manning & Kahana, 2012) and task relatedness (Polyn et al., 2012).

      We revised the sentence and encompassing paragraph to describe the temporal context model more accurately and emphasize how our findings align with the stated version of CMR. The revised text is below:  

      “Next, we asked how gamma spectral activity reflects contextual association between items. In the medial parietal lobe, we observed recurring similarity between items distant in time but adjacent to boundaries. This pattern suggests spectral activity may carry information about an item's relationship to a boundary. These observations align with the Context Maintenance and Retrieval model which extends the predictions of TCM to encompass broader relationships among items. Our results demonstrate boundaries as an important aspect of context and specify the spectral and regional properties of these boundary-related contextual features.”

      (6) Lohnas et al. (2020) Neural fatigue influences memory encoding in the human hippocampus, Neuropsychologia, should be cited when discussing neural fatigue

      Thank you for your suggestion. The citation has been added to the text.

      (7) A within-list, not an across list, similarity analysis should be used to test the interpretation that end-of-list items are more distinct than other list items.

      We believe this recommendation refers to the following line in our text: “These findings suggest end-list items are represented more distinctly, or less similarly, to all succeeding items.” Our statement compares list x, SP12 to all succeeding items (in list x+1, x+2, etc.). Therefore, this statement refers to items in the next lists which is why we performed an across list analysis rather than within-list one.

      (8) It is unclear why it is necessary to use PCA to estimate similarity between items.

      PCA was used to reduce the dimensionality of the time-frequency matrix for the gamma band. This technique allowed us to compare predominant trends in gamma between items. In addition, we added a figure showing 3 example subjects in Figure 3 – supplementary figure 2D to show unique time-frequency components contribute to signal reconstructed from the PCs for each subject. Therefore, the boundary representation may be represented differently for each patient.

      (9) Lags are listed as -4, 4 (Page 8), however with a list length of 12, possible lags should be 11, 11.

      The listed parenthetical statement ‘(-4 to 4)’ referred to Figure 1 where Lag CRP is shown for transitions from -4 to 4. However, we did calculate lag CRP for all possible transitions. Therefore, the referenced phrase was changed to: “Lagged CRP was calculated for all possible transitions (-11 to 11).”

      (10) Hsieh et al. 2014 and Hsieh & Ranganath (2015) are fMRI studies and as such, do not support the statement "Previous work consistent with temporal context models suggests spectral relatedness reduces as a function of distance between words" (Page 3). 

      The statement has been revised to: “Previous work consistent with temporal context models suggests neural pattern similarity reduces as a function of distance between related memories.”

      (11) Although statistically one can measure "How item-item similarity is affected by recollection" (Page 3), this is logically backwards, given that similarity during study necessarily precedes performance during free recall. Additionally, it is erroneous to assume that recalled words are "recollected" without additional measurements (e.g. Mickes et al. (2013) Rethinking familiarity: Remember/Know judgments in free recall, JML).

      The statement was changed to “item-item similarity is affected based on successful recall” given recollection cannot be determined in our paradigm.

      Reviewer 3:

      (1) My primary confusion in the current version of this paper is that the analyses don't seem to directly compare the two proposed models illustrated in Fig 1B, i.e. the temporal context model (with smooth drifts between items, including across lists) versus the boundary model (with similarities across all lists for items near boundaries). After examining smooth drift in the within-list analysis (Fig 2), the across-list analyses (Figs 3-5) use a model with two predictors (boundary proximity and list distance), neither of which is a smoothlydrifting context. Therefore there does not appear to be a quantitative analysis supporting the conclusion that in lateral temporal cortex "drift exhibits a relationship with elapsed time regardless of the presences of intervening boundaries" (lines 272-3).

      We could not use a smoothly drifting regressor due to its collinearity with any model of boundary similarity. Therefore, we chose our two regressors: boundary proximity, which models intra-list changes in similarity and list distance, which models a stepwise decrease in similarity from adjacent lists.

      However, we agree with the comment that the presented data does not directly support the lateral temporal cortex drifts independent of intervening boundaries. Therefore, we amended the statement to: “We found successfully recalled items encoded in distant serial positions drifted significantly more than items from adjacent serial positions (Figure 2C)”. Consistent with the predictions of the temporal context model, the reduced similarity between distant items may reflect reduced contextual overlap proportional time elapsed between them.”

      (2) The feature representation used for the neural response to each item is a gamma power time-frequency matrix. This makes it unclear what characteristics of the neural response are driving the observed similarity effects. It appears that a simple overall scaling of the response after boundaries (stronger responses to initial items during the beginning portion of the 1.6s time window) would lead to the increased cosine similarity between initial items, but wouldn't necessarily reflect meaningful differences in the neural representation or context of these items.

      Our study aims to draw the connection between the neural response after boundaries with neural representation and context of these items. Prior studies (Manning et al. 2011, El Kalliny et al. 2017) have interpreted similarity in neural spectra as a memory relevant phenomenon. We use very similar methods to perform our analysis.  

      In addition, we compare the fit of our boundary similarity model to behavioral performance to show increased boundary representation correlates with improved boundary item recall.

      While our study does not specify which time-frequency components underly the increased similarity, we do limit our analysis to the gamma band. Traditional analyses include log-scaled, broadband time-frequency data (eg. 3-100hz) from which we specify the relevance of a much narrower spectral band.  

      Finally, we tried to study which time–frequency components contributed to the increased similarity, but it varied greatly between patients (see Figure 3 – supplementary figure 2D). Hence, we opted to use principal component analyses to compare the features showing the most variation for each given participant. This added analytical step allows us to detect boundary effects across patients despite individual variability in boundary representation.

      (3) The specific form of the boundary proximity models is not well justified. For initial items, a model of e^(1-d) is used (with d being serial position), but it is not stated how the falloff scale of this model was selected (as opposed to e.g. e^((1-d)/2)). For final items, a different model of d/#items is used, which seems to have a somewhat different interpretation (about drift between boundaries, rather than an effect specific to items near a final boundary). The schematic in Fig 1B appears to show a hypothesis which is not tested, with symmetric effects at initial and final boundaries.

      The boundary proximity models were chosen empirically. Our model was intended to quantify a decreasing relationship across many patients. We acknowledge the constants and variables may not definitively describe underlying neural processes.  

      For start- and end-list boundaries, we used different models because primacy and recency effects are unique phenomena. Primacy memory is classically thought to arise from rehearsal during the encoding time (Polyn et al. 2009, Lohnas et al. 2015). Alternatively, recency memory is thought to arise from strong contextual cues of recency items during recall due to their temporal proximity. Therefore, we have a limited basis on which to assume their spectral representation in relation to task boundaries would be symmetric.

      (4) The main text description of Fig 2 only describes drift effects in lateral temporal cortex, but Fig 2 - supplement 1 shows that there is also drift and a significant subsequent memory effect in the other two ROIs as well. There is not a significant memory x drift slope interaction in these regions; are the authors arguing that the lack of this interaction (different drift rates for remembered versus forgotten items) is critical for interpreting the roles of lateral temporal cortex versus medial parietal and hippocampal regions?

      Yes. Fig 2- Supplement 1 shows that drift occurs in both the HC and MPL. However, the interaction term is not significant, which suggests that the rate of drift between recalled and non-recalled items is not significantly different.  

      In contrast, Fig 2C shows that recalled pairs drift at a higher rate than non-recalled pairs. For the LTC, the interaction term is negative in magnitude and statistically significant. This suggests successfully encoded item pairs encoded far apart share more distinct spectral representations, specifically in the LTC. These findings lead to our interpretation in the discussion that “elevated drift rate might allow the representations of recalled items to remain distinct but ordered in memory.”

      (5) The parameter fits for the "list distance" regressor are not shown or analyzed, though they do appear to be important for the observed similarity structure (e.g. Fig 3E). I would interpret this regressor as also being "boundary-related" in the sense that it assumes discrete changes in similarity at boundaries.

      Parameter fits for the ‘list distance’ regressor are now shown in the supplementary portion of Figures 3 and Figure 5. The difference between regions is non-significant.

      (6) To make strong claims about temporal context versus boundary models as implied by Fig 1B, these two regressors should be fit within the same model to explain across-list similarity. The temporal context model could be based on the number of intervening items (as in Fig 1B) or actual time elapsed between items. The relationship between the smoothly drifting temporal context model and the discretely-jumping list distance models should also be clarified.

      We could not use a smoothly drifting regressor due to its collinearity with any model of boundary similarity. A model which included a ‘temporal context regressor’ would not be able to account for the presence of a boundary effect and would not allow us to demonstrate a boundary representation in the presence of drift. Therefore, we chose our two regressors: boundary proximity, which models intra-list changes in similarity and list distance, which models a stepwise decrease in similarity from adjacent lists. These regressors allow the model to differentiate between intra-list changes (the boundary regressor) verses inter-list changes (the list distance regressor).  

      (7) The features of the time-frequency matrix that are driving similarity between events could be visualized to provide a better understanding of the boundary-related signals. The analysis could also be re-run with reduced versions of the feature space in order to determine the critical components of this signal; for example, responses could be averaged across time to examine only differences across frequencies, or across frequencies to examine purely temporal changes across the 1.6 second window.

      Figure 3 – supplementary figure 2 A-C has been added to show varying the number of principal components (PCs) does not change the trend of boundary sensitivity in the MPL. In addition, we included 3 example subjects in Figure 3 – supplementary figure 2D to show unique time-frequency components contribute to signal reconstructed from the PCs for each subject. Therefore, the boundary representation may be represented differently for each patient.

      (8) If the authors are considering a space of multiple models as "boundary proximity models" (e.g. linear models and exponential models with different scale factors), this should be part of the model-fitting process rather than a single model being selected posthoc.

      We agree with the reviewer’s suggestion that the most ideal way to fit a model to the trend would be using a model-fitting process. However, due to a limitation on the amount of computational resources available, we were not able to perform it given the size of our dataset.

      (9) The interpretation of region differences in the results in Fig 2 and Fig 2 - supplement 1 should be clarified. 

      In discussion, we have added the following text to clarify our interpretation of the regional differences shown in the mentioned figures.  

      “However, across task boundaries, our study did not detect a robust change in drift rate in the medial or lateral temporal cortex. This finding contrasts with significant work (Ezzyat and Davachi, 2014; Griffiths and Fuentemilla, 2020) which shows hippocampal sensitivity to event-boundaries. One interpretation would be that boundary representations in the hippocampus are quite sparse and represented by populations of time-sensitive cells whose activity is indexed to task-related boundaries (Umbach et al 2018). While the sparse representations may not be detectable in gamma activity, perhaps it suggests drift in these regions represents a more abstract set of contextual features accumulated from multiple brain regions (Baldassano et al. 2017). “

      (10) Whether there are significant fits for the list distance regressor, and whether these fits vary across regions, could be stated. The list distance regressor could also be directly compared (in the same model) to a temporal-context regressor, which predicts graded changes in similarity between items rather than the discrete changes between lists.

      We have added parameter fits for the ‘list distance’ regressor in the supplementary portion of Figures 3 and Figure 5. The difference between regions is non-significant. Therefore, our results show very similar stepwise decrease in similarity across lists between regions (list distance regressor; Figure 3 —supplementary figure 1B).

      We could not compare these parameters to a separate model which includes a smoothly drifting ‘temporal-context’ regressor due to the regressors collinearity with any representation of boundary. See our response to Reviewer 3 –comment 6.  

      (11) The authors should clarify their interpretation of the results, and whether they are proposing a tweak to the temporal context model or a substantially different organizational system. 

      In the disucssion we include the following statements to clarify what we suggest regarding the temporal context model.  

      “Our findings suggest a broader scope of contextual association than just prior items, where temporal proximity as well as task structure in the form of boundaries, play intertwined roles in contextual construction. Our data therefore have implications for updated iterations of the temporal context model incorporating (perhaps) specific terms for boundary information. This may in turn provide a more systematic prediction of primacy effects in behavioral data.”  

      (12) Minor typos and corrections: 

      52: using -> use 

      108: patients -> patients'  156: list -> lists 

      The list distance plot is described as "pink" in Fig 3 and Fig 5 - supplement 1, but appears gray in the figures.

      Each of these corrections has been corrected in the text.

    1. Author Response

      Reviewer #1 (Public Review):

      Weaknesses:

      1) The authors should better review what we know of fungal Drosophila microbiota species as well as the ecology of rotting fruit. Are the microbiota species described in this article specific to their location/setting? It would have been interesting to know if similar species can be retrieved in other locations using other decaying fruits. The term 'core' in the title suggests that these species are generally found associated with Drosophila but this is not demonstrated. The paper is written in a way that implies the microbiota members they have found are universal. What is the evidence for this? Have the fungal species described in this paper been found in other studies? Even if this is not the case, the paper is interesting, but there should be a discussion of how generalizable the findings are.

      The reviewer inquires as to whether the microbial species described in this article are ubiquitously associated with Drosophila or not. Indeed, most of the microbes described in this manuscript are generally recognized as species associated with Drosophila spp. For example, species such as Hanseniaspora uvarum, Pichia kluyveri, and Starmerella bacillaris have been detected in or isolated from Drosophila spp. collected in European countries as well as the United States and Oceania (Chandler et al., 2012; Solomon et al., 2019). As for the bacteria, species belonging to the genera Pantoea, Lactobacillus, Leuconostoc, and Acetobacter have also previously been detected in wild Drosophila spp. (Chandler et al., 2011). These elucidations will be incorporated into our revised manuscript.

      Nevertheless, the term “core” in the manuscript title may lead to misunderstanding, as the generality does not ensure the ubiquitous presence of these microbial species in every individual fly. Considering this point, we will replace the term with an expression more appropriate to our context.

      2) Can the authors clearly demonstrate that the microbiota species that develop in the banana trap are derived from flies? Are these species found in flies in the wild? Did the authors check that the flies belong to the D. melanogaster species and not to the sister group D. simulans?

      Can the authors clearly demonstrate that the microbiota species that develop in the banana trap are derived from flies? Are these species found in flies in the wild?

      The reviewer asked whether the microbial species identified in the fermented banana samples were derived from flies. To address this question, additional experiments under more controlled conditions, such as the inoculation of specific species of wild flies onto fresh bananas, would be needed. Nevertheless, the microbes may potentially originate from wild flies, as supported by the literature cited in our response to the Weakness 1).

      Alternative sources for microbial provenance also merit consideration. For example, microbial entities may be inherently present in unfermented bananas through the infiltration of peel injuries (lines 1141-1142 of the original manuscript). In addition, they could be introduced by insects other than flies, given that both rove beetles (Staphylinidae) and sap beetles (Nitidulidae) were observed in some of the traps. These possibilities will be incorporated into the 'MATERIALS AND METHODS' and 'DISCUSSION' sections of our revised manuscript.

      Did the authors check that the flies belong to the D. melanogaster species and not to the sister group D. simulans?

      Our sampling strategy was designed to target not only D. melanogaster but also other domestic Drosophila species, such as D. simulans, that inhabit human residential areas. After adult flies were caught in each trap, we identified the species as shown in Table S1, thereby showing the presence of either or both D. melanogaster and D. simulans. We will provide these descriptions in MATERIALS AND METHODS and DISCUSSION.

      3) Did the microarrays highlight a change in immune genes (ex. antibacterial peptide genes)? Whatever the answer, this would be worth mentioning. The authors described their microarray data in terms of fed/starved in relation to the Finke article. They should clarify if they observed significant differences between species (differences between species within bacteria or fungi, and more generally differences between bacteria versus fungi).

      Did the microarrays highlight a change in immune genes (ex. antibacterial peptide genes)? Whatever the answer, this would be worth mentioning.

      Regarding the antimicrobial peptide genes, statistical comparisons of our RNA-seq data across different conditions were impracticable because most of them showed low expression levels (refer to Author response table 1, which exhibits the RNA-seq data of the yeast-fed larvae; similar expression profiles were observed in the bacteria-fed larvae). While a subset of genes exhibited significantly elevated expression in the non-supportive conditions relative to the supportive ones, this can be due to intra-sample variability rather than due to distinct nutritional environments. Therefore, it would be difficult to discuss a change in immune genes in the paper. Additionally, the previous study that conducted larval microarray analysis (Zinke et al., 2002) did not explicitly focus on immune genes.

      Author response table 1.

      Antimicrobial peptide genes are not up-regulated by any of the microbes. Antimicrobial peptides gene expression profiles of whole bodies of first-instar larvae fed on yeasts. TPM values of all samples and comparison results of gene expression levels in the larvae fed on supportive and non-supportive yeasts are shown. Antibacterial peptide genes mentioned in Hanson and Lemaitre, 2020 are listed. NA or na, not available.

      They should clarify if they observed significant differences between species (differences between species within bacteria or fungi, and more generally differences between bacteria versus fungi).

      We did not observe significant differences between species within bacteria or fungi, or between bacteria and fungi. For example, the gene expression profiles of larvae fed on the various supporting microbes showed striking similarities to each other, as evidenced by the heat map showing the expression of all genes detected in larvae fed either yeast or bacteria (Author response image 1). Similarities were also observed among larvae fed on distinct non-supporting microbes.

      Author response image 1.

      Gene expression profiles of larvae fed on the various supporting microbes show striking similarities to each other. Heat map showing the gene expression of the first-instar larvae that fed on yeasts or bacteria. Freshly hatched germ-free larvae were placed on banana agar inoculated with each microbe and collected after 15 h feeding to examine gene expression of the whole body. Note that data presented in Figures 3A and 4C in the original manuscript, which are obtained independently, are combined to generate this heat map. The labels under the heat map indicate the microbial species fed to the larvae, with three samples analyzed for each condition. The lactic acid bacteria (“LAB”) include Lactiplantibacillus plantarum and Leuconostoc mesenteroides, while the lactic acid bacterium (“AAB”) represents Acetobacter orientalis. “LAB + AAB” signifies mixtures of the AAB and either one of the LAB species. The asterisk in the label highlights a sample in a “LAB” condition (Leuconostoc mesenteroides), which clustered separately from the other “LAB” samples. Brown abbreviations of scientific names are for the yeast-fed conditions. H. uva, Hanseniaspora uvarum; K. hum, Kazachstania humilis; M. asi, Martiniozyma asiatica; S. cra, Saccharomycopsis crataegensis; P. klu, Pichia kluyveri; S. bac, Starmerella bacillaris; S. cer, S. cerevisiae BY4741 strain.

      Only a handful of genes showed different expression patterns between larvae fed on yeast and those fed on bacteria, without any enrichment for specialized gene functions. Thus, it is challenging to discuss the potential differential impacts, if any, of yeast and bacteria on larval growth.

      4) The whole paper - and this is one of its merits - points to a role of the Drosophila larval microbiota in processing the fly food. Are these bacterial and fungal species found in the gut of larvae/adults? Are these species capable of establishing a niche in the cardia of adults as shown recently in the Ludington lab (Dodge et al.,)? Previous studies have suggested that microbiota members stimulate the Imd pathway leading to an increase in digestive proteases (Erkosar/Leulier). Are the microbiota species studied here affecting gut signaling pathways beyond providing branched amino acids?

      The whole paper - and this is one of its merits - points to a role of the Drosophila larval microbiota in processing the fly food. Are these bacterial and fungal species found in the gut of larvae/adults? Are these species capable of establishing a niche in the cardia of adults as shown recently in the Ludington lab (Dodge et al.,)?

      Although we did not investigate the microbiota in the gut of either larvae or adults, we did compare the microbiota within surface-sterilized larvae or adults with those in food samples. We found that adult flies and early-stage food sources, as well as larvae and late-stage food sources, harbor similar microbial species (Figure 1F). Additionally, previous examinations of the gut microbiota in wild adult flies have identified microbial species or taxa congruent with those we isolated from our foods (Chandler et al., 2011; Chandler et al., 2012). We have elaborated on this in our response to Weakness 1).

      While we did not investigate whether these species are capable of establishing a niche in the cardia of adults, we will cite the study by Dodge et al., 2023 in our revised manuscript and discuss the possibility that predominant microbes in adult flies may show a propensity for colonization.

      Previous studies have suggested that microbiota members stimulate the Imd pathway leading to an increase in digestive proteases (Erkosar/Leulier). Are the microbiota species studied here affecting gut signaling pathways beyond providing branched amino acids?

      The reviewer inquires whether the supportive microbes in our study stimulate gut Imd signaling pathways and induce the expression of digestive protease genes, as demonstrated in a previous study (Erkosar et al., 2015). According to our RNA-seq data, it seems unlikely that the supportive microbes stimulate the signaling pathway. Figures contained in Author response image 2 provide the statistical comparisons of expression levels for seven protease genes between the supportive and the non-supportive conditions. These genes did not exhibit a consistent upregulation in the presence of the supportive microbes (H. uva or K. hum in Author response image 2A; Le mes + A. ori in Author response image 2B). Rather, they exhibited a tendency to be upregulated under the non-supportive microbes (St. bac or Pi. klu in Author response image 2A; La. pla in Author response image 2B).

      Author response image 2.

      Most of the peptidase genes reported by Erkosar et al., 2015 are more highly expressed under the non-supportive conditions than the supportive conditions. Comparison of the expression levels of seven peptidase genes derived from the RNA-seq analysis of yeast-fed (A) or bacteria-fed (B) first-instar larvae. A previous report demonstrated that the expression of these genes is upregulated upon association with a strain of Lactiplantibacillus plantarum, and that the PGRP-LE/Imd/Relish signaling pathway, at least partially, mediates the induction (Erkosar et al., 2015). H. uva, Hanseniaspora uvarum; K. hum, Kazachstania humilis; P. klu, Pichia kluyveri; S. bac, Starmerella bacillaris; La. pla, Lactiplantibacillus plantarum; Le. mes, Leuconostoc mesenteroides; A. ori, Acetobacter orientalis; ns, not significant.

      Reviewer #2 (Public Review):

      Weaknesses:

      The experimental setting that, the authors think, reflects host-microbe interactions in nature is one of the key points. However, it is not explicitly mentioned whether isolated microbes are indeed colonized in wild larvae of Drosophila melanogaster who eat bananas. Another matter is that this work is rather descriptive and a few mechanical insights are presented. The evidence that the nutritional role of BCAAs is incomplete, and molecular level explanation is missing in "interspecies interactions" between lactic acid bacteria (or yeast) and acetic acid bacteria that assure their inhabitation. Apart from these matters, the future directions or significance of this work could be discussed more in the manuscript.

      The experimental setting that, the authors think, reflects host-microbe interactions in nature is one of the key points. However, it is not explicitly mentioned whether isolated microbes are indeed colonized in wild larvae of Drosophila melanogaster who eat bananas.

      The reviewer asks whether the isolated microbes were colonized in the larval gut. Previous studies on microbial colonization associated with Drosophila have predominantly focused on adults (Pais et al. PLOS Biology, 2018), rather than larval stages. Developing larvae continually consume substrates which are already subjected to microbial fermentation and abundant in live microbes until the end of the feeding larval stage. Therefore, we consider it difficult to discuss microbial colonization in the larval gut. We will add this point in the DISCUSSION of the revised manuscript.

      Another matter is that this work is rather descriptive and a few mechanical insights are presented. The evidence that the nutritional role of BCAAs is incomplete, and molecular level explanation is missing in "interspecies interactions" between lactic acid bacteria (or yeast) and acetic acid bacteria that assure their inhabitation.

      While recognizing the importance of comprehensive mechanistic analysis, this study includes all experimentally feasible data. Elucidation of more detailed molecular mechanisms lies beyond the scope of this study and will be the subject of future research.

      Regarding the nutritional role of BCAAs, the incorporation of BCAAs enabled larvae fed with the non-supportive yeast to grow to the second instar. This observation suggests that consumption of BCAAs upregulates diverse genes involved in cellular growth processes in larvae. We have discussed the hypothetical interaction between lactic acid bacteria (LAB) and acetic acid bacteria (AAB) in the manuscript (lines 402-405): LAB may facilitate lactate provision to AAB, consequently enhancing the biosynthesis of essential nutrients such as amino acids. To test this hypothesis, future experiments will include the supplementation of lactic acid to AAB culture plates and the co-inoculating LAB mutant strains defective in lactate production with AABs, to assess both larval growth and continuous larval association with AABs. With respect to AAB-yeast interactions, metabolites released from yeast cells might benefit AAB growth, and this possibility will be investigated through the supplementation of AAB culture plates with candidate metabolites identified in the cell suspension supernatants of the late-stage yeasts.

      Apart from these matters, the future directions or significance of this work could be discussed more in the manuscript.

      We appreciate the reviewer's recommendations and will include additional descriptions regarding these aspects in the DISCUSSION section.

      Reviewer #3 (Public Review):

      Weaknesses:

      Despite describing important findings, I believe that a more thorough explanation of the experimental setup and the steps expected to occur in the exposed diet over time, starting with natural "inoculation" could help the reader, in particular the non-specialist, grasp the rationale and main findings of the manuscript. When exactly was the decision to collect early-stage samples made? Was it when embryos were detected in some of the samples? What are the implications of bacterial presence in the no-fly traps? These samples also harbored complex microbial communities, as revealed by sequencing. Were these samples colonized by microbes deposited with air currents? Were they the result of flies that touched the material but did not lay eggs? Could the traps have been visited by other insects? Another interesting observation that could be better discussed is the fact that adult flies showed a microbiome that more closely resembles that of the early-stage diet, whereas larvae have a more late-stage-like microbiome. It is easy to understand why the microbiome of the larvae would resemble that of the late-stage foods, but what about the adult microbiome? Authors should discuss or at least acknowledge the fact that there must be a microbiome shift once adults leave their food source. Lastly, the authors should provide more details about the metabolomics experiments. For instance, how were peaks assigned to leucine/isoleucine (as well as other compounds)? Were both retention times and MS2 spectra always used? Were standard curves produced? Were internal, deuterated controls used?

      When exactly was the decision to collect early-stage samples made? Was it when embryos were detected in some of the samples?

      We collected traps and early-stage samples 2.5 days after setting up the traps. This time frame was determined by pilot experiments. A shorter collection time resulted in a greater likelihood of obtaining no-fly traps, whereas a longer collection time caused larval overcrowding, as well as adults’ deaths from drowning in the liquid seeping out of fruits. These procedural details will be delineated in the MATERIALS AND METHODS section of the revised manuscript.

      What are the implications of bacterial presence in the no-fly traps? These samples also harbored complex microbial communities, as revealed by sequencing. Were these samples colonized by microbes deposited with air currents? Were they the result of flies that touched the material but did not lay eggs? Could the traps have been visited by other insects?

      We assume that the origins of the microbes detected in the no-fly trap foods vary depending on the species. For instance, Colletotrichum musae, the fungus that causes banana anthracnose, may have been present in fresh bananas before trap placement. The filamentous fungi could have originated from airborne spores, but they could also have been introduced by insects that feed on these fungi. We will include these possibilities in the DISCUSSION section of the revised manuscript.

      Another interesting observation that could be better discussed is the fact that adult flies showed a microbiome that more closely resembles that of the early-stage diet, whereas larvae have a more late-stage-like microbiome. It is easy to understand why the microbiome of the larvae would resemble that of the late-stage foods, but what about the adult microbiome? Authors should discuss or at least acknowledge the fact that there must be a microbiome shift once adults leave their food source.

      We are grateful for the reviewer's insightful suggestions regarding shifts in the adult microbiome. We plan to include in the DISCUSSION section of the revised manuscript the possibility that the microbial composition may change substantially during pupal stages and that microbes obtained after eclosion could potentially form the adult gut microbiota.

      Lastly, the authors should provide more details about the metabolomics experiments. For instance, how were peaks assigned to leucine/isoleucine (as well as other compounds)? Were both retention times and MS2 spectra always used? Were standard curves produced? Were internal, deuterated controls used?

      We appreciate the reviewer's advice. Detailed methods of the metabolomic experiments will be included in our revised manuscript.

    1. Author Response

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public Review):

      The modeling approaches are very sophisticated, and clearly demonstrate the selective nature of acute ketamine to reduce the impact of trial losses on subsequent performance, relative to neutral or gain outcomes. The authors then, not unreasonably, suggest that this effect is important in the context of the negative bias in interpreting events that is prominent in depression, in that if ketamine reduces the ability of negative outcomes to alter behavior, this may be a mechanism for its rapid acting antidepressant effects.

      However, there is a very strong assumption in this regard, as shown by the first sentence of the discussion which implies this is a systematic study of ketamine's acute antidepressant effects. In actuality, this is a study of the acute effects of ketamine on reinforcement learning (RL) modeled parameters. A primary concern here is that an effect presented as a "robust antidepressant-like behavioral effect" should be more enduring than just an alteration during the acute administration. As it is, the link to an "anti-depressant effect" is based solely on the selective effects on losses. This is not to say this is not an interesting observation, worthy of exploration. It is noted that a similar lack of enduring effects on outcome evaluation is observed in humans, as shown in supplemental fig. S4, but there is not accompanying citation for the human work.

      We agree with the reviewer that the way we linked the study results to ketamine’s antidepressant action can be misleading and based on a rather strong assumption which was not systematically tested in the study. We made the following changes to the manuscript:

      (1) These results constitute a rare report of a robust antidepressant-like behavioral effect produced by therapeutic doses of ketamine during acute phase (<1 hour) after injection (Introduction, 3rd paragraph, line 8-9 in the original manuscript).

      Changed to: These results constitute a rare report of an acute effect of therapeutic dose of ketamine on the processing of affectively negative events during dynamic decision-making.

      (2) We clarified in the Discussion that our study is to gain insights into, but not a systematic investigation of ketamine’s antidepressant action as follows:

      (2.1) A sentence was added (1st paragraph of Discussion): Using a token-based decision task and extensive computational modeling, we examined the behavioral modulation induced by therapeutic doses of ketamine to gain insights into possible early signs of ketamine’s antidepressant activity.

      (2.2) Consistent with the findings from humans, ketamine’s effect on outcome evaluation was acute and did not last over subsequent days (Supplemental Figure S4) (Discussion, 2nd paragraph, line 6-7 in the original manuscript).

      Changed to: While ketamine’s antidepressant effect is reported to be sustained over a week of period (5), ketamine’s effect on outcome evaluation was acute and did not last over subsequent days (Supplemental Figure S4). This discrepancy might be attributable to the possible differences in the state of brain network between healthy subjects and those with depression as well as the type of measures taken to assess ketamine’s effect.

      (2.3) A sentence was added (Discussion, last sentence of the 2nd paragraph) : Nevertheless, systematic studies are required to understand whether the reduced aversiveness to loss in our task might share the same mechanisms that underlie ketamine’s antidepressant action.

      One question that comes to mind in terms of the selectivity observed is whether similar work has been done to examine the acute effects of any other drugs. If ketamine is unique in this regard, that would be quite interesting.

      We think this is an interesting idea. However, comparing ketamine’s effect to that of other drugs is not the scope of the current study. We hope that we will be able to answer this question with future studies.

      Reviewer #2 (Public Review):

      Oemisch and Seo set out to examine the effects of low-dose ketamine on reinforcement learning, with the idea that alterations in reinforcement learning and/or motivation might inform our understanding of what alterations co-occur with potential antidepressant effects. Macaques performed a reinforced/punished matching pennies task while under effects of saline or ketamine administration and the data were fit to a series of reinforcement learning models to determine which model described behavior under saline most closely and then what parameters of this best-fitting model were altered by ketamine. They found a mixed effect, with two out of three macaques primarily exhibiting an effect of ketamine on processing of losses and one out of three macaques exhibiting an effect of ketamine on processing of losses and perseveration. They found that these effects of ketamine appeared to be dissociable from the nystagmus effects of the ketamine.

      The findings are novel and the data suggesting that ketamine is primarily having its effects on processing of losses (under the procedures used) are solid. However, it is unclear whether the connection between processing of losses and the antidepressant effects of ketamine is justified and the current findings may be more useful for those studying reinforcement learning than those studying depression and antidepressant effects. In addition, the co-occurrence of different behavioral procedures with different patterns of ketamine effects, with one macaque tested with different parameters than the other two exhibiting effects of ketamine that were best fit with a different model than the other two macaques, suggests that there may be difficulty in generalizing these findings to reinforcement learning more generally.

      (1) First, the authors should be more explicit and careful in the connection they are trying to make about the link between loss processing and depression. The authors call their effect a "robust antidepressant-like behavioral effect" but there are no references to support this or discussion of how the altered loss processing would relate directly to the antidepressant effects.

      We agree with the reviewer’s point on the way we made the connection between the study results and ketamine’s antidepressant action. This concern overlaps with the reviewer #1’s concern. Please refer to our response 2, 2-1, 2-2 and 2-3.

      (2) It appears that the monkey P was given smaller rewards and punishers than the other two monkeys and this monkey had an effect of ketamine on perseveration that was not observed in the other two monkeys. Is this believed to be due to the different task, or was this animal given a different task because of some behavioral differences that preceded the experiment? The authors should also discuss what these differences may mean for the generality of their findings. For example, might there be some set of parameters where ketamine would only alter perseveration and not processing of losses?

      Although the best-fitting ketamine model for monkey P includes an additional element – perseveration, we believe that monkey P’s baseline behavior and ketamine’s effect are not significantly different from the other two monkeys for the following reasons.

      First, monkey P was the first animal that we tested ketamine’s effect, and therefore we aimed to match the other two monkeys’ baseline behavior similar to monkey P’s behavior in order to reduce variability in ketamine’s effect potentially attributable to the difference in baseline behavior before pharmacological manipulation. We had to adjust the payoff matrix for the subsequent animals (Y and B) because these monkeys were more sensitive to loss, and seldom chose “risky” target (yielding loss). In order to make the other two monkeys’ behavior similar to that of monkey P, we adjusted the asymmetry between the risky and the safe target in the way that loss (neutral) outcome occurred from the safe (risky) target as well. Eventually, this adjustment made the baseline behavior similar across all three monkeys. The goal of the study was to reliably measure the ketamine’s effect, and not to study individual differences that can naturally occur with the same task parameters. Therefore, we believe that the adjustment of payoff matrix helped to reliably detect ketamine’s effect starting from the common baseline behavior.

      Second, the best-fitting model for monkey P (K-model 7) and that for the other two monkeys (K-model 4) make very similar predictions both qualitatively and quantitatively as are seen in the revised Figure 4. The parameters for outcome values estimated from these two models in monkey P are very similar as is seen in the revised Table 3. In addition, the difference in BIC between the model which includes only perseveration modulation (K-model 6) and the model incorporating outcome value modulation as well (K-model 7) is 441, whereas the difference in BIC between K-model 7 and the model that includes only outcome value modulation (K-model 4) is as small as 4. These BIC results indicate that the variability explained by ketamine’s modulation of outcome evaluation is remarkably larger that that explained by its modulation of perseveration in monkey P.

      Therefore, we conclude that ketamine’s effect was not significantly different between monkey P and the other two monkeys. We clarified this in the revised manuscript by adding the following paragraph in the Result section:

      “Unlike monkey Y and B, the best-fitting model for monkey P indicated that ketamine increased overall tendency to switch choice in addition to outcome-dependent modulation of outcome evaluation. However, BIC differed only slightly (dBIC = 3.99) between the best-fitting (K-model 7) and the second-best model (K-model 4) and the model predictions for choice behavior were very similar both qualitatively and quantitatively (Table 3, Figure 4). We conclude that the behavioral effects of ketamine were consistent across all three monkeys.”

      (3) The authors should discuss whether the plasma ketamine levels they observed are similar to those seen with rapid antidepressant ketamine or are higher or lower.

      We added a sentence in the first paragraph of the Result section as follows with a reference.

      “Plasma concentration and its time course over 60 minutes were also comparable to those measured after 0.5mg/kg in human subjects (35).”

      (35) Zarate CA, Brutsche N, Laje G, Luckenbaugh DA, Venkata SLV, Ramamoorthy A, et al (2012): Relationship of ketamine’s plasma metabolites with response, diagnosis, and side effects in major depression. Biol Psychiatry, 72: 331-338.

      (4) For Figure 4 or S3, the authors should show the data fitted to model 7, which was the best for one of the animals.

      We added the parameters and model predictions from both K-model 7 and K-model 4 for monkey P to help comparison between two models in Table 3, and Figure 4. Revised Table 3 and Figure 4 are as follows:

      Author response table 1.

      Maximum likelihood parameter estimates of the best models for saline and ketamine sessions.

      In all three animals, the model incorporating valence-dependent change in outcome evaluation best fit the choice data from ketamine sessions with (K-model 7 in the parenthesis, P) or without (K-model 4, P and Y/B) additional change in the tendency of choice perseveration (Figure 3, Table 3).

      Author response image 1.

      ketamine-induced behavioral modulation simulated with differential forgetting model (for saline session) and best-fitting K-model (for ketamine session).

    1. Author Response

      The following is the authors’ response to the original reviews.

      Public Reviews:

      The study could also valuably explore what kinds of genes experienced what forms of expression evolution. A brief description of GO terms frequently represented in genes which showed strong patterns of expression evolution might be suggestive of which selective pressures led to the changes in expression in the C. bursa-pastoris lineage, and to what extent they related to adaptation to polyploidization (e.g. cell-cycle regulators), compensating for the initial pollen and seed inviability or adapting to selfing (endosperm- or pollen-specific genes), or adaptation to abiotic conditions. ”

      We did not include a gene ontology (GO) analysis in the first place as we did not have a clear expectation on the GO terms that would be enriched in the genes that are differentially expressed between resynthesized and natural allotetraploids. Even if we only consider adaptive changes, the modifications could occur in various aspects, such as stabilizing meiosis, adapting to the new cell size, reducing hybrid incompatibility and adapting to self-fertilization. And each of these modifications involves numerous biological processes and molecular functions. As we could make post-hoc stories for too many GO terms, extrapolating at this stage have limited implications and could be misleading.

      Nonetheless, we are not the only study that compared newly resynthesized and established allopolyploids. GO terms that were repeatedly revealed by this type of exploratory analysis may give a hint for future studies. For this reason, now we have reported the results of a simple GO analysis.

      Recommendations for the authors: please note that you control which, if any, revisions, to undertake

      The majority of concerns from reviewers and the reviewing editor are in regards to the presentation of the manuscript; that the framing of the manuscript does not help the general reader understand how this work advances our knowledge of allopolyploid evolution in the broad sense. The manuscript may be challenging to read for those who aren't familiar with the study system or the genetic basis of polyploidy/gene expression regulation. Further, it is difficult to understand from the introduction how this work is novel compared to the recently published work from Duan et al and compared to other systems. Because eLife is a journal that caters to a broad readership, re-writing the introduction to bring home the novelty for the reader will be key.

      Additionally, the writing is quite technical and contains many short-hands and acronyms that can be difficult to keep straight. Revising the full text for clarity (and additionally not using acronyms) would help highlight the findings for a larger audience.

      Reviewer #1 (Recommendations For The Authors):

      Most of my suggestions on this interesting and well-written study are minor changes to clarify the writing and the statistical approaches.

      The use of abbreviations throughout for both transcriptional phenomena and lines is logical because of word limits, but for me as a reader, it really added to the cognitive burden. Even though writing out "homoeolog expression bias" or "hybridization-first" every time would add length, I would find it easier to follow and suspect others would too.

      Thank you for this suggestion. Indeed, using less uncommon acronyms or short-hands should increase the readability of the text for broader audience. Now in most places, we refer to “Sd/Sh” and “Cbp” as “resynthesized allotetraploids” and “natural allotetraploids”, respectively. We have also replaced the most occurrences of the acronyms for transcriptional phenomena (ELD, HEB and TRE) with full phrases, unless there are extra attributes before them (such as “Cg-/Co-ELD” and “relic/Cbp-specific ELD”).

      It would be helpful to include complete sample sizes to either a slightly modified Figure 1 or the beginning of the methods, just to reduce mental arithmetic ("Each of the five groups was represented by six "lines", and each line had six individuals" so there were 180 total plants, of which 167 were phenotyped - presumably the other 13 died? - and 30 were sequenced).

      The number 167 only applied to floral morphorlogical traits (“Floral morphological traits were measured for all five groups on 167 plants…”), but the exact total sample size for other traits differed. Now the total sample sizes of other traits have also been added to beginning of the second paragraph of the methods.

      For this study 180 seedings have been transplanted from Petri dishes to soil, but 8 seedlings died right after transplanting, seemingly caused by mechanical damage and insufficient moistening. Later phenotyping (2020.02-2020.05) was also disrupted by the COVID-19 pandemic, and some individuals were not measured as we missed the right life stages. Specifically, 5 individuals were missing for floral morphological traits (sepal width, sepal length, petal width, petal length, pistil width, pistil length, and stamen length), 30 for pollen traits, 1 for stem length, and 2 for flowering time. As for seed traits, we only measured individuals with more than ten fruits, so apart from the reasons mentioned above, individuals that were self-incompatible and had insufficient hand-pollination were also excluded. We spotted another mistake during the revision: two individuals with floral morphological measurements had no positional information (tray ID). These measurements were likely mis-sampled or mislabeled, and were therefore excluded from analysis. We assumed most of these missing values resulted from random technical mistakes and were not directly related to the measured traits.

      In general, the methods did a thorough job of describing the genomics approaches but could have used more detail for the plant growth (were plants randomized in the growth chamber, can you rule out block/position effects) and basic statistics (what statistical software was used to perform which tests comparing groups in each section, after the categories were identified).

      When describing the methods, mention whether the plants; this should be straightforward as a linear model with position as a covariate.

      Data used in the present study and a previously published work (Duan et al., 2023) were different subsets of a single experiment. For this reason, we spent fewer words in describing shared methods in this manuscript but tried to summarize some methods that were essential for understanding the current paper. But as you have pointed out, we did miss many important details that should have been kept. Now we have added some description and a table (Supplementary file 1) in the “Plant material” section for explaining randomization, and added more information of the software used for performing statistic tests in the “Phenotyping” section.

      Although we did not mention in the present manuscript, we used a randomized block design for the experiment (Author response image 1).

      Author response image 1.

      Plant positions inside the growth chamber. Plants used in the present study and Duan et al. (2023) were different subsets of a single experiment. The entire experiment had eight plant groups, including the five plant groups used in the present study (diploid C. orientalis (Co2), diploid C. grandiflora (Cg2), “whole-genome-duplication-first” (Sd) and “hybridization-first”(Sh) resynthesized allotetraploids, and natural allotetraploids, C. bursa pastoris (Cbp), as well as three plant groups that were only used in Duan et al. (2023; tetraploid C. orientalis (Co4), tetraploid C. grandiflora (Cg4) and diploid hybrids (F)). Each of the eight plant groups had six lines and each line represented by six plants, resulting in 288 plants (8 groups x 6 lines x 6 individuals = 288 plants). The 288 plants were grown in 36 trays placed on six shelves inside the same growth chamber. Each tray had exactly one plant from each of the eight groups, and the position of the eight plants within each tray (A-H) were randomized with random.shuffle() method in Python (Supplementary file 1). The position of the 36 trays inside the growth room (1-36) was also random and the positions of all trays were shuffled once again 28 days after germination (randomized with RAND() and sorting in Microsoft Excel Spreadsheet). (a) Plant distribution; (b) An example of one tray; (c) A view inside the growth chamber, showing the six benches.

      With the randomized block design and one round of shuffling, positional effect is very unlikely to bias the comparison among the five plant groups. The main risk of not adding positions to the statistical model is increasing error variance and decreasing the statistical power for detecting group effect. As we had already observed significant among-group variation in all phenotypic traits (p-value <2.2e-16 for group effect in most tests), further increasing statistical power is not our primary concern. In addition, during the experiment we did not notice obvious difference in plant growth related to positions. Although we could have added more variables to account for potential positional effects (tray ID, shelf ID, positions in a tray etc.), adding variables with little effect may reduce statistical power due to the loss of degree of freedom.

      Due to one round of random shuffling, positions cannot be easily added as a single continuous variable. Now we have redone all the statistical tests on phenotypic traits and included tray ID as a categorical factor (Figure 2-Source Data 1). In general, the results were similar to the models without tray ID. The F-values of group effect was only slightly changed, and p-values were almost unchanged in most cases (still < 2.2e-16). The tray effect (df=35) was not significant in most tests and was only significant in petal length (p-value=0.0111), sepal length (p-value=0.0242) and the number of seeds in ten fruits (p-value=0.0367). As expected, positions (tray ID) had limited effect on phenotypic traits.

      Figure 2 - I assume the numbers at the top indicate sample sizes but perhaps add this to the figure caption.

      Statistical power depends on both the total sample size and the sample size of each group, especially the group with the fewest observations. We lost different number of measurements in each phenotypic trait, and for pollen traits we did have a notable loss, so we chose to show sample sizes above each group to increase transparency. Since we had five different sets of sample sizes (for floral morphological traits, stem length, days to flowering, pollen traits and seed traits, respectively), it would be cumbersome to introduce all 25 numbers in figure caption and could be hard for readers to match the sample sizes with results. For this reason, we would like to keep the sample sizes in the figure, and now we have modified the legend to clarify that the numbers above groups are sample sizes.

      ’The trend has been observed in a wide range of organisms, including ...’ - perhaps group Brassica and Raphanobrassica into one clause in the sentence, since separating them out undermines the diversity somewhat.

      Indeed, it is very strange to put “cotton” between two representatives from Brassicaceae. Now the sentence is changed to “… including Brassica (Wu et al., 2018; Li et al., 2020; Wei et al., 2021) and Raphanobrassica (Ye et al., 2016), cotton (Yoo et al., 2013)…”

      The diagrams under the graph in Figure 4B are particularly helpful for understanding the expression patterns under consideration! I appreciated them a lot!

      Thank you for the comment. We also feel the direction of expression level dominance is convoluted and hard to remember, so we adopted the convention of showing the directions with diagrams.

      Reviewer #2 (Recommendations For The Authors):

      The science is very interesting and thorough, so my comments are mostly meant to improve the clarity of the manuscript text:

      • I found it challenging to remember the acronyms for the different gene expression phenomena and had to consistently cross-reference different parts of the manuscript to remind myself. I think using the full phrase once or twice at the start of a paragraph to remind readers what the acronym stands for could improve readability.

      Thank you for this reasonable suggestion. Now we have replaced the most occurrence of acronyms with the full phrases.

      • There are some technical terms, such as "homoeologous synapsis" and "disomic inheritance", which I think are under-defined in the current text.

      Indeed these terms were not well-defined before using in the manuscript. Now we have added a brief explanation for each term.

      • Under the joint action of these forces, allopolyploid subgenomes are further coordinated and degenerated, and subgenomes are often biasedly fractionated" This sentence has some unclear terminology. Does "coordinated" mean co-adapted, co-inherited, or something else? Is "biasedly fractionated" referring to biased inheritance or evolution of one of the parental subgenomes?

      We apologize for not using accurate terms. With “coordinated” we emphasized the evolution of both homoeologs depends on the selection on total expression of both homoeologs, and on both relative and absolute dosages, which may have shifted away from optima after allopolyploidization. “Co-evolved” or “co-adapted” might be a better word.

      But the term "biasedly fractionation" has been commonly used for referring to the phenomenon that genes from one subgenome of polyploids are preferentially retained during diploidization (Woodhouse et al., 2014; Wendel, 2015). Instead of inventing a new term, we prefer to keep the same term for consistency, so readers could link our findings with numerous studies in this field. Now the sentence is changed to “Under the joint action of these forces, allopolyploid subgenomes are further co-adapted and degenerated, and subgenomes are often biasedly retained, termed biased fractionation”.

      • There are a series of paragraphs in the results, starting with "Resynthesized allotetraploids and the natural Cbp had distinct floral morphologies", which consistently reference Figure 1 where they should be referencing Figure 2.

      Thank you for spotting this mistake! Now the numbers have been corrected.

      • ‘The number of pollen grains per flower decreased in natural Cbp’ this wording implies it's the effect of some experimental treatment on Cbp, rather than just measured natural variation.

      Yes, it is not scientifically precise to say this in the Results section, especially when describing details of results. We meant that assuming resynthesized allopolyploids are good approximation of the initial state of natural allotetraploid C. bursa-pastoris, our results indicate that the number of pollen grains had decreased in natural C. bursa-pastoris. But this is an implication, rather than an observation, so the sentence is better rewritten as “Natural allotetraploids had less pollen grains per flower.”

      • ‘The percentage of genes showing complete ELD was altogether limited but doubled between resynthesized allotetraploid groups and natural allotetraploids’ for clarity, I would suggest revising this to something like "doubled in natural allotetraploids relative to resynthesized allotetraploids

      Thank you for the suggestion. The sentence has been revised as suggested.

      • I'm not sure I understand what the difference is between expression-level dominance and homeolog expression bias. It seems to me like the former falls under the umbrella of the latter.

      Expression-level dominance and homeolog expression bias are easily confused, but they are conceptually independent. One gene could have expression-level dominance without any homeolog expression bias, or strong homeolog expression bias without any expression-level dominance. The concepts were well explained in Grover et al., (2012) with nice figures.

      Expression level dominance compares the total expression level of both homoeologs in allopolyploids with the expression of the same gene in parental species, and judges whether the total expression level in allopolyploids is only similar to one of the parental species. The contributions from different homoeologs are not distinguished.

      While homoeolog expression bias compares the relative expression level of each homoeologs in allopolyploids, with no implication on the total expression of both homoeologs.

      Let the expression level of one gene in parental species X and Y be e(X) and e(Y), respectively. And let the expression level of x homoeolog (from species X) and y homoeolog (from species Y) in allopolyploids be e(x) and e(y), respectively.

      Then a (complete) expression level dominance toward species X means: e(x)+e(y)=e(X) and e(x)+e(y)≠e(Y);

      While a homoeolog expression bias toward species X means: e(x) > e(y), or e(x)/e(y) > e(X)/e(Y), depending on the definition of studies.

      Both expression-level dominance and homeolog expression bias have been widely studied in allopolyploids (Combes et al., 2013; Li et al., 2014; Yoo et al., 2014; Hu & Wendel, 2019). As the two phenomena could be in opposite directions, and may be caused by different mechanisms, we think adopting the definitions in Grover et al., (2012) and distinguishing the two concepts would facilitate communication.

      • Is it possible to split up the results in Figure 7 to show which of the two homeologs was lost (i.e. orientalis vs. grandiflora)? Or at least clarify in the legend that these scenarios are pooled together in the figure?

      Maybe using acronyms without explanation made the figure titles hard to understand, but in the original Figure 7 the loss of two homoeologs were shown separately. Figure 7a,c showed the loss of C. orientalis-homoeolog (“co-expession loss”), and Figure 7b,d showed the loss of C. grandiflora-homoeolog (“cg-expession loss”). Now the legends have been modified to explain the Figure.

      • The paragraph starting with "The extant diploid species" is too long, should probably be split into two paragraphs and edited for clarity.

      The whole paragraph was used to explain why the resynthesized allotetraploids could be a realistic approximation of the early stage of C. bursa-pastoris with two arguments:

      1) The further divergence between C. grandiflora and C. orientalis after the formation of C. bursa-pastoris should be small compared to the total divergence between the two parental species; 2) The mating systems of real parental populations were most likely the same as today. Now the two arguments were separated as two paragraphs, and the second paragraph has been shortened.

      • On the other hand, the number of seeds per fruit" implies this is evidence for an alternative hypothesis, when I think it's really just more support for the same idea.

      “On the other hand” was used to contrast the reduced number of pollen grains and the increased number of seeds in natural allotetraploids. As both changes are typical selfing syndrome, indeed the two support the same idea. We replaced the “On the other hand” with “Moreover”.

      • ‘has become self-compatible before the formation" "has become" should be "became".

      The tense of the word has been changed.

      • If natural C. bursa-pastoris indeed originated from the hybridization between C. grandiflora-like outcrossing plants and C. orientalis-like self-fertilizing plants, the selfing syndrome in C. bursa-pastoris does not reflect the instant dominance effect of the C. orientalis alleles, but evolved afterward.’ This sentence should be closer to the end of the paragraph, after the main morphological results are summarized.

      Thank you for the suggestion. The paragraph is indeed more coherent after moving the conclusion sentence.

      References

      Combes, M.C., Dereeper, A., Severac, D., Bertrand, B. & Lashermes, P. (2013) Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures. New Phytologist, 200, 251–260.

      Grover, C.E., Gallagher, J.P., Szadkowski, E.P., Yoo, M.J., Flagel, L.E. & Wendel, J.F. (2012) Homoeolog expression bias and expression level dominance in allopolyploids. New Phytologist, 196, 966–971.

      Hu, G. & Wendel, J.F. (2019) Cis – trans controls and regulatory novelty accompanying allopolyploidization. New Phytologist, 221, 1691–1700.

      Li, A., Liu, D., Wu, J., Zhao, X., Hao, M., Geng, S., et al. (2014) mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in

      Nascent Hexaploid Wheat. The Plant Cell, 26, 1878–1900. Wendel, J.F. (2015) The wondrous cycles of polyploidy in plants. American Journal of Botany, 102, 1753–1756.

      Woodhouse, M.R., Cheng, F., Pires, J.C., Lisch, D., Freeling, M. & Wang, X. (2014) Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Proceedings of the National Academy of Sciences of the United States of America, 111, 5283–5288.

      Yoo, M.J., Liu, X., Pires, J.C., Soltis, P.S. & Soltis, D.E. (2014) Nonadditive Gene Expression in Polyploids. https://doi.org/10.1146/annurev-genet-120213-092159, 48, 485–517.

    1. Author response:

      The following is the authors’ response to the original reviews.

      As you will see, the main changes in the revised manuscript pertain to the structure and content of the introduction. Specifically, we have tried to more clearly introduce our paradigm, the rationale behind the paradigm, why it is different from learning paradigms, and why we study “relief”.

      In this rebuttal letter, we will go over the reviewers’ comments one-by-one and highlight how we have adapted our manuscript accordingly. However, because one concern was raised by all reviewers, we will start with an in-depth discussion of this concern.

      The shared concern pertained to the validity of the EVA task as a model to study threat omission responses. Specifically, all reviewers questioned the effectivity of our so-called “inaccurate”, “false” or “ruse” instructions in triggering an equivalent level of shock expectancy, and relatedly, how this effectivity was affected by dynamic learning over the course of the task.

      We want to thank the reviewers for raising this important issue. Indeed, it is a vital part of our design and it therefore deserves considerable attention. It is now clear to us that in the previous version of the manuscript we may have focused too little on why we moved away from a learning paradigm, and how we made sure that the instructions were successful at raising the necessary expectations; and how the instructions were affected by learning. We believe this has resulted in some misunderstandings, which consequently may have cast doubts on our results. In the following sections, we will go into these issues.

      The rationale behind our instructed design

      The main aim of our study was to investigate brain responses to unexpected omissions of threat in greater detail by examining their similarity to the reward prediction error axioms (Caplin & Dean, 2008), and exploring the link with subjective relief. Specifically, we hypothesized that omission-related responses should be dependent on the probability and the intensity of the expected-but-omitted aversive event (i.e., electrical stimulation), meaning that the response should be larger when the expected stimulation was stronger and more expected, and that fully predicted outcomes should not trigger a difference in responding.

      To this end, we required that participants had varying levels of threat probability and intensity predictions, and that these predictions would most of the time be violated. Although we fully agree with the reviewers that fear conditioning and extinction paradigms can provide an excellent way to track the teaching properties of prediction error responses (i.e., how they are used to update expectancies on future trials), we argued that they are less suited to create the varying probability and intensity-related conditions we required (see Willems & Vervliet, 2021). Specifically, in a standard conditioning task participants generally learn fast, rendering relatively few trials on which the prediction is violated. As a result, there is generally little intraindividual variability in the prediction error responses. This precludes an in-depth analysis of the probability-related effects. Furthermore, conditioning paradigms generally only include one level of aversive outcome: the electrical stimulation is either delivered or omitted. As a result, intensity-related effects cannot be tested. Finally, because CS-US contingencies change over the course of a fear conditioning and extinction study (e.g. from acquisition to extinction), there is never complete certainty about when the US will (not) follow. This precludes a direct comparison of fully predicted outcomes.

      Another added value of studying responses to the prediction error at threat omission outside a learning context is that it can offer a way to disentangle responses to the violation of threat expectancy, with those of subsequent expectancy updating.

      Also note that Rutledge and colleagues (2010), who were the first to show that human fMRI responses in the Nucleus Accumbens comply to the reward prediction error axioms also did not use learning experiences to induce expectancy. In that sense, we argued it was not necessary to adopt a learning paradigm to study threat omission responses.

      Adaptations in the revised manuscript: We included two new paragraphs in the introduction of the revised manuscript to elaborate on why we opted not to use a learning paradigm in the present study (lines 90-112).

      “However, is a correlation with the theoretical PE over time sufficient for neural activations/relief to be classified as a PE-signal? In the context of reward, Caplin and colleagues proposed three necessary and sufficient criteria all PE-signals should comply to, independent of the exact operationalizations of expectancy and reward (the socalled axiomatic approach24,25; which has also been applied to aversive PE26–28). Specifically, the magnitude of a PE signal should: (1) be positively related to the magnitude of the reward (larger rewards trigger larger PEs); (2) be negatively related to likelihood of the reward (more probable rewards trigger smaller PEs); and (3) not differentiate between fully predicted outcomes of different magnitudes (if there is no error in prediction, there should be no difference in the PE signal).”

      “It is evident that fear conditioning and extinction paradigms have been invaluable for studying the role of the threat omission PE within a learning context. However, these paradigms are not tailored to create the varying intensity and probability-related conditions that are required to evaluate the threat omission PE in the light of the PE axioms. First, conditioning paradigms generally only include one level of aversive outcome: the electrical stimulation is either delivered or omitted. As a result, the magnitude-related axiom cannot be tested. Second, in conditioning tasks people generally learn fast, rendering relatively few trials on which the prediction is violated. As a result, there is generally little intra-individual variability in the PE responses. Moreover, because of the relatively low signal to noise ratio in fMRI measures, fear extinction studies often pool across trials to compare omission-related activity between early and late extinction16, which further reduces the necessary variability to properly evaluate the probability axiom. Third, because CS-US contingencies change over the course of the task (e.g. from acquisition to extinction), there is never complete certainty about whether the US will (not) follow. This precludes a direct comparison of fully predicted outcomes. Finally, within a learning context, it remains unclear whether PErelated responses are in fact responses to the violation of expectancy itself, or whether they are the result of subsequent expectancy updating.”

      Can verbal instructions be used to raise the expectancy of shock?

      The most straightforward way to obtain sufficient variability in both probability and intensityrelated predictions is by directly providing participants with instructions on the probability and intensity of the electrical stimulation. In a previous behavioral study, we have shown that omission responses (self-reported relief and omission SCR) indeed varied with these instructions (Willems & Vervliet, 2021). In addition, the manipulation checks that are reported in the supplemental material provided further support that the verbal instructions were effective at raising the associated expectancy of stimulation. Specifically, participants recollected having received more stimulations after higher probability instructions (see Supplemental Figure 2). Furthermore, we found that anticipatory SCR, which we used as a proxy of fearful expectation, increased with increasing probability and intensity (see Supplemental Figure 3). This suggests that it is not necessary to have expectation based on previous experience if we want to evaluate threat omission responses in the light of the prediction error axioms.

      Adaptations in the revised manuscript: We more clearly referred to the manipulation checks that are presented in the supplementary material in the results section of the main paper (lines 135-141).

      “The verbal instructions were effective at raising the expectation of receiving the electrical stimulation in line with the provided probability and intensity levels. Anticipatory SCR, which we used as a proxy of fearful expectation, increased as a function of the probability and intensity instructions (see Supplementary Figure 3). Accordingly, post-experimental questions revealed that by the end of the experiment participants recollected having received more stimulations after higher probability instructions, and were willing to exert more effort to prevent stronger hypothetical stimulations (see Supplementary Figure 2).”

      How did the inconsistency between the instructed and experienced probability impact our results?

      All reviewers questioned how the inconsistency between the instructed and experienced probability might have impacted the probability-related results. However, judging from the way the comments were framed, it seems that part of the concern was based on a misunderstanding of the design we employed. Specifically, reviewer 1 mentions that “To ensure that the number of omissions is similar across conditions, the task employs inaccurate verbal instructions; I.e., 25% of shocks are omitted regardless of whether subjects are told that the probability is 100%, 75%, 50%, 25%, 0%.”, and reviewer 3 states that “... the fact remains that they do not get shocks outside of the 100% probability shock. So learning is occurring, at least for subjects who realize the probability cue is actually a ruse.” We want to emphasize that this was not what we did, and if it were true, we fully agree with the reviewers that it would have caused serious trust- and learning related issues, given that it would be immediately evident to participants that probability instructions were false. It is clear that under such circumstances, dynamic learning would be a big issue.

      However, in our task 0% and 100% instructions were always accurate. This means that participants never received a stimulus following 0% instructions and always received the stimulation of the given intensity on the 100% instructions (see Supplemental Figure 1 for an overview of the trial types). Only for the 25%, 50% and 75% trials an equal reinforcement rate (25%) was maintained, meaning that the stimulation followed in 25% of the trials, irrespective of whether a 25%, 50% or 75% instruction was given. The reason for this was that we wanted to maximize and balance the number of omission trials across the different probability levels, while also keeping the total number of presentations per probability instruction constant. We reasoned that equating the reinforcement rate across the 25%, 50% and 75% instructions should not be detrimental, because (1) in these trials there was always the possibility that a stimulation would follow; and (2) we instructed the participants that each trial is independent of the previous ones, which should have discouraged them to actively count the number of shocks in order to predict future shocks.

      Adaptations in the revised manuscript: We have tried to further clarify the design in several sections of the manuscript, including the introduction (lines 121-125), results (line 220) and methods (lines 478-484) sections:

      Adaptation in the Introduction section: “Specifically, participants received trial-by-trial instructions about the probability (0%, 25%, 50%, 75% and 100%) and intensity (weak, moderate, strong) of a potentially painful upcoming electrical stimulation, time-locked by a countdown clock (see Fig.1A). While stimulations were always delivered on 100% trials and never on 0% trials, most of the other trials (25%-75%) did not contain the expected stimulation and hence provoked an omission PE.”

      Adaptation in the Results section: “Indeed, the provided instructions did not map exactly onto the actually experienced probabilities, but were all followed by stimulation in 25% on the trials (except for the 0% trials and the 100% trials).”

      Adaptation in the Methods section: “Since we were mainly interested in how omissions of threat are processed, we wanted to maximize and balance the number of omission trials across the different probability and intensity levels, while also keeping the total number of presentations per probability and intensity instruction constant. Therefore, we crossed all non-0% probability levels (25, 50, 75, 100) with all intensity levels (weak, moderate, strong) (12 trials). The three 100% trials were always followed by the stimulation of the instructed intensity, while stimulations were omitted in the remaining nine trials. Six additional trials were intermixed in each run: Three 0% omission trials with the information that no electrical stimulation would follow (akin to 0% Probability information, but without any Intensity information as it does not apply); and three trials from the Probability x Intensity matrix that were followed by electrical stimulation (across the four runs, each Probability x Intensity combination was paired at least once, and at most twice with the electrical stimulation).”

      Could the incongruence between the instructed and experienced reinforcement rate have detrimental effects on the probability effect? We agree with reviewer 2 that it is possible that the inconsistency between instructed and experienced reinforcement rates could have rendered the exact probability information less informative to participants, which might have resulted in them paying less attention to the probability information whenever the probability was not 0% or 100%. This might to some extent explain the relatively larger difference in responding between 0% and 25% to 75% trials, but the relatively smaller differences between the 25% to 75% trials.

      However, there are good reasons to believe that the relatively smaller difference between 25% to 75% trials was not caused by the “inaccurate” nature of our instructions, but is inherent to “uncertain” probabilities.

      We added a description of these reasons to the supplementary materials in a supplementary note (supplementary note 4; lines 97-129 in supplementary materials), and added a reference to this note in the methods section (lines 488-490).

      “Supplementary Note 4: “Accurate” probability instructions do not alter the Probability-effect

      A question that was raised by the reviewers was whether the inconsistency between the probability instruction and the experienced reinforcement rate could have detrimental effects on the Probability-related results; especially because the effect of Probability was smaller when only including non-0% trials.

      However, there are good reasons to believe that the relatively smaller difference between 25% to 75% trials was not caused by the “inaccurate” nature of our instructions, but that they are inherent to “uncertain” probabilities.

      First, in a previously unpublished pilot study, we provided participants with “accurate” probability instructions, meaning that the instruction corresponded to the actual reinforcement rate (e.g., 75% instructions were followed by a stimulation in 75% of the trials etc.). In line with the present results and our previous behavioral study (Willems & Vervliet, 2021), the results of this pilot (N = 20) showed that the difference in the reported relief between the different probability levels was largest when comparing 0% and the rest (25%, 50% and 75%). Furthermore the overall effect size of Probability (excluding 0%) matched the one of our previous behavioral study (Willems & Vervliet, 2021): ηp2 = +/- 0.50.”

      Author response image 1.

      Main effect of Probability including 0% : F(1.74,31.23) = 53.94, p < .001, ηp2 = 0.75. Main effect of Probability excluding 0%: F(1.50, 28.43) = 21.03, p < .001, ηp2 = 0.53.

      Second, also in other published studies that used CSs with varying reinforcement rates (which either included explicit written instructions of the reinforcement rates or not) showed that the difference in expectations, anticipatory SCR or omission SCR was largest when comparing the CS0% to the other CSs of varying reinforcement rates (Grings & Sukoneck, 1971; Öhman et al., 1973; Ojala et al., 2022).

      Together, this suggests that when there is a possibility of stimulation, any additional difference in probability will have a smaller effect on the omission responses, irrespective of whether the underlying reinforcement rate is accurate or not.

      Adaptation to methods section: “Note that, based on previous research, we did not expect the inconsistency between the instructed and perceived reinforcement rate to have a negative effect on the Probability manipulation (see Supplementary Note 4).”

      Did dynamic learning impact the believability of the instructions?

      Although we tried to minimize learning in our paradigm by providing instructions that trials are independent from one another, we agree with the reviewers that this cannot preclude all learning. Any remaining learning effects should present themselves by downweighing the effect of the probability instructions over time. We controlled for this time-effect by including a “run” regressor in our analyses. Results of the Run regressor for subjective relief and omission-related SCR are presented in Supplemental Figure 5. These figures show that although there was a general drop in reported relief pleasantness and omission SCR over time, the effects of probability and intensity remained present until the last run. This indicates that even though some learning might have taken place, the main manipulations of probability and intensity were still present until the end of the task.

      Adaptations in the revised manuscript: We more clearly referred to the results of the Blockregressor which were presented in the supplementary material in the results section of the main paper (lines 159-162).

      Note that while there was a general drop in reported relief pleasantness and omission SCR over time, the effects of Probability and Intensity remained present until the last run (see Supplementary Figure 5). This further confirms that probability and intensity manipulations were effective until the end of the task.

      In the following sections of the rebuttal letter, we will go over the rest of the comments and our responses one by one.

      Reviewer #1 (Public Review):

      Summary:

      Willems and colleagues test whether unexpected shock omissions are associated with reward-related prediction errors by using an axiomatic approach to investigate brain activation in response to unexpected shock omission. Using an elegant design that parametrically varies shock expectancy through verbal instructions, they see a variety of responses in reward-related networks, only some of which adhere to the axioms necessary for prediction error. In addition, there were associations between omission-related responses and subjective relief. They also use machine learning to predict relief-related pleasantness, and find that none of the a priori "reward" regions were predictive of relief, which is an interesting finding that can be validated and pursued in future work.

      Strengths:

      The authors pre-registered their approach and the analyses are sound. In particular, the axiomatic approach tests whether a given region can truly be called a reward prediction error. Although several a priori regions of interest satisfied a subset of axioms, no ROI satisfied all three axioms, and the authors were candid about this. A second strength was their use of machine learning to identify a relief-related classifier. Interestingly, none of the ROIs that have been traditionally implicated in reward prediction error reliably predicted relief, which opens important questions for future research.

      Weaknesses:

      To ensure that the number of omissions is similar across conditions, the task employs inaccurate verbal instructions; i.e. 25% of shocks are omitted, regardless of whether subjects are told that the probability is 100%, 75%, 50%, 25%, or 0%. Given previous findings on interactions between verbal instruction and experiential learning (Doll et al., 2009; Li et al., 2011; Atlas et al., 2016), it seems problematic a) to treat the instructions as veridical and b) average responses over time. Based on this prior work, it seems reasonable to assume that participants would learn to downweight the instructions over time through learning (particularly in the 100% and 0% cases); this would be the purpose of prediction errors as a teaching signal. The authors do recognize this and perform a subset analysis in the 21 participants who showed parametric increases in anticipatory SCR as a function of instructed shock probability, which strengthened findings in the VTA/SN; however given that one-third of participants (n=10) did not show parametric SCR in response to instructions, it seems like some learning did occur. As prediction error is so important to such learning, a weakness of the paper is that conclusions about prediction error might differ if dynamic learning were taken into account.

      We thank the reviewer for raising this important concern. We believe we replied to all the issues raised in the general reply above.

      Lastly, I think that findings in threat-sensitive regions such as the anterior insula and amygdala may not be adequately captured in the title or abstract which strictly refers to the "human reward system"; more nuance would also be warranted.

      We fully agree with this comment and have changed the title and abstract accordingly.

      Adaptations in the revised manuscript: We adapted the title of the manuscript.

      “Omissions of Threat Trigger Subjective Relief and Prediction Error-Like Signaling in the Human Reward and Salience Systems”

      Adaptations in the revised manuscript: We adapted the abstract (lines 27-29).

      “In line with recent animal data, we showed that the unexpected omission of (painful) electrical stimulation triggers activations within key regions of the reward and salience pathways and that these activations correlate with the pleasantness of the reported relief.”

      Reviewer #2 (Public Review):

      The question of whether the neural mechanisms for reward and punishment learning are similar has been a constant debate over the last two decades. Numerous studies have shown that the midbrain dopamine neurons respond to both negative and salient stimuli, some of which can't be well accounted for by the classic RL theory (Delgado et al., 2007). Other research even proposed that aversive learning can be viewed as reward learning, by treating the omission of aversive stimuli as a negative PE (Seymour et al., 2004).

      Although the current study took an axiomatic approach to search for the PE encoding brain regions, which I like, I have major concerns regarding their experimental design and hence the results they obtained. My biggest concern comes from the false description of their task to the participants. To increase the number of "valid" trials for data analysis, the instructed and actual probabilities were different. Under such a circumstance, testing axiom 2 seems completely artificial. How does the experimenter know that the participants truly believe that the 75% is more probable than, say, the 25% stimulation? The potential confusion of the subjects may explain why the SCR and relief report were rather flat across the instructed probability range, and some of the canonical PE encoding regions showed a rather mixed activity pattern across different probabilities. Also for the post-hoc selection criteria, why pick the larger SCR in the 75% compared to the 25% instructions? How would the results change if other criteria were used?

      We thank the reviewer for raising this important concern. We believe the general reply above covers most of the issues raised in this comment. Concerning the post-hoc selection criteria, we took 25% < 75% as criterium because this was a quite “lenient” criterium in the sense that it looked only at the effects of interest (i.e., did anticipatory SCR increase with increasing instructed probability?). However, also when the criterium was more strict (e.g., selecting participants only if their anticipatory SCR monotonically increased with each increase in instructed probability 0% < 25% < 50% < 75% < 100%, N = 11 participants), the probability effect (ωp2 = 0.08), but not the intensity effect, for the VTA/SN remained.

      To test axiom 3, which was to compare the 100% stimulation to the 0% stimulation conditions, how did the actual shock delivery affect the fMRI contrast result? It would be more reasonable if this analysis could control for the shock delivery, which itself could contaminate the fMRI signal, with extra confound that subjects may engage certain behavioral strategies to "prepare for" the aversive outcome in the 100% stimulation condition. Therefore, I agree with the authors that this contrast may not be a good way to test axiom 3, not only because of the arguments made in the discussion but also the technical complexities involved in the contrast.

      We thank the reviewer for addressing this additional confound. It was indeed impossible to control for the delivery of shock since the delivery of the shock was always present on the 100% trials (and thus completely overlapped with the contrast of interest). We added this limitation to our discussion in the manuscript. In addition, we have also added a suggestion for a contrast that can test the “no surprise equivalence” criterium.

      Adaptations in the revised manuscript: We adapted lines 358-364.

      “Thus, given that we could not control for the delivery of the stimulation in the 100% > 0% contrast (the delivery of the stimulation completely overlapped with the contrast of interest), it is impossible to disentangle responses to the salience of the stimulation from those to the predictability of the outcome. A fairer evaluation of the third axiom would require outcomes that are roughly similar in terms of salience. When evaluating threat omission PE, this implies comparing fully expected threat omissions following 0% instructions to fully expected absence of stimulation at another point in the task (e.g. during a safe intertrial interval).”

      Reviewer #3 (Public Review):

      We thank the reviewer for their comments. Overall, based on the reviewer’s comments, we noticed that there was an imbalance between a focus on “relief” in the introduction and the rest of the manuscript and preregistration. We believe this focus raised the expectation that all outcome measures were interpreted in terms of the relief emotion. However, this was not what we did nor what we preregistered. We therefore restructured the introduction to reduce the focus on relief.

      Adaptations in the revised manuscript: We restructured the introduction of the manuscript. Specifically, after our opening sentence: “We experience a pleasurable relief when an expected threat stays away1” we only introduce the role of relief for our research in lines 79-89.

      “Interestingly, unexpected omissions of threat not only trigger neural activations that resemble a reward PE, they are also accompanied by a pleasurable emotional experience: relief. Because these feelings of relief coincide with the PE at threat omission, relief has been proposed to be an emotional correlate of the threat omission PE. Indeed, emerging evidence has shown that subjective experiences of relief follow the same time-course as theoretical PE during fear extinction. Participants in fear extinction experiments report high levels of relief pleasantness during early US omissions (when the omission was unexpected and the theoretical PE was high) and decreasing relief pleasantness over later omissions (when the omission was expected and the theoretical PE was low)22,23. Accordingly, preliminary fMRI evidence has shown that the pleasantness of this relief is correlated to activations in the NAC at the time of threat omission. In that sense, studying relief may offer important insights in the mechanism driving safety learning.”

      Summary:

      The authors conducted a human fMRI study investigating the omission of expected electrical shocks with varying probabilities. Participants were informed of the probability of shock and shock intensity trial-by-trial. The time point corresponding to the absence of the expected shock (with varying probability) was framed as a prediction error producing the cognitive state of relief/pleasure for the participant. fMRI activity in the VTA/SN and ventral putamen corresponded to the surprising omission of a high probability shock. Participants' subjective relief at having not been shocked correlated with activity in brain regions typically associated with reward-prediction errors. The overall conclusion of the manuscript was that the absence of an expected aversive outcome in human fMRI looks like a reward-prediction error seen in other studies that use positive outcomes.

      Strengths:

      Overall, I found this to be a well-written human neuroimaging study investigating an often overlooked question on the role of aversive prediction errors, and how they may differ from reward-related prediction errors. The paper is well-written and the fMRI methods seem mostly rigorous and solid.

      Weaknesses:

      I did have some confusion over the use of the term "prediction-error" however as it is being used in this task. There is certainly an expectancy violation when participants are told there is a high probability of shock, and it doesn't occur. Yet, there is no relevant learning or updating, and participants are explicitly told that each trial is independent and the outcome (or lack thereof) does not affect the chances of getting the shock on another trial with the same instructed outcome probability. Prediction errors are primarily used in the context of a learning model (reinforcement learning, etc.), but without a need to learn, the utility of that signal is unclear.

      We operationalized “prediction error” as the response to the error in prediction or the violation of expectancy at the time of threat omission. In that sense, prediction error and expectancy violation (which is more commonly used in clinical research and psychotherapy; Craske et al., 2014) are synonymous. While prediction errors (or expectancy violations) are predominantly studied in learning situations, the definition in itself does not specify how the “expectancy” or “prediction” arises: whether it was through learning based on previous experience or through mere instruction. The rationale why we moved away from a conditioning study in the present manuscript is discussed in our general reply above.

      We agree with the reviewer that studying prediction errors outside a learning context limits the ecological validity of the task. However, we do believe there is also a strength to this approach. Specifically, the omission-related responses we measure are less confounded by subsequent learning (or updating of the wrongful expectation). Any difference between our results and prediction error responses in learning situation can therefore point to this exact difference in paradigm, and can thus identify responses that are specific to learning situations.

      An overarching question posed by the researchers is whether relief from not receiving a shock is a reward. They take as neural evidence activity in regions usually associated with reward prediction errors, like the VTA/SN . This seems to be a strong case of reverse inference. The evidence may have been stronger had the authors compared activity to a reward prediction error, for example using a similar task but with reward outcomes. As it stands, the neural evidence that the absence of shock is actually "pleasurable" is limited-albeit there is a subjective report asking subjects if they felt relief.

      We thank the reviewer for cautioning us and letting us critically reflect on our interpretation. We agree that it is important not to be overly enthusiastic when interpreting fMRI results and to attribute carelessly psychological functions to mere activations. Therefore, we will elaborate on the precautions we took not to minimize detrimental reverse inference.

      First, prior to analyzing our results, we preregistered clear hypotheses that were based on previous research, in addition to clear predictions, regions of interest and a testing approach on OSF. With our study, we wanted to investigate whether unexpected omissions of threat: (1) triggered activations in the VTA/SN, putamen, NAc and vmPFC (as has previously been shown in animal and human studies); (2) represent PE signals; and (3) were related to self-reported relief, which has also been shown to follow a PE time-curve in fear extinction (Vervliet et al., 2017). Based on previous research, we selected three criteria all PE signals should comply to. This means that if omission-related activations were to represent true PE signals, they should comply to these criteria. However, we agree that it would go too far to conclude based on our research that relief is a reward, or even that the omission-related activations represent only PE signals. While we found support for most of our hypotheses, this does not preclude alternative explanations. In fact, in the discussion, we acknowledge this and also discuss alternative explanations, such as responding to the salience (lines 395-397; “One potential explanation is therefore that the deactivation resulted from a switch from default mode to salience network, triggered by the salience of the unexpected threat omission or by the salience of the experienced stimulation.”), or anticipation (line 425-426; “... we cannot conclusively dismiss the alternative interpretation that we assessed (part of) expectancy instead”).

      Second, we have deliberately opted to only use descriptive labels such as omission-related activations when we are discussing fMRI results. Only when we are talking about how the activations were related to self-reported relief, we talk about relief-related activations.

      I have some other comments, and I elaborate on those above comments, below:

      (1) A major assumption in the paper is that the unexpected absence of danger constitutes a pleasurable event, as stated in the opening sentence of the abstract. This may sometimes be the case, but it is not universal across contexts or people. For instance, for pathological fears, any relief derived from exposure may be short-lived (the dog didn't bite me this time, but that doesn't mean it won't next time or that all dogs are safe). And even if the subjective feeling one gets is temporary relief at that moment when the expected aversive event is not delivered, I believe there is an overall conflation between the concepts of relief and pleasure throughout the manuscript. Overall, the manuscript seems to be framed on the assumption that "aversive expectations can transform neutral outcomes into pleasurable events," but this is situationally dependent and is not a common psychological construct as far as I am aware.

      We thank the reviewer for their comment. We have restructured the introduction because we agree with the reviewer that the introduction might have set false expectations concerning our interpretation of the results. The statements related to relief have been toned down in the revised manuscript.

      Still, we want to note that the initial opening statement “unexpected absence of danger constitutes the pleasurable emotion relief” was based on a commonly used definition of relief that states that relief refers to “the emotion that is triggered by the absence of expected or previously experienced negative stimulation ” (Deutsch, 2015). Both aspects that it is elicited by the absence of an otherwise expected aversive event and that it is pleasurable in nature has received considerable empirical support in emotion and fear conditioning research (Deutsch et al., 2015; Leknes et al., 2011; Papalini et al., 2021; Vervliet et al., 2017; Willems & Vervliet, 2021).

      That said, the notion that the feeling of relief is linked to the (reward) prediction error underlying the learning of safety is included in several theoretical papers in order to explain the commonly observed dopaminergic response at the time of threat omission (both in animals and humans; Bouton et al., 2020; Kalisch et al., 2019; Pittig et al., 2020).

      Together, these studies indicate that the definition of relief, and its potential role in threat omission-driven learning is – at least in our research field – established. Still, we felt that more direct research linking feelings of relief to omission-related brain responses was warranted.

      One of the main reasons why we specifically focus on the “pleasantness” of the relief is to assess the hedonic impact of the threat omission, as has been done in previous studies by our lab and others (Leknes et al., 2011; Leng et al., 2022; Papalini et al., 2021; Vervliet et al., 2017; Willems & Vervliet, 2021). Nevertheless, we agree with the reviewer that the relief we measure is a short-lived emotional state that is subjected to individual differences (as are all emotions).

      (2) The authors allude to this limitation, but I think it is critical. Specifically, the study takes a rather simplistic approach to prediction errors. It treats the instructed probability as the subjects' expectancy level and treats the prediction error as omission related activity to this instructed probability. There is no modeling, and any dynamic parameters affected by learning are unaccounted for in this design . That is subjects are informed that each trial is independently determined and so there is no learning "the presence/absence of stimulations on previous trials could not predict the presence/absence of stimulation on future trials." Prediction errors are central to learning. It is unclear if the "relief" subjects feel on not getting a shock on a high-probability trial is in any way analogous to a prediction error, because there is no reason to update your representation on future trials if they are all truly independent. The construct validity of the design is in question.

      (3) Related to the above point, even if subjects veered away from learning by the instruction that each trial is independent, the fact remains that they do not get shocks outside of the 100% probability shock. So learning is occurring, at least for subjects who realize the probability cue is actually a ruse.

      We thank the reviewer for raising these concerns. We believe that the general reply above covers the issues raised in points 2 and 3.

      (4) Bouton has described very well how the absence of expected threat during extinction can create a feeling of ambiguity and uncertainty regarding the signal value of the CS. This in large part explains the contextual dependence of extinction and the "return of fear" that is so prominent even in psychologically healthy participants. The relief people feel when not receiving an expected shock would seem to have little bearing on changing the long-term value of the CS. In any event, the authors do talk about conditioning (CS-US) in the paper, but this is not a typical conditioning study, as there is no learning.

      We fully agree with the reviewer that our study is no typical conditioning study. Nevertheless, because our research mostly builds on recent advances in the fear extinction domain, we felt it was necessary to introduce the fear extinction procedure and related findings. In the context of fear extinction learning, we have previously shown that relief is an emotional correlate of the prediction error driving acquisition of the novel safety memory (CSnoUS; Papalini et al., 2021; Vervliet et al., 2017). The ambiguity Bouton describes is the result of extinguished CS holding multiple meanings once the safety memory is acquired. Does it signal danger or safety? We agree with Bouton that the meaning of the CS for any new encounter will depend on the context, and the passage of time, but also on the initial strength of the safety acquisition (which is dependent on the size of the prediction error, and hence the amount of relief; Craske et al., 2014). However, it was not our objective to directly study the relation of relief to subsequent CS value, and our design is not tailored to do so post hoc.

      (5) In Figure 2 A-D, the omission responses are plotted on trials with varying levels of probability. However, it seems to be missing omission responses in 0% trials in these brain regions. As depicted, it is an incomplete view of activity across the different trial types of increasing threat probability.

      We thank the reviewer for pointing out this unclarity. The betas that are presented in the figures represent the ROI averages from each non-0% vs 0% contrasts (i.e., 25%>0%; 50%>0%; and 75%>0% for the weak, moderate and strong intensity levels). Any positive beta therefore indicates a stronger activation in the given region compared to a fully predicted omission. Any negative beta indicates a weaker activation.

      Adaptations in the revised manuscript: We have adapted the figure captions of figures 2 and 3.

      “The extracted beta-estimates in figures A-D represent the ROI averages from each non0% > 0% contrast (i.e., 25%>0%; 50%>0%; and 75%>0% for the weak, moderate and strong intensity levels). Any positive beta therefore indicates a stronger activation in the given region compared to a fully predicted omission. Any negative beta indicates a weaker activation.”

      (6) If I understand Figure 2 panels E-H, these are plotting responses to the shock versus no-shock (when no-shock was expected). It is unclear why this would be especially informative, as it would just be showing activity associated with shocks versus no-shocks. If the goal was to use this as a way to compare positive and negative prediction errors, the shock would induce widespread activity that is not necessarily reflective of a prediction error. It is simply a response to a shock. Comparing activity to shocks delivered after varying levels of probability (e.g., a shock delivered at 25% expectancy, versus 75%, versus 100%) would seem to be a much better test of a prediction error signal than shock versus no-shock.

      We thank the reviewer for this comment. The purpose of this preregistered contrast was to test whether fully predicted outcomes elicited equivalent activations in our ROIs (corresponding to the third prediction error axiom). Specifically, if a region represents a pure prediction error signal, the 100% (fully predicted shocks) > 0% (fully predicted shock omissions) contrast should be nonsignificant, and follow-up Bayes Factors would further provide evidence in favor of this null-hypothesis.

      We agree with the reviewer that the delivery of the stimulation triggers widespread activations in our regions of interest that confounded this contrast. However, given that it was a preregistered test for the prediction error axioms, we cannot remove it from the manuscript. Instead, we have argued in the discussion that future studies who want to take an axiomatic stance should consider alternative tests to examine this axiom.

      Adaptations in the revised manuscript: We adapted lines 358-364.

      “Thus, given that we could not control for the delivery of the stimulation in the 100% > 0% contrast (the delivery of the stimulation completely overlapped with the contrast of interest), it is impossible to disentangle responses to the salience of the stimulation from those to the predictability of the outcome. A fairer evaluation of the third axiom would require outcomes that are roughly similar in terms of salience. When evaluating threat omission PE, this implies comparing fully expected threat omissions following 0% instructions to fully expected absence of stimulation at another point in the task (e.g. during a safe intertrial interval).”

      Also note that our task did not lend itself for an in-depth analysis of aversive (worse-thanexpected) prediction error signals, given that there was only one stimulation trial for each probability x intensity level (see Supplemental Figure 1). The most informative contrast that can inform us about aversive prediction error signals contrasts all non-100% stimulation trials with all 100% stimulation trials. The results of this contrast are presented in Supplemental Figure 16 and Supplemental Table 11 for completeness.

      (7) I was unclear what the results in Figure 3 E-H were showing that was unique from panels A-D, or where it was described. The images looked redundant from the images in A-D. I see that they come from different contrasts (non0% > 0%; 100% > 0%), but I was unclear why that was included.

      We thank the reviewer for this comment. Our answer is related to that of the previous comment. Figure 3 presents the results of the axiomatic tests within the secondary ROIs we extracted from a wider secondary mask based on the non0%>0% contrast.

      (8) As mentioned earlier, there is a tendency to imply that subjects felt relief because there was activity in "the reward pathway ."

      We thank the reviewer for their comment, but we respectfully disagree. Subjective relief was explicitly probed when the instructed stimulations stayed away. In the manuscript we only talk about “relief” when discussing these subjective reports. We found that participants reported higher levels of relief-pleasantness following omissions of stronger and more probable threat. This was an observation that matches our predictions and replicates our previous behavioral study (Willems & Vervliet, 2021).

      The fMRI evidence is treated separately from the “pleasantness” of the relief. Specifically, we refrain from calling the threat omission-related neural responses “relief-activity” as this would indeed imply that the activation would only be attributed to this psychological function. Instead, we talked about omission-related activity, and we assessed whether it complied to the prediction error criteria as specified by the axiomatic approach.

      Only afterwards, because we hypothesized that omission-related fMRI activation and selfreported relief-pleasantness were related, and because we found a similar response pattern for both measures, we examined how relief and omission-related fMRI activations within our ROIs were related on a trial-by-trial basis. To this end, we entered relief-pleasantness ratings as a parametric modulator to the omission regressor.

      By no means do we want to reduce an emotional experience (relief) to fMRI activations in isolated regions in the brain. We agree with the reviewer that this would be far too reductionist. We therefore also ran a pre-registered LASSO-PCR analysis in order to identify whether a whole-brain pattern of activations can predict subjective relief (independent from the exact instructions we gave, and independent of our a priori ROIs). This analysis used trialby-trial patterns of activation across all voxels in the brain as the predictor and self-reported relief as the outcome variable. It is therefore completely data-driven and can be seen as a preregistered exploratory analysis that is intended to inform future studies.

      (9) From the methods, it wasn't entirely clear where there is jitter in the course of a trial. This centers on the question of possible collinearity in the task design between the cue and the outcome. The authors note there is "no multicollinearity between anticipation and omission regressors in the firstlevel GLMs," but how was this quantified? b The issue is of course that the activity coded as omission may be from the anticipation of the expected outcome.

      We thank the reviewer for pointing out this unclarity. Jitter was introduced in all parts of the trial: i.e., the duration of the inter-trial interval (4-7s), countdown clock (3-7s), and omission window (4-8s) were all jittered (see fig. 1A and methods section, lines 499-507). We added an additional line to the method section.

      Adaptations in the revised manuscript: We added an additional line of to the methods section to further clarify the jittering (lines 498-500).

      “The scale remained on the screen for 8 seconds or until the participant responded, followed by an intertrial interval between 4 and 7 seconds during which only a fixation cross was shown. Note that all phases in the trial were jittered (i.e., duration countdown clock, duration outcome window, duration intertrial interval).”

      Multicollinearity between the omission and anticipation regressors was assessed by calculating the variance inflation factor (VIF) of omission and anticipation regressors in the first level GLM models that were used for the parametric modulation analyses.

      Adaptations in the revised manuscript: We replaced the VIF abbreviation with “variance inflation factor” (line 423-424).

      “Nevertheless, there was no multicollinearity between anticipation and omission regressors in the first-level GLMs (VIFs Variance Inflation Factor, VIF < 4), making it unlikely that the omission responses purely represented anticipation.”

      (10) I did not fully understand what the LASSO-PCR model using relief ratings added. This result was not discussed in much depth, and seems to show a host of clusters throughout the brain contributing positively or negatively to the model. Altogether, I would recommend highlighting what this analysis is uniquely contributing to the interpretation of the findings.

      The main added value of this analyses is that it uses a different approach altogether. Where the (mass univariate) parametric modulation analysis estimated in each voxel (and each ROI) whether the activity in this voxel/ROI covaried with the reported relief, a significant activation only indicated that this voxel was related to relief. However, given that each voxel/ROI is treated independently in this analysis, it remains unclear how the activations were embedded in a wider network across the brain, and which regions contributed most to the prediction of relief. The multivariate LASSO-PCR analysis approach we took attempts to overcome this limitation by examining if a more whole-brain pattern can predict relief. Because we use the whole-brain pattern (and not only our a priori ROIs), this analysis is completely data-driven and is intended to inform future studies. In addition, the LASSO-PCR model was cross-validated using five-fold cross-validation, which is also a difference (and a strength) compared to the mass univariate GLM approach.

      One interesting finding that only became evident when we combined univariate and multivariate approaches is that despite that the parametric modulation analysis showed that omission-related fMRI responses in the ROIs were modulated by the reported relief, none of these ROIs contributed significantly to the prediction of relief based on the identified signature. Instead, some of the contributing clusters fell within other valuation and errorprocessing regions (e.g. lateral OFC, mid cingulate, caudate nucleus). This suggests that other regions than our a priori ROIs may have been especially important for the subjective experience of relief, at least in this task. However, all these clusters were small and require further validation in out of sample participants. More research is necessary to test the generalizability and validity of the relief signature to new individuals and tasks, and to compare the signature with other existing signature models (e.g., signature of pain, fear, reward, pleasure). However, this was beyond the scope of the present study.

      Adaptations in the revised manuscript: We altered the explanation of the LASSO-PCR approach in the results section (lines 286-295) and the discussion (lines 399-402)

      Adaptations in the Results section: “The (mass univariate) parametric modulation analysis showed that omission-related fMRI activity in our primary and secondary ROIs correlated with the pleasantness of the relief. However, given that each voxel/ROI is treated independently in this analysis, it remains unclear how the activations were embedded in a wider network of activation across the brain, and which regions contributed most to the prediction of relief. To overcome these limitations, we trained a (multivariate) LASSO-PCR model (Least Absolute Shrinkage and Selection Operator-Regularized Principle Component Regression) in order to identify whether a spatially distributed pattern of brain responses can predict the perceived pleasantness of the relief (or “neural signature” of relief)31. Because we used the whole-brain pattern (and not only our a priori ROIs), this analysis is completely data driven and can thus identify which clusters contribute most to the relief prediction.”

      Adaptations in the Discussion section: “In addition to examining the PE-properties of neural omission responses in our a priori ROIs, we trained a LASSO-PCR model to establish a signature pattern of relief. One interesting finding that only became evident when we compared the univariate and multivariate approach was that none of our a priori ROIs appeared to be an important contributor to the multivariate neural signature, even though all of them (except NAc) were significantly modulated by relief in the univariate analysis.”

      In addition to the public peer review, the reviewers provided some recommendation on how to further improve our manuscript. We will reply to the recommendations below.

      Reviewer #1 (Recommendations For The Authors):

      Given that you do have trial-level estimates from the classifier analysis, it would be very informative to use learning models and examine responses trial-by-trial to test whether there are prediction errors that vary over time as a function of learning.

      We thank the reviewer for the suggestion. However, based on the results of the run-regressor, we do not anticipate large learning effects in our paradigm. As we mentioned in our responses above, we controlled for time-related drops in omission-responding by including a “run” regressor in our analyses. Results of this regressor for subjective relief and omission-related SCR showed that although there was a general drop in reported relief pleasantness and omission SCR over time, the effects of probability and intensity remained present until the last run. This suggests that even though some learning might have taken place, its effect was likely small and did not abolish our manipulations of probability and intensity. In any case, we cannot use the LASSO-PCR signature model to investigate learning, as this model uses the trial-level brain pattern at the time of US omission to estimate the associated level of relief. These estimates can therefore not be used to examine learning effects.

      Reviewer #2 (Recommendations For The Authors):

      The LASSO-PCR model feels rather disconnected from the rest of the paper and does not add much to the main theme. I would suggest to remove this part from the paper.

      We thank the reviewer for this suggestion. However, the LASSO-PCR analysis was a preregistered. We therefore cannot remove it from the manuscript. We hope to have clarified its added value in the revised version of the manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Valk and Engert et al. examined the potential relations between three different mental training modules, hippocampal structure and functional connectivity, and cortisol levels over a 9-month period. They found that among the three types of mental training: Presence (attention and introspective awareness), Affect (socio-emotional - compassion and prosocial motivation), and Perspective (socio-cognitive - metacognition and perspective taking) modules; Affect training most consistently related to changes in hippocampal structure and function - specifically, CA1-3 subfields of the hippocampus. Moreover, decreases in diurnal cortisol correlated to bilateral increases in volume, and decreases in diurnal and chronic cortisol left CA1-3 functional connectivity. Chronic cortisol levels also related to right CA4/DG volume and left subiculum function. The authors demonstrate that mindfulness training programs impact hippocampus and are a potential avenue for stress interventions, a potential avenue to improve health. The data contribute to the literature on plasticity of hippocampal subfields during adulthood, the impact of mental training interventions on the brain, and the link between CA1-3 and both short- and long-term stress changes. Additional clarification and extension of the methods is needed to strengthen the authors' conclusions.

      We thank the Reviewer for their positive evaluation and summary of our findings and work. We made additional changes as suggested by the Reviewer and hope this clarified any open points.

      (1) The authors thoughtfully approached the study of hippocampal subfields, utilizing a method designed for T1w images that outperformed Freesurfer 5.3 and that produced comparable results to an earlier version of ASHS. However, given the use of normalized T1-weighted images to delineate hippocampal subfield volume, some caution may be warranted (Wisse et al. 2020). While the authors note the assessment of quality control processes, the difficulty in ensuring valid measurement is an ongoing conversation in the literature. This also extends to the impact of functional co-registration using segmentations. I appreciate the inclusion of Table 5 in documenting reasons for missing data across subjects. Providing additional details on the distribution of quality ratings across subfields would help contextualize the results and ensure there is equal quality of segmentations across subfields.

      We thank the Reviewer for bringing up this point. In the current work, we assessed the overall segmentation of all six subfields per individual. Thus, unfortunately, we have no data of quality of segmentation of individual subfields beyond our holistic assessment. Indeed, registration of hippocampal subfields remains a challenge and we have further highlighted this limitation in the Discussion of the current work.

      “It is of note that the current work relies on a segmentation approach of hippocampal subfields including projection to MNI template space, an implicit correction for total brain volume through the use of a stereotaxic reference frame. Some caution for this method may be warranted, as complex hippocampal anatomy can in some cases lead to over- as well as underestimation of subfield volumes, as well as subfield boundaries may not always be clearly demarcated (1). Future work, studying the hippocampal surface at higher granularity, for example though unfolding the hippocampal sheet (2-5), may further help with both alignment and identification of not only subfield-specific change but also alterations as a function of the hippocampal long axis, a key dimension of hippocampal structural and functional variation that was not assessed in the current work (6, 7).”

      (2) Given the consistent pattern of finding results with CA1-3, in contrast to other subfields, it would help to know if the effects of the different training modules on subfields differed from each other statistically (i.e., not just that one is significant, and one is not) to provide an additional context of the strength of results focused on Affect training and CA1-3 (for example, those shown in Figure 3).

      Our work investigated i) whether the effects of the individual Training Modules differed from each other statistically. We found that the Affect Training Module showed increases in CA1-3 volume, and that these increases remained when testing effects relative to changes in this subfield following Perspective training and in retest controls. Moreover, in CA1-3 we found changes in functional connectivity when comparing the Affect to Perspective training Module. These changes were only present in this contrast, but not significant in each of the Training Modules per se. To test for specificity, we additionally evaluated whether subfield-specific changes were present above and beyond changes in the other ipsilateral hippocampal subfields. Relative to other subfields, right CA1-3 showed increases in the Affect vs Perspective contrast (left: t-value: 2.298, p=0.022, Q>0.1; right: t-value: 3.045, p=0.0025, Q=0.015). No other subfield showed significant changes. We now include this statement in the revised Results and Supplementary Tables.

      “Moreover, associations between CA1-3 and Affect, relative to Perspective, seemed to go largely above and beyond changes in the other subfields (left: t-value: 2.298, p=0.022, Q>0.1; right: t-value: 3.045, p=0.0025, Q=0.015, see further Supplementary File 1h).”

      Author response table 1.

      Subfield-specific changes following the Training Modules, controlling for the other two ipsilateral subfields

      Reviewer #1 (Recommendations For The Authors):

      (1) In Figure 1, using different colors for subfields versus the modules (yellow, red, green) would help as it could lead the reader to try to draw connections between the two when it is namely a depiction of the delineations.

      As suggested, we updated Figure 1 accordingly and present the subfields in different shades of purple for clarity. Please find the updated figure below.

      Author response image 1.

      (2) In the Results, it was at times hard to follow when Affect off Perspective where the focus of the results. Perhaps the authors could restructure or add additional context for clarity.

      We are happy to clarify. For the first analysis on Module-specific changes in hippocampal subfield volume, we compared effects across Training Modules. Here, main contrasts were ran between subjects: Presence vs active control and within subjects: Affect versus Perspective. In additional secondary contrasts, we studied training effects vs retest control. After observing consistent increases in bilateral CA1-3 following Affect, in the following analysis, we evaluated 1) intrinsic functional networks in main and supplementary contrasts and 2) diurnal cortisol measures within the Training modules only and all three Training Modules combined, and also adopted 3) a multivariate approach (PLS) (see comments Reviewer 2). We now also report effects of cortisol change on structural and functional subfield change in Presence and Perspective, for additional completeness and clarity.

      “To study whether there was any training module-specific change in hippocampal subfield volumes following mental training, we compared training effects between all three Training Modules (Presence, Affect, and Perspective). Main contrasts were: Presence vs Active control (between subjects) and Affect vs Perspective (within subjects). Supplementary comparisons were made vs retest controls and within training groups.”

      “Overall, for all hippocampal subfields, findings associated with volume increases in CA1-3 fol-lowing the Affect training were most consistent across timepoints and contrasts (Supplementary File 1a-f).”

      “Subsequently, we studied whether hippocampal CA1-3 would show corresponding changes in intrinsic function following the Affect mental training.”

      “In particular, the moderately consistent CA1-3 volume increases following Affect training were complemented with differential functional connectivity alterations of this subfield when comparing Affect to Perspective training”

      “Last, we probed whether group-level changes in hippocampal subfield CA1-3 volume would correlate with individual-level changes in diurnal cortisol indices (Presence: n= 86; Affect: n=92; Perspective: n=81), given that the hippocampal formation is a nexus of the HPA-axis (8). We took a two-step approach. First, we studied associations between cortisol and subfield change, particularly focusing on the Affect module and CA1-3 volume based on increases in CA1-3 volume identified in our group-level analysis.”

      “We observed that increases in bilateral CA1-3 following Affect showed a negative association with change in total diurnal cortisol output […]”

      “We did not observe alterations in CA1-3 volume in relation to change in cortisol markers in Presence or Perspective. Yet, for Presence, we observed association between slope and LCA4/DG change (t=-2.89, p=0.005, q=0.03), (Supplementary File 1uv).”

      “In case of intrinsic function, we also did not observe alterations in CA1-3 in relation to change in cortisol markers in Presence or Perspective, nor in other subfields (Supplementary File 1wx).”

      Author response table 2.

      Correlating change in subfield volume and diurnal cortisol indices in Presence. Main focus was on CA1-3 based on volumetric observations and are highlighted in bold.

      Author response table 3.

      Correlating change in subfield volume and diurnal cortisol indices in Perspective. Main focus was on CA1-3 based on volumetric observations and are highlighted in bold.

      Author response table 4.

      Association between stress-markers and within functional network sub-regions in Affect and Perspective.

      Author response table 5.

      Correlating change in subfield function and diurnal cortisol indices in Presence. Main focus was on CA1-3 based on volumetric observations and are highlighted in bold. For these multiple comparisons (FDRq, corrected for two subfields) values are reported if uncorrected p values are below p<.05.

      Author response table 6.

      Correlating change in subfield function and diurnal cortisol indices in Perspective. Main focus was on CA1-3 based on volumetric observations and are highlighted in bold. For these multiple comparisons (FDRq, corrected for two subfields) values are reported if uncorrected p values are below p<.05.

      (3) In the Methods, the authors note that corrections for multiple comparisons were used where needed, throughout the manuscript there is some switching between corrected and uncorrected p-values. At times, this made it difficult to follow in terms of when these corrections were needed.

      For clarity, we added explicit multiple comparisons information a) in main and supplementary results, and b) wherever extra information was needed. Also, we only included main contrasts in Table 1-3 to avoid confusion and moved the information on changes in SUB and CA4/DG to the Supplementary tables.

      (4) Typically, when correcting for intracranial volume the purpose is the ensure that sexual dimorphism in the size of the brain is accounted for. I would recommend the authors assess whether sex differences are accounted for by the MNI normalization approach taken. In the reading of the original Methods paper for the patch-based algorithm used, ICV was used to transform to MNI152 space. It would help to have additional information on how the normalization was done in the current study in order to draw comparisons to other findings in the literature.

      We are happy to further clarify. In the current work, we used the same approach as in the original paper. Volumes were linearly registered to the MNI template using FSL flirt. We now provided this additional information in the revised methods.

      “Hippocampal volumes were estimated based on T1w data that were linearly registered to MNI152 using FSL flirt (http://www.fmrib.ox.ac.uk/fsl/), such that intracranial volume was implicitly controlled for.”

      We agree with the Reviewer that sex differences may still be present, and investigated this. At baseline, sex differences were found in all subfields in the left hemisphere, and right CA4/DG (FDRq<0.05). Regressing out ICV resolved remaining sex differences. We then evaluated whether main results of volumetric subfield change were impacted by ICV differences. Differences between Affect and Perspective remained stable. We have now added this additional analysis in the Supplementary Materials.

      “Although stereotaxic normalization to MNI space would in theory account for global sex differences in intra-cranial volume, we still observed sex differences in various subfield volumes at baseline. Yet, accounting for ICV did not impact our main results suggesting changes in CA1-3 following Affect were robust to sex differences in overall brain volume (Supplementary File1j).”

      Author response table 7.

      Sex differences (female versus male) in hippocampal subfield volumes.

      Reviewer #2 (Public Review):

      In this study, Valk, Engert et al. investigated effects of stress-reducing behavioral intervention on hippocampal structure and function across different conditions of mental training and in relation to diurnal and chronic cortisol levels. The authors provide convincing multimodal evidence of a link between hippocampal integrity and stress regulation, showing changes in both volume and intrinsic functional connectivity, as measured by resting-state fMRI, in hippocampal subfield CA1-3 after socio-affective training as compared to training in a socio-cognitive module. In particular, increased CA1-3 volume following socio-affective training overlapped with increased functional connectivity to medial prefrontal cortex, and reductions in cortisol. The conclusions of this paper are well supported by the data, although some aspects of the data analysis would benefit from being clarified and extended.

      A main strength of the study is the rigorous design of the behavioral intervention, including test-retest cohorts, an active control group, and a previously established training paradigm, contributing to an overall high quality of included data. Similarly, systematic quality checking of hippocampal subfield segmentations contributes to a reliable foundation for structural and functional investigations.

      We thank the Reviewer for the thoughtful summary and appreciation of our work, as well as requests for further clarification and analyses. We addressed each of them in a point by point fashion below.

      Another strength of the study is the multimodal data, including both structural and functional markers of hippocampal integrity as well as both diurnal and chronic estimates of cortisol levels.

      (1) However, the included analyses are not optimally suited for elucidating multivariate interrelationships between these measures. Instead, effects of training on structure and function, and their links to cortisol, are largely characterized separately from each other. This results in the overall interpretation of results, and conclusions, being dependent on a large number of separate associations. Adopting multivariate approaches would better target the question of whether there is cortisol-related structural and functional plasticity in the hippocampus after mental training aimed at reducing stress.

      We thank the Reviewer for this suggestion. Indeed, our project combined different univariate analyses to uncover the association between hippocampal subfield structure, function, and cortisol markers. While systematic, a downside of this approach is indeed that interpretation of our results depend on a large number of analyses. To further explore the question whether there is cortisol-related structural and functional plasticity in the hippocampus, we followed the Reviewer’s suggestion and additionally adopted a multivariate partial least squares (PLS) model. We ran two complementary models. One focusing on the bilateral CA1-3, as this region showed increases in volume following Affect training and differential change between Affect and Perspective training in our resting state analyses and one model including all subfields. Both models included all stress markers. We found that both models could significantly relate stress markers to brain measures, and that in particular Affect showed strong associations with significant the latent markers. Both analyses showed inverse effects of structure and function in relation to stress markers and both slope and AUC changes showed strongest loadings. We now include these analyses the revised manuscript.

      Abstract

      “Of note, using a multivariate approach we found that other subfields, showing no group-level changes, also contributed to alterations in cortisol levels, suggesting circuit-level alterations within the hippocampal formation.”

      Methods

      “Partial least squares analysis

      To assess potential relationships between cortisol change and hippocampal subfield volume and functional change, we performed a partial least squares analysis (PLS) (9, 10). PLS is a multivariate associative model that to optimizes the covariance between two matrices, by generating latent components (LCs), which are optimal linear combinations of the original matrices (9, 10). In our study, we utilized PLS to analyze the relationships between change in volume and intrinsic function of hippocampal subfields and diurnal cortisol measures. Here we included all Training Modules and regressed out effects of age, sex, and random effects of subject on the brain measures before conducting the PLS analysis. The PLS process involves data normalization within training groups, cross-covariance, and singular value decomposition. Subsequently, subfield and behavioral scores are computed, and permutation testing (1000 iterations) is conducted to evaluate the significance of each latent factor solution (FDR corrected). We report then the correlation of the individual hippocampal and cortisol markers with the latent factors. To estimate confidence intervals for these correlations, we applied a bootstrapping procedure that generated 100 samples with replacement from subjects’ RSFC and behavioral data.”

      Results

      “Last, to further explore the question whether there is concordant cortisol-related structural and functional plasticity in the hippocampus we adopted a multivariate partial least square approach, with 1000 permutations to account for stability (9, 10) and bootstrapping (100 times) with replacement. We ran two complementary models including all Training Modules whilst regressing out age, sex and random effects of subject. First, we focused on the bilateral CA1-3, as this region showed increases in volume following Affect training and differential change between Affect and Perspective training in our resting state analyses. In the second model included structural and functional data of all subfields. Both models included all stress markers. We found that both models could identify significant associations between cortisol stress markers and hippocampal plasticity (FDRq<0.05), and that in particular Affect showed strongest associations with the latent markers for CA1-3 (Table 5). Both analyses showed inverse effects of subfield structure and function in relation to stress markers and both slope and AUC changes showed strongest associations with the latent factor.”

      Author response table 8.

      Multivariate PLS analyses linking cortisol markers to hippocampal subfield volume and function.

      Discussion

      “Last, performing multivariate analysis, we again observed associations between CA1-3 volume and function plasticity and stress change, strongest in Affect. Yet combining all subfields in a single model indicated that other subfields also link to stress alterations, indicating that ultimately circuit-level alterations within the hippocampal formation relate to latent changes in diurnal stress markers across Training Modules.”

      “This interpretation is also supported by our multivariate observations.”

      “In line with our observations in univariate analysis, we found multivariate associations between hippocampal subfield volume, intrinsic function and cortisol markers. Again, the contribution of volume and intrinsic function was inverse. This may possibly relate to the averaging procedure of the functional networks. Combined, outcomes of our univariate and multivariate analyses point to an association between change in hippocampal subfields and stress markers, and that these changes, at the level of the individual, ultimately reflect complex interactions within and across hippocampal subfields and may capture different aspects of diurnal stress. Future work may more comprehensively study the plasticity of the hippocampal structure, and link this to intrinsic functional change and cortisol to gain full insights in the specificity and system-level interplay across subfields, for example using more detailed hippocampal models (3). Incorporating further multivariate, computational, models is needed to further unpack and investigate the complex and nuanced association between hippocampal structure and function, in particular in relation to subfield plasticity and short and long-term stress markers.”

      “…based on univariate analysis. Our multivariate analysis further nuanced this observation, but again pointed to an overall association between hippocampal subfield changes and cortisol changes, but this time more at a systems level.”

      “Lastly, our multivariate analyses also point to a circuit level understanding of latent diurnal stress scores.”

      Author response image 2.

      Multivariate associations between changes in structure and function of hippocampal subfield volume and markers of stress change in Affect. A) Multivariate associations between bilateral CA1-3 volume and intrinsic function and stress markers. Left: Scatter of loadings, colored by Training Module; Right upper: individual correlations of stress markers; Right lower: individual correlation of subfields; B). Multivariate associations between all subfields’ volume and intrinsic function and stress markers. Left: Scatter of loadings, colored by Training Module; Right upper: individual correlations of stress markers; Right lower: individual correlation of subfields.

      (2) The authors emphasize a link between hippocampal subfield CA1-3 and stress regulation, and indeed, multiple lines of evidence converge to highlight a most consistent role of CA1-3. There are, however, some aspects of the results that limit the robustness of this conclusion. First, formal comparisons between subfields are incomplete, making it difficult to judge whether the CA1-3, to a greater degree than other subfields, display effects of training.

      We thank the Reviewer for this comment. To further test for specificity, we additionally evaluated subfield-specific changes relative to other subfields for our main contrasts (Presence versus Active Control and Affect versus Perspective). Relative to other subfields, right CA1-3 showed increases in the Affect vs Perspective contrast (left: t-value: 2.298, p=0.022, Q>0.1; right: t-value: 3.045, p=0.0025, Q=0.015); no other subfield showed significant changes. We now include this statement in Results and Supplementary Tables.

      “Moreover, associations between CA1-3 and Affect, relative to Perspective, seemed to go largely above and beyond changes in the other subfields (left: t-value: 2.298, p=0.022, Q>0.1; right: t-value: 3.045, p=0.0025, Q=0.015, see further Supplementary File 1h).”

      Author response table 9.

      Subfield-specific changes following the Training Modules, controlling for the other two ipsilateral subfields

      (3) Relatedly, it would be of interest to assess whether changes in CA1-3 make a significant contribution to explaining the link between hippocampal integrity and cortisol, as compared to structure and functional connectivity of the whole hippocampus.

      We thank the Reviewer for this comment. Please see the PLS analysis performed above (R2Q1). Indeed, not only CA1-3 but also other subfields seem to show a relationship with cortisol, in line with circuit level accounts on stress regulation and hippocampal circuit alterations (8, 11-15).

      (4) Second, both structural and functional effects (although functional to a greater degree), were most pronounced in the specific comparison of "Affect" and "Perspective" training conditions, possibly limiting the study's ability to inform general principles of hippocampal stress-regulation.

      We agree with the Reviewer that the association between stress and hippocampal plasticity, on the one hand, and mental training and hippocampal plasticity, on the other hand, make it not very straightforward to inform general principles on hippocampal stress regulation. However, as underscored in the discussion, in previous work we could also link mental training to stress reductions(16-18). We hope that the additional analyses and explanations further explain the multilevel insights of the current work, on the one hand using group-level analysis to investigate and illustrate the association between mental training and hippocampal subfield volume and intrinsic function, and on the other hand using individual level analysis to unpack the association between cortisol change and hippocampal subfield change.

      Reviewer #2 (Recommendations For The Authors):

      (1) In the Results, the description of how the hippocampal subfields' functional networks were defined would benefit from some clarification. It is also somewhat unclear what is meant by (on page 10): "Evaluating functional connectivity changes, we found that connectivity of the right CA1-3 functional network showed differential changes when comparing Affect training to Perspective training (2.420, p=0.016, FDRq=0.032, Cohens D =0.289), but not versus retest control (Table 1 and Supplementary Table 8-14)." Were there significant changes in CA1-3 FC following both training conditions (but these differed from each other)? A description of what this difference reflected would increase the reader's understanding.

      We are happy to clarify. We included information of change of individual modules in the Supplementary materials, Supplementary Table 1 and 2, 9 and 10. Changes for functional connectivity were largely due to the differences in Modules, but did not show strong effects in one Module alone. We now include information on Affect and Perspective un-contrasted change in the main results text:

      “… which could be attributed to decreases in right CA1-3 mean FC following Perspective (t=-2.012, p=0.045, M:-0.024, std: 0.081, CI [-0.041 -0.006]), but not Affect (t=1.691, p=0.092, M: 0.010, std: 0.098, CI [-0.01 0.031]); changes were not present when comparing Affect training versus retest control (Table 1 and Supplementary File 1k-q).”

      (2) As described in the Public Review, the lack of multivariate assessments may risk selling the data short. Including analyses of concomitant functional and structural changes, in relation to cortisol, seems like an approach better adapted to characterize meaningful interrelationships between these measures.

      We thank the Reviewer for suggesting multivariate assessments. To understand the interrelation between behavioral intervention, hippocampal plasticity, and cortisol changes, the current work first evaluates a simpler operationalization of the relationship between hippocampal subfield structure and volume, and cortisol as a function of mental training. Thus, given the complex nature of the study, we initially opted for a model where we assess structural and functional changes independently, with structural changes as the basis of our investigations. Now we have also included a multivariate approach (PLS) to further test the association between hippocampal subfields and cortisol markers, please see our additions to the manuscript above. We now highlighted multivariate associations in the Discussion as well, and suggest this as an important next step for more detailed, future investigations.

      “Incorporating further multivariate, computational, models is needed to further unpack and investigate the complex and nuanced association between hippocampal structure and function, in particular in relation to subfield plasticity and short and long-term stress markers.”

      (3) A minor comment regards the Figures. Some main effects should be visualized in a clearer manner. For instance, the scatterplots in Figure 1, panel D. Also, some of the current headings within the figures could be made more intuitive to the reader.

      We thank the Reviewer for this comment. To improve clarity, we updated figure headings. For Figure 1D, the challenge is that the data are quite scattered and we aimed to visualize our observations in a naturalistic way. Therefore, we added additional y-axis information to further clarify the figures. Creating more overlap or differentiation would make other elements of the figure less clear, hence we remained with the current set-up detailing the intra- and inter-individual alterations of the current model.

      (1) Wisse LEM, Chetelat G, Daugherty AM, de Flores R, la Joie R, Mueller SG, et al. (2021): Hippocampal subfield volumetry from structural isotropic 1 mm(3) MRI scans: A note of caution. Hum Brain Mapp. 42:539-550.

      (2) DeKraker J, Kohler S, Khan AR (2021): Surface-based hippocampal subfield segmentation. Trends Neurosci. 44:856-863.

      (3) DeKraker J, Haast RAM, Yousif MD, Karat B, Lau JC, Kohler S, et al. (2022): Automated hippocampal unfolding for morphometry and subfield segmentation with HippUnfold. Elife. 11.

      (4) Vos de Wael R, Lariviere S, Caldairou B, Hong SJ, Margulies DS, Jefferies E, et al. (2018): Anatomical and microstructural determinants of hippocampal subfield functional connectome embedding. Proc Natl Acad Sci U S A. 115:10154-10159.

      (5) Bernhardt BC, Bernasconi A, Liu M, Hong SJ, Caldairou B, Goubran M, et al. (2016): The spectrum of structural and functional imaging abnormalities in temporal lobe epilepsy. Ann Neurol. 80:142-153.

      (6) Vogel JW, La Joie R, Grothe MJ, Diaz-Papkovich A, Doyle A, Vachon-Presseau E, et al. (2020): A molecular gradient along the longitudinal axis of the human hippocampus informs large-scale behavioral systems. Nat Commun. 11:960.

      (7) Genon S, Bernhardt BC, La Joie R, Amunts K, Eickhoff SB (2021): The many dimensions of human hippocampal organization and (dys)function. Trends Neurosci. 44:977-989.

      (8) McEwen BS (1999): Stress and hippocampal plasticity. Annu Rev Neurosci. 22:105-122.

      (9) Kebets V, Holmes AJ, Orban C, Tang S, Li J, Sun N, et al. (2019): Somatosensory-Motor Dysconnectivity Spans Multiple Transdiagnostic Dimensions of Psychopathology. Biol Psychiatry. 86:779-791.

      (10) McIntosh AR, Lobaugh NJ (2004): Partial least squares analysis of neuroimaging data: applications and advances. Neuroimage. 23 Suppl 1:S250-263.

      (11) Paquola C, Benkarim O, DeKraker J, Lariviere S, Frassle S, Royer J, et al. (2020): Convergence of cortical types and functional motifs in the human mesiotemporal lobe. Elife. 9.

      (12) DeKraker J, Ferko KM, Lau JC, Kohler S, Khan AR (2018): Unfolding the hippocampus: An intrinsic coordinate system for subfield segmentations and quantitative mapping. Neuroimage. 167:408-418.

      (13) McEwen BS, Nasca C, Gray JD (2016): Stress Effects on Neuronal Structure: Hippocampus, Amygdala, and Prefrontal Cortex. Neuropsychopharmacology. 41:3-23.

      (14) Sapolsky RM (2000): Glucocorticoids and hippocampal atrophy in neuropsychiatric disorders. Arch Gen Psychiatry. 57:925-935.

      (15) Jacobson L, Sapolsky R (1991): The role of the hippocampus in feedback regulation of the hypothalamic-pituitary-adrenocortical axis. Endocr Rev. 12:118-134.

      (16) Engert V, Hoehne K, Singer T (2023): Specific reduction in the cortisol awakening response after socio-affective mental training. Mindfulness.

      (17) Puhlmann LMC, Vrticka P, Linz R, Stalder T, Kirschbaum C, Engert V, et al. (2021): Contemplative Mental Training Reduces Hair Glucocorticoid Levels in a Randomized Clinical Trial. Psychosom Med. 83:894-905.

      (18) Engert V, Kok BE, Papassotiriou I, Chrousos GP, Singer T (2017): Specific reduction in cortisol stress reactivity after social but not attention-based mental training. Sci Adv. 3:e1700495.

    1. Author Response

      The following is the authors’ response to the original reviews.

      Reviewer #1

      Strengths:

      This study uses a carefully constructed experiment design and decision-making task that allows separation of multiple electroencephalographic (EEG) signals thought to track different stages of decision-making. For example, the steady-state visual evoked potential measures can be cleanly dissociated from more anterior beta-band activity over the motor cortex. They also allow evaluation of how cued expectancy effects may unfold over a number of testing sessions. This is important because the most consistent evidence of expectation-related modulations of electrophysiological measures (using EEG, local field potentials, or single neuron firing rates) is from studies of nonhuman primates that involved many days of cue-stimulus contingency learning, and there is a lack of similar work using several testing sessions in humans. Although there were several experimental conditions included in the study, careful trial-balancing was conducted to minimise biases due to incidental differences in the number of trials included for analyses across each condition. Performance for each individual was also carefully calibrated to maximise the possibility of identifying subtle changes in task performance by expectation and avoid floor or ceiling effects.

      We would like to thank Reviewer 1 for these very positive comments.

      Weaknesses:

      Although the experiment and analysis methods are cohesive and well-designed, there are some shortcomings that limit the inferences that can be drawn from the presented findings.

      Comment #1

      The first relates to the measures of SSVEPs and their relevance for decision-making in the task. In order to eliminate the influence of sporadic pulses of contrast changes that occurred during stimulus presentation, a time window of 680-975 ms post-stimulus onset was used to measure the SSVEPs. The mean response times for the valid and neutral cues were around 850-900 ms for correct responses, and within the same time window for errors in the invalid cue condition. In addition, a large portion of response times in perceptual decision-making tasks are substantially faster than the mean due to right-skewed response time distributions that are typically observed. As it has also been estimated to require 70-100 ms to execute a motor action (e.g., a keypress response) following the commitment to a decision. This raises some concerns about the proportion of trials in which the contrast-dependent visual responses (indexed by the SSVEPs) indexed visual input that was actually used to make the decision in a given trial. Additional analyses of SSVEPs that take the trial-varying pulses into account could be run to determine whether expectations influenced visual responses earlier in the trial.

      The reviewer raises a very valid point and, indeed, it is an issue that we grappled with in our analyses. Actually, in this study, the RT distributions were not right-skewed, but appear to be relatively normal (RT distributions shown below). This is something that we have previously observed when using tasks that involve an initial zero-evidence lead in at the start of each trial which means that participants cannot start accumulating at stimulus onset and must rely on their knowledge of the lead-in duration to determine when the physical evidence has become available (e.g. Kelly et al 2021, Nat Hum Beh). We agree that it is important to establish whether the reported SSVEP modulations occur before or after choice commitment. In our original submission we had sought to address this question through our analysis of the response-locked ‘difference SSVEP’. Figure 4D clearly indicates that the cue modulations are evident before as well as after response.

      However, we have decided to include an additional Bayesian analysis of the response-locked signal to offer more evidence that the cue effect is not a post-response phenomenon.

      Manuscript Changes

      To quantify the evidence that the cue effect was not driven by changes in the signal after the response, we ran Bayesian one-way ANOVAs on the SSVEP comparing the difference across cue conditions before and after the response. If the cue effect only emerged after the response, we would expect the difference between invalid and neutral or invalid and valid cues to increase in the post-response window. There was no compelling evidence of an increase in the effect when comparing invalid to neutral (BF10 = 1.58) or valid cues (BF10 = 0.32).

      Comment #2

      Presenting response time quantile plots may also help to determine the proportions of motor responses (used to report a decision) that occurred during or after the SSVEP measurement window.

      We agree that it may be helpful for the reader to be able to determine the proportion of responses occurring at different phases of the trial, so we have included the requested response time quantile plot (shown below) as a supplementary figure.

      Author response image 1.

      Reaction time quantiles across cue conditions. The plot illustrates the proportion of trials where responses occurred at different stages of the trial. The SSVEP analysis window is highlighted in purple.

      Comment #3

      In addition, an argument is made for changes in the evidence accumulation rate (called the drift rate) by stimulus expectancy, corresponding to the observed changes in SSVEP measures and differences in the sensory encoding of the stimulus. This inference is limited by the fact that evidence accumulation models (such as the Diffusion Decision Model) were not used to test for drift rate changes as could be determined from the behavioural data (by modelling response time distributions). There appear to be ample numbers of trials per participant to test for drift rate changes in addition to the starting point bias captured in earlier models. Due to the very high number of trials, models could potentially be evaluated for each single participant. This would provide more direct evidence for drift rate changes than the findings based on the SSVEPs, particularly due to the issues with the measurement window relating to the response times as mentioned above.

      The focus of the present study was on testing for sensory-level modulations by predictive cues, rather than testing any particular models. Given that the SSVEP bears all the characteristics of a sensory evidence encoding signal, we believe it is reasonable to point out that its modulation by the cues would very likely translate to a drift rate effect. But we do agree with the reviewer that any connection between our results and previously reported drift rate effects can only be confirmed with modelling and we have tried to make this clear in the revised text. We plan to comprehensively model the data from this study in a future project. While we do indeed have the benefit of plenty of trials, the modelling process will not be straightforward as it will require taking account of the pulse effects which could have potentially complicated, non-linear effects. In the meantime, we have made changes to the text to qualify the suggestion and stress that modelling would be necessary to determine if our hypothesis about a drift rate effect is correct.

      Manuscript Changes

      (Discussion): [...] We suggest that participants may have been able to stabilise their performance across task exposure, despite reductions in the available sensory evidence, by incorporating the small sensory modulation we detected in the SSVEP. This would suggest that the decision process may not operate precisely as the models used in theoretical work describe. Instead, our study tentatively supports a small number of modelling investigations that have challenged the solitary role of starting point bias, implicating a drift bias (i.e. a modulation of the evidence before or upon entry to the decision variable) as an additional source of prior probability effects in perceptual decisions (Dunovan et al., 2014; Hanks et al., 2011; Kelly et al., 2021; van Ravenzwaaij et al., 2012 Wyart et al., 2012) and indicates that these drift biases could, at least partly, originate at the sensory level. However, this link could only be firmly established with modelling in a future study.

      Recommendations For The Authors:

      Comment #4

      The text for the axis labels and legends in the figures is quite small relative to the sizes of the accompanying plots. I would recommend to substantially increase the sizes of the text to aid readability.

      Thank you for this suggestion. We have increased the size of the axis labels and made the text in the figure legends just 1pt smaller than the text in the main body of the manuscript.

      Comment #5

      It is unclear if the scalp maps for Figure 5 (showing the mu/beta distributions) are on the same scale or different scales. I assume they are on different scales (adjusted to the minimum/maximum within each colour map range), as a lack of consistent signals (in the neutral condition) would be expected to lead to a patchy pattern on the scalp as displayed in that figure (due to the colour range shrinking to the degree of noise across electrodes). I would recommend to include some sort of colour scale to show that, for example, in the neutral condition there are no large-amplitude mu/ beta fluctuations distributed somewhat randomly across the scalp.

      Thank you to the reviewer for pointing this out. They were correct, the original topographies were plotted according to their own scale. The topographies in Figure 5 have now been updated to put them on a common scale and we have included a colour bar (as shown below). The caption for Figure 5 has also been updated to confirm that the topos are on a common scale.

      Author response image 2.

      Manuscript Changes

      (Figure 5 Caption): [...] The topography of MB activity in the window - 200:0 ms before evidence onset is plotted on a common scale for neutral and cued conditions separately.

      Comment #6

      In Figure 2, the legend is split across the two panels, despite the valid/invalid/neutral legend also applying to the first panel. This gives an initial impression that the legend is incomplete for the first panel, which may confuse readers. I would suggest putting all of the legend entries in the first panel, so that all of this information is available to readers at once.

      We are grateful to the reviewer for spotting this. Figure 2 has been updated so that the full legend is presented in the first panel, as shown below.

      Author response image 3.

      Comment #7

      Although linear mixed-effects models (using Gaussian families) for response times are standard in the literature, they incorrectly specify the distributions of response times to be Gaussian instead of substantially right-skewed. Generalised linear mixed-effects models using gamma families and identity functions have been shown to more accurately model distributions of response times (see Lo and Andrews, 2015. Frontiers in Psychology). The authors may consider using these models in line with good practice, although it might not make a substantial difference relating to the patterns of response time differences.

      We appreciate this thoughtful comment from Reviewer 1. Although RT distributions are often right skewed, we have previously observed that RT distributions can be closer to normal when the trial incorporates a lead-in phase with no evidence (e.g. Kelly et al 2021, Nat Hum Beh). Indeed, the distributions we observed in this study were markedly Gaussian (as shown in the plot below). Given the shape of these distributions and the reviewer’s suggestion that adopting alternative models may not lead to substantial differences to our results, we have decided to leave the mixed effects models as they are in the manuscript, but we will take note of this advice in future work.

      Author response image 4.

      Reviewer #2

      Strengths:

      The work is executed expertly and focuses cleverly on two features of the EEG signals that can be closely connected to specific loci of the perceptual decision-making process - the SSVEP which connects closely to sensory (visual) encoding, and Mu-Beta lateralisation which connects closely to movement preparation. This is a very appropriate design choice given the authors' research question.

      Another advantage of the design is the use of an unusually long training regime (i.e., for humans) - which makes it possible to probe the emergence of different expectation biases in the brain over different timecourses, and in a way that may be more comparable to work with nonhuman animals (who are routinely trained for much longer than humans).

      We are very grateful for these positive comments from Reviewer 2.

      Weaknesses:

      In my view, the principal shortcoming of this study is that the experimental task confounds expectations about stimulus identity with expectations about to-be-performed responses. That is, cues in the task don't just tell participants what they will (probably) see, but what they (probably) should do.

      In many respects, this feature of the paradigm might seem inevitable, as if specific stimuli are not connected to specific responses, it is not possible to observe motor preparation of this kind (e.g., de Lange, Rahnev, Donner & Lau, 2013 - JoN).

      However, the theoretical models that the authors focus on (e.g., drift-diffusion models) are models of decision (i.e., commitment to a proposition about the world) as much as they are models of choice (i.e., commitment to action). Expectation researchers interested in these models are often interested in asking whether predictions influence perceptual processing, perceptual decision, and/ or response selection stages (e.g., Feuerriegel, Blom & Hoogendorn, 2021 - Cortex), and other researchers have shown that parameters like drift bias and start point bias can be shifted in paradigms where observers cannot possibly prepare a response (e.g., Thomas, Yon, de Lange & Press, 2020 - Psych Sci).

      The present paradigm used by Walsh et al makes it possible to disentangle sensory processing from later decisional processes, but it blurs together the processes of deciding about the stimulus and choosing/initiating the response. This ultimately limits the insights we can draw from this study - as it remains unclear whether rapid changes in motor preparation we see reflect rapid acquisition of new decision criterion or simple cue-action learning. I think this would be important for comprehensively testing the models the authors target - and a good avenue for future work.

      Thank you to Reviewer 2 for these observations. We adopted this paradigm because it is typical of the perceptual decision making literature and our central focus in this study was to test for a sensory-level modulation as a source of a decision bias. We are pleased that the Reviewer agrees that the paradigm successfully disentangles sensory encoding from later decisional processes since this was our priority. However, we agree with Reviewer 2 that because the response mapping was known to the participants, the cues predicted both the outcome of the perceptual decision (“Is this a left- or right-tilted grating?”) and the motor response that the participant should anticipate making (“It’s probably going to be a left click on this trial”). They are correct that this makes it difficult to know whether the changes in motor preparation elicited by the predictive cues reflect action-specific preparation or a more general shift in the boundaries associated with the alternate perceptual interpretations. We fully agree that it remains an interesting and important question and in our future work we hope to conduct investigations that better dissect the distinct components of the decision process during prior-informed decisions. In the interim, we have made some changes to the manuscript to reflect the Reviewer’s concerns and better address this limitation of the study design (these are detailed in the response to the comment below).

      Recommendations For The Authors:

      Comment #8

      As in my public review, my main recommendation to the authors is to think a bit more in the presentation of the Introduction and Discussion about the difference between 'perceiving', 'deciding', and 'responding'.

      The paper is presently framed in terms of the debates around whether expectations bias decision or bias perception - and these debates are in turn mapped onto different aspects of the driftdiffusion model. Biases in sensory gain, for instance, are connected to biases in the drift rate parameter, while decisional shifts are connected to parameters like start points.

      In line with this kind of typology, the authors map their particular EEG signals (SSVEP and MB lateralisation) onto perception and decision. I see the logic, but I think the reality of these models is more nuanced.

      In particular, strictly speaking, the process of evidence accumulation to bound is the formation of a 'decision' (i.e., a commitment to having seen a particular stimulus). Indeed, the dynamics of this process have been beautifully described by other authors on this paper in the past. Since observers in this task simultaneously form decisions and prepare actions (because stimuli and responses are confounded) it is unclear whether changes in motor preparation are reflecting changes in what perceivers 'decide' (i.e., changes in what crosses the decision threshold) or what they 'do' (i.e., changes in the motor response threshold). This is particularly important for the debate around whether expectations change 'perception' or 'decision' because - in some accounts - is the accumulation of evidence to the bound that is hypothesised to cause the perceptual experience observers actually have (Pereira, Perrin & Faivre, 2022 - TiCS). The relevant 'bound' here though is not the bound to push the button, but the bound for the brain to decide what one is actually 'seeing'.

      I completely understand the logic behind the authors' choices, but I would have liked more discussion of this issue. In particular, it seems strange to me to talk about the confounding of stimuli and responses as a particular 'strength' of this design in the manuscript - when really it is a 'necessary evil' for getting the motor preparation components to work. Here is one example from the Introduction:

      "While some have reported expectation effects in humans using EEG/MEG, these studies either measured sensory signals whose relevance to the decision process is uncertain (e.g. Blom et al., 2020; Solomon et al., 2021; Tang et al., 2018) and/or used cues that were implicit or predicted a forthcoming stimulus but not the correct choice alternative (e.g. Aitken et al., 2020; Feuerriegel et al., 2021b; Kok et al., 2017). To assess whether prior probabilities modulate sensory-level signals directly related to participants' perceptual decisions, we implemented a contrast discrimination task in which the cues explicitly predicted the correct choice and where sensory signals that selectively trace the evidence feeding the decision process could be measured during the process of deliberation."

      I would contend that this design allows you to pinpoint signals related to participant's 'choices' or 'actions' but not necessarily their 'decisions' in the sense outlined above.

      As I say though, I don't think this is fatal and I think the paper is extremely interesting in any case. But I think it would be strengthened if some of these nuances were discussed a bit more explicitly, as a 'perceptual decision' is more than pushing a button. Indeed, the authors might want to consider discussing work that shows the neural overlap between deciding and acting breaks down when Ps cannot anticipate which actions to use to report their choices ahead of time (Filimon, Philiastides, Nelson, Kloosterman & Heekeren, 2013 - JoN) and/or work which has combined expectations with drift diffusion modelling to show how expectations change drift bias (Yon, Zainzinger, de Lange, Eimer & Press, 2020 - JEP:General) and/or start bias (Thomas, Yon, de Lange & Press, 2020 - Psych Sci) even when Ps cannot prepare a motor response ahead of time.

      While our focus was on testing for sensory-level modulations, we think the question of whether the motor-level effects we observed are attributable to the task design or represents a more general perceptual bound adjustment is an important question for future research. In our previous work, we have examined this distinction between abstract, movement-independent evidence accumulation (indexed by the centro-parietal positivity, CPP) and response preparation in detail. The CPP has been shown to trace evidence accumulation irrespective of whether the sensory alternatives are associated with a specific response or not (Twomey et al 2016, J Neurosci). When speed pressure is manipulated in tasks with fixed stimulus-response mappings we have found that the CPP undergoes systematic adjustments in its pre-response amplitude that closely accord with the starting-level modulations observed in mu/beta, suggesting that motor-level adjustments do still translate to differences at the perceptual level under these task conditions (e.g. Kelly et al 2021, Nat Hum Beh; Steinemann et al., 2018, Nat Comms). We have also observed that the CPP and mu-beta exhibit corresponding adjustments in response to predictive cues (Kelly et al., 2021) that are consistent with both a starting-point shift and drift rate bias. However, the Kelly et al. study did not include a signature of sensory encoding and therefore could not test for sensory-level modulations.

      We have added some remarks to the discussion to acknowledge this issue with the interpretation of the preparatory shifts in mu-beta activity we observed when the predictive cues were presented, and we have included references to the papers that the reviewer helpfully provided. We have also offered some additional consideration of the features of the task design that may have influenced the SSVEP results.

      Manuscript Changes

      An implication of using cues that predict not just the upcoming stimulus, but the most likely response, is that it becomes difficult to determine if preparatory shifts in mu-beta (MB) activity that we observed reflect adjustments directly influencing the perceptual interpretation of the stimulus or simply preparation of the more probable action. When perceptual decisions are explicitly tied to particular modes of response, the decision state can be read from activity in motor regions associated with the preparation of that kind of action (e.g. de Lafuente et al., 2015; Ding & Gold, 2012; Shadlen & Newsome, 2001; Romo et al., 2004), but these modules appear to be part of a constellation of decision-related areas that are flexibly recruited based on the response modality (e.g. Filimon et al., 2013). When the response mapping is withheld or no response is required, MB no longer traces decision formation (Twomey et al., 2015), but an abstract decision process is still readily detectable (e.g. O’Connell et al., 2012), and modelling work suggests that drift biases and starting point biases (Thomas et al., 2020; Yon et al., 2021) continue to influence prior-informed decision making. While the design of the present study does not allow us to offer further insight about whether the MB effects we observed were inherited from strategic adjustments at this abstract level of the decision process, we hope to conduct investigations in the future that better dissect the distinct components of prior-informed decisions to address this question.

      Several other issues remain unaddressed by the present study. One, is that it is not clear to what extent the sensory effects may be influenced by features of the task design (e.g. speeded responses under a strict deadline) and if these sensory effects would generalise to many kinds of perceptual decision-making tasks or whether they are particular to contrast discrimination.

      Comment #9

      On a smaller, unrelated point - I thought the discussion in the Discussion section about expectation suppression was interesting, but I did not think it was completely logically sound. The authors suggest that they may see relative suppression (rather than enhancement) of their marginal SSVEP under a 'sharpening' account because these accounts suggest that there is a relative suppression of off-channel sensory units, and there are more off-channel sensory units than onchannel sensory units (i.e., there are usually more possibilities we don't expect than possibilities that we do, and suppressing the things we don't expect should therefore yield overall suppression).

      However, this strikes me as a non-sequitur given that the marginal SSVEP only reflects featurespecific visual activity (i.e., activity tuned to one of the two grating stimuli used). The idea that there are more off-channel than on-channel units makes sense for explaining why we would see overall signal drops on expected trials e.g., in an entire visual ROI in an fMRI experiment. But surely this explanation cannot hold in this case, as there is presumably an equal number of units tuned to each particular grating?

      My sense is that this possibility should probably be removed from the manuscript - and I suspect it is more likely that the absence of a difference in marginal SSVEP for Valid vs Neutral trials has more to do with the fact that participants appear to be especially attentive on Neutral trials (and so any relative enhancement of feature-specific activity for expected events is hard to detect against a baseline of generally high-precision sensory evidence on these highly attentive, neutral trials).

      We thank the reviewer for flagging that we did not clearly articulate our thoughts in this section of the manuscript. Our primary purpose in mentioning this sharpening account was simply to point out that, where at first blush our results seem to conflict with expectation suppression effects in the fMRI literature, the sharpening account provides an explanation that can reconcile them. In the case of BOLD data, the sharpening account proposes that on-channel sensory units are boosted and off-channel units are suppressed and, due to the latter being more prevalent, this leads to an overall suppression of the global signal. In the case of the SSVEP, the signal isolates just the onunits and so the sharpening account would predict that when there is a valid cue, the SSVEP signal associated with the high-contrast, expected stimulus should be boosted and the SSVEP signal associated with the low-contrast, unexpected stimulus should be weakened; this would result in a larger difference between these signals and therefore, a larger ‘marginal SSVEP’. Conversely, when there is an invalid cue, the SSVEP signal associated with the, now unexpected, high-contrast stimulus should be relatively weakened and the SSVEP signal associated with the expected, but low-contrast stimulus should be relatively boosted; this would result in a smaller difference between these signals and therefore, a lower amplitude marginal SSVEP. We do not think that this account needs to make reference to any channels beyond those feature-specific channels driving the two SSVEP signals. Again our central point is simply that the sharpening account offers a means of reconciling our SSVEP findings with expectation suppression effects previously reported in the fMRI literature.

      We suspect that this was not adequately explained in the discussion. We have adjusted the way this section is phrased to make it clear that we are not invoking off-channel activity to explain the SSVEP effect we observed and we thank the Reviewer for pointing out that this was unclear in the original text.

      Manuscript Changes

      An alternative account for expectation suppression effects, which is consistent with our SSVEP results, is that they arise, not from a suppression of expected activity, but from a ‘sharpening’ effect whereby the response of neurons that are tuned to the expected feature are enhanced while the responses of neurons tuned to unexpected features are suppressed (de Lange et al., 2018). On this account, the expectation suppression commonly reported in fMRI studies arises because voxels contain intermingled populations with diverse stimulus preferences and the populations tuned to the unexpected features outnumber those tuned to the expected feature. In contrast to these fMRI data, the SSVEP represents the activity of sensory units driven at the same frequency as the stimulus, and thus better isolates the feature-specific populations encoding the task-relevant sensory evidence. Therefore, according to the sharpening account, an invalid cue would have enhanced the SSVEP signal associated with the low contrast grating and weakened the SSVEP signal associated with the high contrast grating. As this would result in a smaller difference between these signals, and therefore, a lower amplitude marginal SSVEP compared to the neutral cue condition, this could explain the effect we observed. 

      Reviewer #3

      Observers make judgements about expected stimuli faster and more accurately. How expectations facilitate such perceptual decisions remains an ongoing area of investigation, however, as expectations may exert their effects in multiple ways. Expectations may directly influence the encoding of sensory signals. Alternatively (or additionally), expectations may influence later stages of decision-making, such as motor preparation, when they bear on the appropriate behavioral response.

      In the present study, Walsh and colleagues directly measured the effect of expectations on sensory and motor signals by making clever use of the encephalogram (EEG) recorded from human observers performing a contrast discrimination task. On each trial, a predictive cue indicated which of two superimposed stimuli would likely be higher contrast and, therefore, whether a left or right button press was likely to yield a correct response. Deft design choices allowed the authors to extract both contrast-dependent sensory signals and motor preparation signals from the EEG. The authors provide compelling evidence that, when predictive cues provide information about both a forthcoming stimulus and the appropriate behavioral response, expectation effects are immediately manifest in motor preparation signals and only emerge in sensory signals after extensive training.

      Future work should attempt to reconcile these results with related investigations in the field. As the authors note, several groups have reported expectation-induced modulation of sensory signals (using both fMRI and EEG/MEG) on shorter timescales (e.g. just one or two sessions of a few hundred trials, versus the intensive multi-session study reported here). One interesting possibility is that perceptual expectations are not automatic but demand the deployment of feature-based attention, while motor preparation is comparatively less effortful and so dominates when both sources of information are available, as in the present study. This hypothesis is consistent with the authors' thoughtful analysis showing decreased neural signatures of attention over posterior electrodes following predictive cues. Therefore, observing the timescale of sensory effects using the same design and methods (facilitating direct comparison with the present work), but altering task demands slightly such that cues are no longer predictive of the appropriate behavioral response, could be illuminating.

      We would like to thank Reviewer 3 for their positive comments and thoughtful suggestions for future work.

      Recommendations For The Authors:

      Comment #10

      In the methods, the term 'session' is used early on but only fleshed out at the end of the 'Procedure' subsection and never entirely explained (e.g., did sessions take place over multiple days?). A brief sentence laying this out early on, perhaps in 'Participants' after the (impressive) trial counts are reported, might be helpful.

      Thank you to Reviewer 3 for pointing out that this was not clear in the original draft. We have amended the text in the Methods section to better explain the relationship between sessions, days, and trial bins.

      Manuscript Changes

      (Methods - Participants): [...] All procedures were approved by the Trinity College Dublin School of Psychology Ethics Committee and were in accordance with the Declaration of Helsinki. Participants completed between 4 and 6 testing sessions, each on a different day. While the sample size was small, on average, participants completed 5750 (SD = 1066) trials each.

      (Methods - Data Analysis): [...] As there were two lengths of testing session and participants completed different numbers of sessions, we analysed the effect of task exposure by pooling trials within-subjects and dividing them into five ‘trial bins’. The first bin represents the participants’ earliest exposure to the task and the final bin represents trials at the end of their participation, when they had had substantial task exposure. All trials with valid responses and reaction times greater than 100 ms were included in the analyses of behavioural data and the SSVEP.

      Comment #11

      On a related note: participants completed a variable number of trials/sessions. To facilitate comparison across subjects, training effects are reported by dividing each subject's data into 5 exposure bins. This is entirely reasonable but does leave the reader wondering about whether you found any effects of rest or sleep between sessions.

      We agree with the reviewer that this is an interesting question that absolutely merits further investigation. As different participants completed different numbers of sessions, different session lengths, and had variable gaps between their sessions, we do not think a per-session analysis would be informative. We think it may be better addressed in a future study, perhaps one with a larger sample where we could collect data specifically about sleep and more systematically control the intervals between testing sessions.

      Comment #12

      Fig 2B: the 'correct' and 'neutral' labels in the legend are switched

      Thank you to the reviewer for spotting that error, the labels in Figure 2 have been corrected.

      Comment #13

      Fig 4B: it's a bit difficult to distinguish which lines are 'thick' and 'thin'

      We have updated Figure 4.B to increase the difference in line thickness between the thick and thin lines (as shown below).

      Author response image 5.

      Comment #14

      Fig 4C: missing (I believe?) the vertical lines indicating median reaction time

      We have updated Figure 4.C to include the median reaction times.

      Author response image 6.

    1. Author Response

      The following is the authors’ response to the original reviews.

      eLife assessment

      This important study enhances our understanding of the effects of landscape context on grassland plant diversity and biomass. Notably, the authors use a well-designed field sampling method to separate the effects of habitat loss and fragmentation per se. Most of the data and analyses provide solid support for the findings that habitat loss weakens the positive relationship between grassland plant richness and biomass.

      Response: Thanks very much for organizing the review of the manuscript. We are grateful to you for the recognition. We have carefully analyzed all comments of the editors and reviewers and revised our manuscript to address them. All comments and recommendations are helpfully and constructive for improving our manuscript. We have described in detail our response to each of comment below.

      In addition to the reviewers' assessments, we have the following comments on your paper.

      (1) Some of the results are not consistent between figures. The relationships between overall species richness and fragmentation per se are not consistent between Figs. 3 and 5. The relationships between aboveground biomass and habitat loss are not consistent between Figs. 4 and 5. How shall we interpret these inconsistent results?

      Response: Thanks for your insightful comments. The reason for these inconsistencies is that the linear regression model did not take into account the complex causal relationships (including direct and indirect effects) among the different influencing factors. The results in Figures 3 and 4 just represent the pairwise relationship pattern and relative importance, respectively. The causal effects of habitat loss and fragmentation per se on plant richness and above-ground biomass should be interpreted based on the structural equation model results (Figure 6). We have revised the data analysis to clear these inconsistent results. Line 225-228

      In the revised manuscript, we have added the interpretation for these inconsistent results. The inconsistent effects between Figures 3 and 6 suggest that fragmentation per se actually had a positive effect on plant richness after accounting for the effects of habitat loss and environmental factors simultaneously.

      The inconsistent effects between Figures 4 and 6 are because the effects of habitat loss and fragmentation per se on above-ground biomass were mainly mediated by plant richness and environmental factors, which had no significant direct effect (Figure 6). Thus, habitat loss and fragmentation per se showed no significant relative effects on above-ground biomass after controlling the effects of plant richness and environmental factors (Figure 4).

      (2) One of the fragmentation indices, mean patch area metric, seems to be more appropriate as a measure of habitat loss, because it represents "a decrease in grassland patch area in the landscape".

      Response: Thanks for your insightful comments. We apologize for causing this confusion. The mean patch area metric in our study represents the mean size of grassland patches in the landscape for a given grassland amount. Previous studies have often used the mean patch metric as a measure of fragmentation, which can reflect the processes of local extinction in the landscape (Fahrig, 2003; Fletcher et al., 2018). We have revised the definition of the mean patch area metric and added its ecological implication in the revised manuscript to clarify this confusion.

      (3) It is important to show both the mean and 95% CI (or standard error) of the slope coefficients regarding to Figs. 3 and 6.

      Response: Thanks for your suggestions. We have added the 95% confidence intervals to the Figure 3 and Figure 6 in the revised manuscript.

      (4) It would be great to clarify what patch-level and landscape-level studies are in lines 302-306. Note that this study assesses the effects of landscape context on patch-level variables (i.e., plot-based plant richness and plot-based grassland biomass) rather than landscape-level variables (i.e., the average or total amount of biomass in a landscape).

      Response: Thanks for your insightful comment. We agree with your point that our study investigated the effect of fragmented landscape context (habitat loss and fragmentation per se) on plot-based plant richness and plot-based above-ground biomass rather than landscape-level variables.

      Therefore, we no longer discussed the differences between the patch-level and landscape-level studies here, instead focusing on the different ecological impacts of habitat loss and fragmentation per se in the revised manuscript.

      Line 369-374:

      “Although habitat loss and fragmentation per se are generally highly associated in natural landscapes, they are distinct ecological processes that determine decisions on effective conservation strategies (Fahrig, 2017; Valente et al., 2023). Our study evaluated the effects of habitat loss and fragmentation per se on grassland plant diversity and above-ground productivity in the context of fragmented landscapes in the agro-pastoral ecotone of northern China, with our results showing the effects of these two facets to not be consistent.”

      (5) One possible way to avoid the confusion between "habitat fragmentation" and "fragmentation per se" could be to say "habitat loss and fragmentation per se" when you intend to express "habitat fragmentation".

      Response: Thanks for your constructive suggestions. To avoid this confusion, we no longer mention habitat fragmentation in the revised manuscript but instead express it as habitat loss and fragmentation per se.

      Reviewer #1 (Public Review):

      This is a well-designed study that explores the BEF relationships in fragmented landscapes. Although there are massive studies on BEF relationships, most of them were conducted at local scales, few considered the impacts of landscape variables. This study used a large dataset to specifically address this question and found that habitat loss weakened the BEF relationships. Overall, this manuscript is clearly written and has important implications for BEF studies as well as for ecosystem restoration.

      Response: We are grateful to you for the recognition and constructive comments. All the comments and suggestions are very constructive for improving this manuscript. We have carefully revised the manuscript following your suggestions. All changes are marked in red font in the revised manuscript.

      My only concern is that the authors should clearly define habitat loss and fragmentation. Habitat loss and fragmentation are often associated, but they are different terms. The authors consider habitat loss a component of habitat fragmentation, which is not reasonable. Please see my specific comments below.

      Response: We agree with your point. In the revised manuscript, we no longer consider habitat loss and fragmentation per se as two facets of habitat fragmentation. We have clearly defined habitat loss and fragmentation per se and explicitly evaluated their relative effects on plant richness, above-ground biomass, and the BEF relationship.

      Reviewer #1 (Recommendations For The Authors):

      Title: It is more proper to say habitat loss, rather than habitat fragmentation.

      Response: Thanks for your suggestion. We have revised the title to “Habitat loss weakens the positive relationship between grassland plant richness and above-ground biomass”

      Line 22, remove "Anthropogenic", this paper is not specifically discussing habitat fragmentation driven by humans.

      Response: Thanks for your suggestion. We have removed the “Anthropogenic” from this sentence.

      Line 26, revise to "we investigated the effects of habitat loss and fragmentation per se on plant richness... in grassland communities by using a structural equation model".

      Response: Thanks for your suggestion. We have revised this sentence.

      Line 25-28:

      “Based on 130 landscapes identified by a stratified random sampling in the agro-pastoral ecotone of northern China, we investigated the effects of landscape context (habitat loss and fragmentation per se) on plant richness, above-ground biomass, and the relationship between them in grassland communities using a structural equation model.”

      Line 58-60, habitat fragmentation generally involves habitat loss, but habitat loss is independent of habitat fragmentation, it is not a facet of habitat fragmentation.

      Response: Thanks for your insightful comment. We have no longer considered habitat loss and fragmentation per se as two facets of habitat fragmentation. In the revised manuscript, we consider habitat loss and fragmentation as two different processes in fragmented landscapes.

      Line 65-67, this sentence is not very relevant to this paragraph and can be deleted.

      Response: Thanks for your suggestion. We have deleted this sentence from the paragraph.

      Line 87-90, these references are mainly based on microorganisms, are there any references based on plants? These references are more relevant to this study. In addition, this is a key mechanism mentioned in this study, this section needs to be strengthened with more evidence and further exploration.

      Response: Thanks for your comment and suggestion. Thanks for your comment and suggestion. We have added some references based on plants here to strengthen the evidence and mechanism of habitat specialisation determines the BEF relationship.

      Line 89-95:

      “In communities, specialists with specialised niches in resource use may contribute complementary roles to ecosystem functioning, whereas generalists with unspecialised in resource use may contribute redundant roles to ecosystem functioning due to overlapping niches (Dehling et al., 2021; Denelle et al., 2020; Gravel et al., 2011; Wilsey et al., 2023). Therefore, communities composed of specialists should have a higher niche complementarity effect in maintaining ecosystem functions and a more significant BEF relationship than communities composed of generalists.”

      Denelle, P., Violle, C., DivGrass, C., Munoz, F. 2020. Generalist plants are more competitive and more functionally similar to each other than specialist plants: insights from network analyses. Journal of Biogeography 47: 1922-1933.

      Dehling, D.M., Bender, I.M.A., Blendinger, P.G., Böhning-Gaese, K., Muñoz, M.C., Neuschulz, E.L., Quitián, M., Saavedra, F., Santillán, V., Schleuning, M., Stouffer, D.B. 2021. Specialists and generalists fulfil important and complementary functional roles in ecological processes. Functional Ecology 35: 1810-1821.

      Wilsey, B., Martin, L., Xu, X., Isbell, F., Polley, H.W. 2023. Biodiversity: Net primary productivity relationships are eliminated by invasive species dominance. Ecology Letters.

      Line 129-130, Although you can use habitat loss in the discussion or the introduction, here preferably use habitat amount or habitat area, rather than habitat loss in this case. Habitat loss represents changes in habitat area, but the remaining grasslands could be the case of natural succession or other processes, rather than loss of natural habitat.

      Response: Thanks for your insightful comment. We agree with your point. In the revised manuscript, we have explicitly stated that habitat loss was represented by the loss of grassland amount in the landscape.

      Since the remaining grassland fragments in this region were mainly caused by grassland loss due to human activities such as cropland expansion (Chen et al., 2019; Yang et al., 2020), we used the percentage of non-grassland cover in the landscape to represent habitat loss in our study.

      Line 132-135:

      “Habitat loss was represented by the loss of grassland amount in the landscape. As the remaining grassland fragments in this region were mainly caused by grassland loss due to human activities such as cropland expansion (Chen et al., 2019; Yang et al., 2020), the percentage of non-grassland cover in the landscape was used in our study to represent habitat loss.”

      Lines 245-246, please also give more details of the statistical results, such as n, r value et al in the text.

      Response: Thanks for your suggestion. We have added the details of the statistical results in the revised manuscript.

      Line 283-290:

      “Habitat loss was significantly negatively correlated with overall species richness (R = -0.21, p < 0.05, Figure 3a) and grassland specialist richness (R = -0.41, p < 0.01, Figure 3a), but positively correlated with weed richness (R = 0.31, p < 0.01, Figure 3a). Fragmentation per se was not significantly correlated with overall species richness and grassland specialist richness, but was significantly positively correlated with weed richness (R = 0.26, p < 0.01, Figure 3b). Habitat loss (R = -0.39, p < 0.01, Figure 3c) and fragmentation per se (R = -0.26, p < 0.01, Figure 3d) were both significantly negatively correlated with above-ground biomass.”

      Fig. 5, is there any relationship between habitat amount and fragmentation per se in this study?

      Response: Thanks for your insightful comment. We have considered a causal relationship between habitat loss and fragmentation per se in the structural equation model. We have discussed this relationship in the revised manuscript.

      Line 290-293, how about the BEF relationships with different fragmentation levels? I may have missed something somewhere, but it was not shown here.

      Response: Thanks for your insightful comment. We have added the BEF relationships with different fragmentation per se levels here.

      Line 323-340:

      “The linear regression models showed that habitat loss had a significant positive modulating effect on the positive relationship between plant richness and above-ground biomass, and fragmentation per se had no significant modulating effect (Figure 5). The positive relationship between plant richness and above-ground biomass weakened with increasing levels of habitat loss, strengthened and then weakened with increasing levels of fragmentation per se.

      Author response image 1.

      Relationships between grassland plant richness and above-ground biomass at different levels of habitat loss and fragmentation per se from 130 landscapes in the Tabu River Basin, a typical agro-pastoral ecotone of northern China: (a) high habitat loss and low fragmentation per se, (b) high habitat loss and moderate fragmentation per se, (c) high habitat loss and high fragmentation per se, (d) moderate habitat loss and low fragmentation per se, (e) moderate habitat loss and moderate fragmentation per se, (f) moderate habitat loss and high fragmentation per se, (g) low habitat loss and low fragmentation per se, (h) low habitat loss and moderate fragmentation per se. The R2 values in each panel are from linear regression models. The n in each panel is the number of surveying sites used in the linear regression models. The blue solid and dashed trend lines represent the significant and not significant effects, respectively. The shaded area around the trend line represents the 95% confidence interval. * represent significance at the 0.05 level. ** represent significance at the 0.01 level.”

      Discussion

      The Discussion (Section 4.2) needs to be revised and focused on your key findings, it is habitat loss, not fragmentation per se, that weakens the BEF relationships.

      Response: Thanks for your insightful comment and suggestion. In the revised manuscript, we have rephrased the Discussion (Section 4.2) to mainly discuss the inconsistent effects of habitat loss and fragmentation per se on the BEF relationship.

      Line 414-416:

      “4.2 Habitat loss rather than fragmentation per se weakened the magnitude of the positive relationship between plant diversity and ecosystem function”

      The R2 in the results are low (e.g., Fig. 3), please also mention other variables that might influence the observed pattern in the Discussion, such as soil and topography, though I understand it is difficult to collect such data in this study.

      Response: Thanks for your insightful comment and suggestion. We agree with you and reviewer 3 that the impact of environmental factors should also be considered.

      Therefore, we have considered two environmental factors related to water and temperature (soil water content and land surface temperature) in the analysis and discussed their impacts on plant diversity and above-ground biomass in the revised manuscript.

      Lines 344-345, its relative importance was stronger in the intact landscape than that of the fragmented landscape?

      Response: We apologize for making this confusion. We have rephrased this sentence.

      Line 422-426:

      “Our study found grassland plant diversity showed a stronger positive impact on above-ground productivity than landscape context and environmental factors. This result is consistent with findings by Duffy et al. (2017) in natural ecosystems, indicating grassland plant diversity has an important role in maintaining grassland ecosystem functions in the fragmented landscapes of the agro-pastoral ecotone of northern China.”

      Reviewer #2 (Public Review):

      Summary:

      In this manuscript, Yan et al. assess the effect of two facets of habitat fragmentation (i.e., habitat loss and habitat fragmentation per se) on biodiversity, ecosystem function, and the biodiversity-ecosystem function (BEF) relationship in grasslands of an agro-pastoral ecotone landscape in northern China. The authors use stratified random sampling to select 130 study sites located within 500m-radius landscapes varying along gradients of habitat loss and habitat fragmentation per se. In these study sites, the authors measure grassland specialist and generalist plant richness via field surveys, as well as above-ground biomass by harvesting and dry-weighting the grass communities in each 3 x 1m2 plots of the 130 study sites. The authors find that habitat loss and fragmentation per se have different effects on biodiversity, ecosystem function and the BEF relationship: whereas habitat loss was associated with a decrease in plant richness, fragmentation per se was not; and whereas fragmentation per se was associated with a decrease in above-ground biomass, habitat loss was not. Finally, habitat loss, but not fragmentation per se was linked to a decrease in the magnitude of the positive biodiversity-ecosystem functioning relationship, by reducing the percentage of grassland specialists in the community.

      Strengths:

      This study by Yan et al. is an exceptionally well-designed, well-written, clear and concise study shedding light on a longstanding, important question in landscape ecology and biodiversity-ecosystem functioning research. Via a stratified random sampling approach (cf. also "quasi-experimental design" Butsic et al. 2017), Yan et al. create an ideal set of study sites, where habitat loss and habitat fragmentation per se (usually highly correlated) are decorrelated and hence, separate effects of each of these facets on biodiversity and ecosystem function can be assessed statistically in "real-world" (and not experimental, cf. Duffy et al. 2017) communities. The authors use adequate and well-described methods to investigate their questions. The findings of this study add important empirical evidence from real-world grassland ecosystems that help to advance our theoretical understanding of landscape-moderation of biodiversity effects and provide important guidelines for conservation management.

      Weaknesses:

      I found only a few minor issues, mostly unclear descriptions in the study that could be revised for more clarity.

      Response: Thanks very much for your review of the manuscript. We are grateful to you for the recognition. All the comments and suggestions are very insightful and constructive for improving this manuscript. We have carefully studied the literature you recommend and revised the manuscript carefully following your suggestions. All changes are marked in red font in the revised manuscript.

      Reviewer #2 (Recommendations For The Authors):

      Specific comments

      (1) Some aspects of the Methods section were not entirely clear to me, could you revise them for more clarity?

      (a) Whereas you describe 4 main facets of fragmentation per se that are used to create the PC1 as a measure of overall fragmentation per se, it looks as if this PC1 is mainly driven by 3 facets only (ED, PD and AREA_MN), and patch isolation (nearest neighbour distance, ENN) having a relatively low loading on PC1 (Figure A1). I think it would be good to discuss this fact and the consequences of it, that your definition of fragmentation is focused more on edge density, patch density and mean patch area, and less on patch isolation in your Discussion section?

      Response: Thanks for your insightful comment and suggestion. We agree with your point. We have discussed this fact and its implications for understanding the effects of fragmentation per se in our study.

      Line 384-389:

      “However, it is important to stress that the observed positive effect of fragmentation per se does not imply that increasing the isolation of grassland patches would promote biodiversity, as the metric of fragmentation per se used in our study was more related to patch density, edge density and mean patch area while relatively less related to patch isolation (Appendix Table A1). The potential threats from isolation still need to be carefully considered in the conservation of biodiversity in fragmented landscapes (Haddad et al., 2015).”

      (b) Also, from your PCA in Figure A1, it seems that positive values of PC1 mean "low fragmentation", whereas high values of PC1 mean "high fragmentation", however, in Figure A2, the inverse is shown (low values of PC1 = low fragmentation, high values of PC1 = high fragmentation). Could you clarify in the Methods section, if you scaled or normalized the PC1 to match this directionality?

      Response: We apologize for making this confusion. In order to be consistent with the direction of change in fragmentation per se, we took the inverse of the PC1 as a single fragmentation per se index, which was positively correlated with patch density, edge density, mean nearest-neighbor distance metric, and negatively with mean patch area (Appendix Figure A1 and Table A1). We have clarified this point in the Method section.

      Line 160-163:

      “We took the inverse of the PC1 as a single fragmentation per se index, which was positively correlated with patch density, edge density, mean nearest-neighbor distance metric, and negatively with mean patch area (Appendix Figure A1 and Table A1).”

      (c) On line 155 you describe that you selected at least 20 landscapes using stratified sampling from each of the eight groups of habitat amount and fragmentation combination. Could you clarify: 1) did you randomly sample within these groups with a minimum distance condition or was it a non-random selection according to other criteria? (I think you could move the "To prevent overlapping landscapes..." sentence up here to the description of the landscape selection process) 2) Why did you write "at least 20 landscapes" - were there in some cases more or less landscapes selected? 130 study landscapes divided by 8 groups only gives you 16.25, hence, at least for some groups there were less than 20 landscapes? Could you describe your final dataset in more detail, i.e. the number of landscapes per group and potential repercussions for your analysis?

      Response: Thanks for your insightful comments. In the revised manuscript, we have rephrased the method to provide more detail for the sampling landscape selection.

      (1) Line 169-172

      We randomly selected at least 20 grassland landscapes with a minimum distance condition using stratified sampling from each of the remaining eight grassland types as alternative sites for field surveys. The minimum distance between each landscape was at least 1000 m to prevent overlapping landscapes and potential spatial autocorrelation.

      (2) Line 184-191

      The reason for selecting at least 20 grassland landscapes of each type in this study was to ensure enough alternative sites for the field survey. This is because the habitat type of some selected sites was not the natural grasslands, such as abandoned agricultural land. Some of the selected sites may not be permitted for field surveys.

      Thus, we finally established 130 sites in the field survey. The types of the 130 sites were: 19 high-moderate, 14 high-low, 19 moderate-high, 16 moderate-moderate, 18 moderate-low, 16 low-high, 17 low-moderate, 11 low-low habitat amount and fragmentation per se.

      (d) On line 166, you describe that you established 130 sites of 30 m by 30 m - I assume they were located (more or less) exactly in the centre of the selected 500 m - radius landscapes? Were they established so that they were fully covered with grassland? And more importantly, how did you establish the 10 m by 10 m areas and the 1 m2 plots within the 30 m by 30 m sites? Did you divide the 30 m by 30 m areas into three rectangles of 10 m by 10 m and then randomly established 1 m2 plots? Were the 1 m2 plots always fully covered with grassland/was there a minimum distance to edge criterion? Please describe with more detail how you established the 1 m2 study sites, and how many there were per landscape.

      Response: Thanks for your insightful comments. In the revised manuscript, we have provided more detailed information on how to set up 130 sites of 30 m by 30 m and three plots of 1 m by 1 m.

      (1) As these 130 sites were selected based on the calculation of the moving window, they were located (more or less) exactly in the centre of the 500-m radius buffer.

      (2) These sites were fully covered with grassland because their size (30 m by 30 m) was the same as the size of the grassland cell (30 m by 30 m) used in the calculation of the moving window.

      (3) We randomly set up three 1 m * 1 m plots in a flat topographic area at the 10 m * 10 m centre of each site. Thus, there was a minimum distance of 10 m to the edge for each 1 m * 1 m plot.

      (4) There are three 1 m * 1 m plots per landscape.

      Line 182-191:

      “Based on the alternative sites selected above, we established 130 sites (30 m * 30 m) between late July to mid-August 2020 in the Tabu River Basin in Siziwang Banner, Inner Mongolia Autonomous Region (Figure 1). The types of the 130 sites were: 19 high-moderate, 14 high-low, 19 moderate-high, 16 moderate-moderate, 18 moderate-low, 16 low-high, 17 low-moderate, 11 low-low habitat amount and fragmentation per se. In order to exclude the impact of historical agricultural activities, the habitat type of the established sites was natural grasslands with regional vegetation characteristics. Each site was not abandoned agricultural land, and there was no sign of agricultural reclamation.

      At the 10 m * 10 m center of each site, we randomly set up three 1 m * 1 m plots in a flat topographic area to investigate grassland vascular plant diversity and above-ground productivity.”

      (e) Line 171: could you explain what you mean by reclaimed?

      Response: Thanks for your comment. The “reclaimed” means that historical agricultural activities. We have rephrased this sentence to make it more explicit.

      Line 186-189:

      “In order to exclude the impact of historical agricultural activities, the habitat type of the established sites was natural grasslands with regional vegetation characteristics. Each site was not abandoned agricultural land, and there was no sign of agricultural reclamation.”

      (f) Line 188 ff.: Hence your measure of productivity is average-above ground biomass per 1 m2. I think it would add clarity if you highlighted this more explicitly.

      Response: Thanks for your suggestion. We have highlighted that the productivity in our study was the average above-ground biomass per 1 m * 1 m plots in each site.

      Line 215-217:

      “For each site, we calculated the mean vascular plant richness of the three 1 m * 1 m plots, representing the vascular plant diversity, and mean above-ground biomass of the three 1 m * 1 m plots, representing the above-ground productivity.”

      (2) All figures are clear and well-designed!

      (a) Just as a suggestion: in Figures 3 and 6, you could maybe add the standard errors of the mean as well?

      Response: Thanks for your suggestion. In the revised manuscript, we have added the standard errors of the mean in Figures 3 and 6.

      (b) Figure 4: Could you please clarify: Which models were the optimal models on which these model-averaged standardized parameter estimates were based on? And hence, the optimal models contained all 4 predictors (otherwise, no standardized parameter estimate could be calculated)? Or do these model-averaged parameters take into account all possible models (and not only the optimal ones)?

      Response: Thanks for your suggestion. We selected the four optimal models based on the AICc value to calculate the model-averaged standardized parameter estimates. The four optimal models contained all predictors in Figure 4. We have added the four optimal models in Appendix Table A3.

      Appendix:

      Author response table 1.

      Four optimal models of landscape context, environment factors, and plant diversity affecting above-ground biomass.

      Note: AGB: above-ground biomass; HL: habitat loss; FPS: fragmentation per se; SWT: soil water content; LST: land surface temperature; GSR: grassland specialist richness; WR: weed richness; **: significance at the 0.01 level.”

      (c) Please add in all Figures (i.e., Figures 4, 5 and 6, Figure 6 per "high, moderate and low-class") the number of study units the analyses were based on.

      Response: Thanks for your suggestion. In the revised manuscript, we have added the number of study units the analyses were based on in all Figures.

      (d) Figure 6: I think it would be more consistent to add a second plot where the BEF-relationship is shown for low, moderate and high levels of habitat fragmentation per se. Could you also add a clearer description in the Methods and/or Results section of how you assessed if habitat amount or fragmentation per se affected the BEF-relationship? I.e. based on the significance of the interaction term (habitat amount x species richness) in a linear model?

      Response: Thanks for your insightful comment and suggestion. We have added a second plot in Figure 5 to show the BEF relationship at low, moderate and high levels of fragmentation per se.

      Line 328-340:

      Author response image 2.

      Relationships between grassland plant richness and above-ground biomass at different levels of habitat loss and fragmentation per se from 130 landscapes in the Tabu River Basin, a typical agro-pastoral ecotone of northern China: (a) high habitat loss and low fragmentation per se, (b) high habitat loss and moderate fragmentation per se, (c) high habitat loss and high fragmentation per se, (d) moderate habitat loss and low fragmentation per se, (e) moderate habitat loss and moderate fragmentation per se, (f) moderate habitat loss and high fragmentation per se, (g) low habitat loss and low fragmentation per se, (h) low habitat loss and moderate fragmentation per se. The R2 values in each panel are from linear regression models. The n in each panel is the number of surveying sites used in the linear regression models. The blue solid and dashed trend lines represent the significant and not significant effects, respectively. The shaded area around the trend line represents the 95% confidence interval. * represent significance at the 0.05 level. ** represent significance at the 0.01 level.”

      We determined whether habitat loss and fragmentation per se moderated the BEF relationship by testing the significance of their interaction term with plant richness. We have added a clearer description in the Methods section of the revised manuscript.

      Line 245-250:

      “We then assessed the significance of interaction terms between habitat loss and fragmentation per se and plant richness in the linear regression models to evaluate whether they modulate the relationship between plant richness and above-ground biomass. Further, we used a piecewise structural equation model to investigate the specific pathways in which habitat loss and fragmentation per se modulate the relationship between plant richness and above-ground biomass.”

      (3) While reading your manuscript, I missed a discussion on the potential non-linear effects of habitat amount and fragmentation per se. In your study, it seems that the effects of habitat amount and fragmentation per se on biodiversity and ecosystem function are quite linear, which contrasts previous research highlighting that intermediate levels of fragmentation/heterogeneity could maximise spatial asynchrony, biodiversity and ecosystem function (e.g. Redon et al. 2014, Thompson & Gonzalez 2016, Tscharntke et al. 2012, Wilcox et al. 2017). I think it would add depth to your study if you discussed your finding of linear effects of habitat amount and fragmentation on biodiversity, ecosystem functioning and BEF. For example:

      Response: Thanks for your constructive suggestions. We have carefully studied the literature (e.g. Redon et al. 2014, Thompson & Gonzalez 2016, Tscharntke et al. 2012, Wilcox et al. 2017), which highlights that intermediate levels of fragmentation/heterogeneity could maximise spatial asynchrony, biodiversity and ecosystem function.

      In the revised manuscript, we have added the discussion about the linear positive effects of fragmentation on plant diversity and above-ground productivity and discussed possible reasons for this linear effect.

      Line 402-413:

      “In our study, a possible mechanism for the positive impacts of fragmentation per se on plant diversity and above-ground productivity (indirect positive impact via plant diversity) is that fragmentation per se increases the habitat heterogeneity in the landscape, which can promote biodiversity through spatial asynchrony and spatial insurance effects (Tscharntke et al., 2012). Previous studies indicated that heterogeneity typically has nonlinear effects on biodiversity and ecosystem function, as moderate heterogeneity can maximise spatial asynchrony (Redon et al., 2014; Wilcox et al., 2017). However, our study did not observe nonlinear patterns between fragmentation per se and plant diversity and above-ground productivity. This may be due to the low spatial heterogeneity of this area as a result of agricultural intensification (Benton et al., 2003; Chen et al., 2019). The gradient of fragmentation per se in our study may not cover the optimal heterogeneity levels for maximising plant diversity and above-ground productivity (Thompson and Gonzalez, 2016).”

      Meanwhile, we also discussed the nonlinear pattern of the BEF relationship with increasing levels of fragmentation per se to add depth to the discussion.

      Line 442-451:

      “In addition, our study found that the BEF relationship showed a nonlinear pattern with increasing levels of fragmentation per se. For a given level of habitat loss, the positive BEF relationship was strongest at moderate fragmentation per se level and became neutral at high fragmentation per se level. This can be explained by the increased spatial asynchrony at moderate fragmentation per se level, which can promote niche complementary among species in the community and thus strengthen the BEF relationship (Gonzalez et al., 2020; Thompson and Gonzalez, 2016; Tscharntke et al., 2012). The neutral BEF relationship at high fragmentation per se level may be due to edge effects enhancing environmental filtering, thereby leading to functional redundancy among species and decoupling the BEF relationship (Fetzer et al., 2015; Hu et al., 2016; Zambrano et al., 2019).”

      (a) Line 74-75: I was wondering if you also thought of spatial insurance effects or spatial asynchrony effects that can emerge with habitat fragmentation, which could lead to increased ecosystem functioning as well? (refs. above).

      Response: Thanks for your constructive suggestions. In the revised manuscript, we have explicitly considered the spatial insurance effect or spatial asynchrony as the important mechanism for fragmentation per se to increase plant diversity, ecosystem function, and the BEF relationship.

      Line 74-77:

      “In theory, habitat loss and fragmentation per se can regulate ecosystem function and the BEF relationship by altering species composition, interactions, and spatial asynchrony regardless of changes in species richness (Liu et al., 2018; Thompson and Gonzalez, 2016; Tscharntke et al., 2012).”

      Line 402-408:

      “In our study, a possible mechanism for the positive impacts of fragmentation per se on plant diversity and above-ground productivity (indirect positive impact via plant diversity) is that fragmentation per se increases the habitat heterogeneity in the landscape, which can promote biodiversity through spatial asynchrony and spatial insurance effects (Tscharntke et al., 2012). Previous studies indicated that heterogeneity typically has nonlinear effects on biodiversity and ecosystem function, as moderate heterogeneity can maximise spatial asynchrony (Redon et al., 2014; Wilcox et al., 2017).”

      Line 442-451:

      “In addition, our study found that the BEF relationship showed a nonlinear pattern with increasing levels of fragmentation per se. For a given level of habitat loss, the positive BEF relationship was strongest at moderate fragmentation per se level and became neutral at high fragmentation per se level. This can be explained by the increased spatial asynchrony at moderate fragmentation per se level, which can promote niche complementary among species in the community and thus strengthen the BEF relationship (Gonzalez et al., 2020; Thompson and Gonzalez, 2016; Tscharntke et al., 2012). The neutral BEF relationship at high fragmentation per se level may be due to edge effects enhancing environmental filtering, thereby leading to functional redundancy among species and decoupling the BEF relationship (Fetzer et al., 2015; Hu et al., 2016; Zambrano et al., 2019).”

      (b) I was wondering, if this result of linear effects could also be the result of a fragmentation gradient that does not cover the whole range of potential values? Maybe it would be good to compare the gradient in habitat fragmentation in your study with a theoretical minimum maximum/considering that there might be an optimal medium degree of fragmentation.

      Response: Thanks for your insightful comment. We agree with your point that the linear effect of fragmentation per se in our study may be due to the fact that the gradient of fragmentation per se in this region may not cover the optimal heterogeneity levels for maximising spatial asynchrony. This is mainly because the agricultural intensification in the agro-pastoral ecotone of northern China could lead to lower spatial heterogeneity in this region. We have explicitly discussed this point in the revised manuscript.

      Line 406-413:

      “Previous studies indicated that heterogeneity typically has nonlinear effects on biodiversity and ecosystem function, as moderate heterogeneity can maximise spatial asynchrony (Redon et al., 2014; Wilcox et al., 2017). However, our study did not observe nonlinear patterns between fragmentation per se and plant diversity and above-ground productivity. This may be due to the low spatial heterogeneity of this area as a result of agricultural intensification (Benton et al., 2003; Chen et al., 2019). The gradient of fragmentation per se in our study may not cover the optimal heterogeneity levels for maximising plant diversity and above-ground productivity (Thompson and Gonzalez, 2016).”

      (4) Some additional suggestions:

      (a) Line 3: Maybe add "via reducing the percentage of grassland specialists in the community"?

      Response: Thanks for your suggestion. We have revised this sentence.

      Line 19:

      “Habitat loss can weaken the positive BEF relationship via reducing the percentage of grassland specialists in the community”

      (b) Lines 46-48: Maybe add "but see: Duffy, J.E., Godwin, C.M. & Cardinale, B.J. (2017). Biodiversity effects in the wild are common and as strong as key drivers of productivity. Nature."

      Response: Thanks for your suggestion. We have added this reference here.

      Line 47-49:

      “When research expands from experiments to natural systems, however, BEF relationships remain unclear in the natural assembled communities, with significant context dependency (Hagan et al., 2021; van der Plas, 2019; but see Duffy et al., 2017).”

      (c) Lines 82-87 and lines 90-93: Hence, your study actually is in contrast to these findings, i.e., fragmented landscapes do not necessarily have a lower fraction of grassland specialists? If yes, could you highlight this more explicitly?

      Response: Thanks for your insightful comment. We have explicitly highlighted this point in the revised manuscript.

      Line 434-439:

      “Meanwhile, our study demonstrates that habitat loss, rather than fragmentation per se, can decrease the degree of habitat specialisation by leading to the replacement of specialists by generalists in the community, thus weakening the BEF relationship. This is mainly because fragmentation per se did not decrease the grassland specialist richness in this region, whereas habitat loss decreased the grassland specialist richness and led to the invasion of more weeds from the surrounding farmland into the grassland community (Yan et al., 2022; Yan et al., 2023).”

      (d) Line 360: Could you add some examples of these multiple ecosystem functions you refer to?

      Response: Thanks for your suggestion. We have added some examples of these multiple ecosystem functions here.

      Line 456-457:

      “Therefore, future studies are needed to focus on multiple ecosystem functions, such as below-ground productivity, litter decomposition, soil carbon stocks, etc.”

      Reviewer #3 (Public Review):

      Summary:

      The authors aim to solve how landscape context impacts the community BEF relationship. They found habitat loss and fragmentation per se have inconsistent effects on biodiversity and ecosystem function. Habitat loss rather than fragmentation per se can weaken the positive BEF relationship by decreasing the degree of habitat specialization of the community.

      Strengths:

      The authors provide a good background, and they have a good grasp of habitat fragmentation and BEF literature. A major strength of this study is separating the impacts of habitat loss and fragmentation per se using the convincing design selection of landscapes with different combinations of habitat amount and fragmentation per se. Another strength is considering the role of specialists and generalists in shaping the BEF relationship.

      Response: We are grateful to you for the recognition and constructive comments. All the comments and suggestions are very constructive for improving this manuscript. We have carefully revised the manuscript following your suggestions. All changes are marked in red font in the revised manuscript.

      Weaknesses:

      (1) The authors used five fragmentation metrics in their study. However, the choice of these fragmentation metrics was not well justified. The ecological significance of each fragmentation metric needs to be differentiated clearly. Also, these fragmentation metrics may be highly correlated with each other and redundant. I suggest author test the collinearity of these fragmentation metrics for influencing biodiversity and ecosystem function.

      Response: Thanks for your constructive suggestion. The fragmentation metrics used in our study represent the different processes of breaking apart of habitat in the landscape, which are widely used by previous studies (Fahrig, 2003; Fahrig, 2017). In the revised manuscript, we have provided more detailed information about the ecological significance of these fragmentation indices.

      Line 142-148:

      “The patch density metric reflects the breaking apart of habitat in the landscape, which is a direct reflection of the definition of fragmentation per se (Fahrig et al., 2019). The edge density metric reflects the magnitude of the edge effect caused by fragmentation (Fahrig, 2017). The mean patch area metric and the mean nearest-neighbor distance metric are associated with the area and distance effects of island biogeography, respectively, reflecting the processes of local extinction and dispersal of species in the landscape (Fletcher et al., 2018).”

      Meanwhile, we have calculated the variance inflation factors (VIF) for each fragmentation metric to assess their collinearity. The VIF of these fragmentation metrics were all less than four, suggesting no significant multicollinearity for influencing biodiversity and ecosystem function.

      Author response table 2.

      Variance inflation factors of habitat loss and fragmentation per se indices for influencing plant richness and above-ground biomass.

      (2) I found the local environmental factors were not considered in the study. As the author mentioned in the manuscript, temperature and water also have important impacts on biodiversity and ecosystem function in the natural ecosystem. I suggest authors include the environmental factors in the data analysis to control their potential impact, especially the structural equation model.

      Response: Thanks for your constructive suggestion. We agree with you that environmental factors should be considered in our study. In the revised manuscript, we have integrated two environmental factors related to water and temperature (soil water content and land surface temperature) into the data analysis to control their potential impact. The main results and conclusions of the revised manuscript are consistent with those of the previous manuscript.

      Reviewer #3 (Recommendations For The Authors):

      (1) L60-63. The necessity to distinguish between habitat loss and fragmentation per se is not clearly stated. More information about biodiversity conservation strategies can be given here.

      Response: Thanks for your suggestion. In the revised manuscript, we have provided more evidence about the importance of distinguishing between habitat loss and fragmentation per se for biodiversity conservation.

      Line 62-67:

      “Habitat loss is often considered the major near-term threat to the biodiversity of terrestrial ecosystems (Chase et al., 2020; Haddad et al., 2015), while the impact of fragmentation per se remains debated (Fletcher Jr et al., 2023; Miller-Rushing et al., 2019). Thus, habitat loss and fragmentation per se may have inconsistent ecological consequences and should be considered simultaneously to establish effective conservation strategies in fragmented landscapes (Fahrig et al., 2019; Fletcher et al., 2018; Miller-Rushing et al., 2019).”

      (2) L73-77. The two sentences are hard to follow. Please rephrase to improve the logic. And I don't understand the "however" here. There is no twist.

      Response: Thanks for your suggestion. We have rephrased the two sentences to improve their logic.

      Line 74-79:

      “In theory, habitat loss and fragmentation per se can regulate ecosystem function and the BEF relationship by altering species composition, interactions, and spatial asynchrony regardless of changes in species richness (Liu et al., 2018; Thompson and Gonzalez, 2016; Tscharntke et al., 2012). This is because species in communities are not ecologically equivalent and may respond differently to habitat loss and fragmentation per se, and contribute unequally to ecosystem function (Devictor et al., 2008; Wardle and Zackrisson, 2005).”

      (3) L97. Are grasslands really the largest terrestrial ecosystem? Isn't it the forest?

      Response: We apologize for making this confusion. We have rephrased this sentence here.

      Line 101-104:

      “Grasslands have received considerably less attention, despite being one of the largest terrestrial ecosystems, and suffering severe fragmentation due to human activities, such as agricultural reclamation and urbanisation (Fardila et al., 2017).”

      (4) Fig.1, whether the four sample plots presented in panel b are from panel a. Please add the scale bar in panel b.

      Response: Thanks for your comment. The four sample plots presented in panel b are from panel a in Figure 1. We have also added the scale bar in panel b.

      (5) L105. This statement is too specific. Please remove and consider merging this paragraph with the next.

      Response: Thanks for your suggestion. We have removed this sentence and merged this paragraph with the next.

      (6) L157. The accuracy and kappa value of the supervised classification should be given.

      Response: Thanks for your suggestion. We have added the accuracy and kappa value of the supervised classification in the revised manuscript.

      Line 176-177:

      “The overall classification accuracy was 84.3 %, and the kappa coefficient was 0.81.”

      (7) I would recommend the authors provide the list of generalists and specialists surveyed in the supplementary. Readers may not be familiar with the plant species composition in this area.

      Response: Thanks for your suggestion. We agree with your point. We have provided the list of generalists and specialists surveyed in the Appendix Table A4.

      Line 282-283:

      “A total of 130 vascular plant species were identified in our study sites, including 91 grassland specialists and 39 weeds (Appendix Table A4).”

      (8) Fig.4, it is better to add the results of variation partition to present the relative contribution of habitat fragmentation, environmental factors, and plant diversity.

      Response: Thanks for your suggestion. We have integrated the landscape context, environmental factors, and plant diversity into the multi-model averaging analysis and redraw Figure 4 to present their relative importance for above-ground biomass.

      Line 313-319:

      Author response image 3.

      Standardised parameter estimates and 95% confidence intervals for landscape context, plant diversity, and environmental factors affecting above-ground biomass from 130 landscapes in the Tabu River Basin, a typical agro-pastoral ecotone of northern China. Standardised estimates and 95% confidence intervals are calculated by the multi-model averaging method based on the four optimal models affecting above-ground biomass (Appendix Table A3). ** represent significance at the 0.01 level.

      (9) Please redraw Fig.2 and Fig.5 to integrate the environmental factors. Add the R-square to Fig 5.

      Response: Thanks for your suggestion. We have integrated two environmental factors into the structural equation model and redraw Figure 2 and Figure 5 in the revised manuscript. And we have added the R-square to the Figure 5.

      (10) L354. The authors should be careful to claim that habitat loss could reduce the importance of plant diversity to ecosystem function. This pattern observed may depend on the type of ecosystem function studied.

      Response: Thanks for your suggestion. We have avoided this claim in the revised manuscript and explicitly discussed the importance of simultaneously focusing on multiple ecosystem functions, such as below-ground productivity, litter decomposition, soil carbon stocks, etc.

      Line 454-457:

      “This inconsistency can be explained by trade-offs between different ecosystem functions that may differ in their response to fragmentation per se (Banks-Leite et al., 2020). Therefore, future studies are needed to focus on multiple ecosystem functions, such as below-ground productivity, litter decomposition, soil carbon stocks, etc.”

    1. Author Response

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Transcriptional readthrough, intron retention, and transposon expression have been previously shown to be elevated in mammalian aging and senescence by multiple studies. The current manuscript claims that the increased intron retention and readthrough could completely explain the findings of elevated transposon expression seen in these conditions. To that end, they analyze multiple RNA-seq expression datasets of human aging, human senescence, and mouse aging, and establish a series of correlations between the overall expression of these three entities in all datasets.

      While the findings are useful, the strength of the evidence is incomplete, as the individual analyses unfortunately do not support the claims. Specifically, to establish this claim there is a burden of proof on the authors to analyze both intron-by-intron and gene-by-gene, using internal matched regions, and, in addition, thoroughly quantify the extent of transcription of completely intergenic transposons and show that they do not contribute to the increase in aging/senescence. Furthermore, the authors chose to analyze the datasets as unstranded, even though strand information is crucial to their claim, as both introns and readthrough are stranded, and if there is causality, than opposite strand transposons should show no preferential increase in aging/senescence. Finally, there are some unclear figures that do not seem to show what the authors claim. Overall, the study is not convincing.

      Major concerns: 1) Why were all datasets treated as unstanded? Strand information seems critical, and should not be discarded. Specifically, stranded information is crucial to increase the confidence in the causality claimed by the authors, since readthrough and intron retention are both strand specific, and therefore should influence only the same strand transposons and not the opposite-strand ones.

      This is an excellent suggestion. Since only one of our datasets was stranded, we did not run stranded analyses for the sake of consistency. We would like to provide two analyses here that consider strandedness:

      First, we find that within the set of all expressed transposons (passing minimal read filtering), 86% of intronic transposons match the strand of the intron (3147 out of 3613). In contrast, the number is 51% after permutation of the strands. Similarly, when we randomly select 1000 intronic transposons 45% match the strandedness of the intron (here we select from the set of all transposons). This is consistent with the idea that most transposons are only detectable because they are co-expressed on the sense strand of other features that are highly expressed.

      As for the readthrough data, 287 out of 360 transposons (79%) within readthrough regions matched the strand of the gene and its readthrough.

      Second, in the model we postulate, the majority of transposon transcription occurs as a co-transcriptional artifact. This applies equally to genic transposons (gene expression), intronic (intron retention) and gene proximal (readthrough or readin) transposons. Therefore, we performed the following analysis for the set of all transposons in the Fleischer et al. fibroblast dataset.

      When we invert the strand annotation for transposons, before counting and differential expression, we would expect the counts and log fold changes to be lower compared to using the “correct” annotation file.

      Indeed, we show that out of 6623 significantly changed transposons with age only 226 show any expression in the “inverted run” (-96%). (Any expression is defined as passing basic read filtering.)

      Out of the 226 transposons that can be detected in both runs most show lower counts (A) and age-related differential expression converging towards zero (B) in the inverted run (Fig. L1).

      Author response image 1.

      Transposons with inverted strandedness (“reverse”) show lower expression levels (log counts; A) and no differential expression with age (B) when compared to matched differentially expressed transposons (“actual”). For this analysis we selected all transposons showing significant differential expression with age in the actual dataset that also showed at least minimal expression in the strand-inverted analysis (n=226). Data from Fleischer et al. (2018). (A) The log (counts) are clipped because we only used transposons that passed minimal read filtering in this analysis. (B) The distribution of expression values in the actual dataset is bimodal and positive since some transposons are significantly up- or downregulated. This bimodal distribution is lost in the strand-inverted analysis.

      2) "Altogether this data suggests that intron retention contributes to the age-related increase in the expression of transposons" - this analysis doesn't demonstrate the claim. In order to prove this they need to show that transposons that are independent of introns are either negligible, or non-changing with age.

      We would like to emphasize that we never claimed that intron retention and readthrough can explain all of the age-related increases in transposon expression. In fact, our data is compatible with a multifactorial origin of transposons expression. Age- and senescence-related transposon expression can occur due to: 1/ intron retention, 2/ readthrough, 3/ loss of intergenic heterochromatin. Specifically, we do not try to refute 3.

      However, since most transposons are found in introns or downstream of genes, this suggests that intron retention and readthrough will be major, albeit non-exclusive, drivers of age-related changes in transposons expression. Even if the fold-change for intergenic transposons with aging or senescence were higher this would not account for the broadscale expression patterns seen in RNAseq data.

      To further illustrate this, we analyzed transposons located in introns, genes, downstream (ds) or upstream (us) of genes (distance to gene < 25 kb) or in intergenic regions (distance to gene > 25 kb). Indeed, we find that although intergenic transposons show similar log-fold changes to other transposon classes (Fig. L2A), their total contribution to read counts is negligible (Fig. L2B, Fig. Fig. S15). We have also now added a more nuanced explanation of this issue to the discussion.

      Author response image 2.

      We analyzed transposons located in introns, genes, downstream (ds) or upstream (us) of genes (distance to gene < 25 kb) or in intergenic regions (distance to gene > 25 kb). Independent of their location, transposons show similar differential expression with aging or cellular senescence (A). In contrast, the expression of transposons (log counts) is highly dependent on their location and the median log(count) value decreases in the order: genic > intronic > ds > us > intergenic.

      Author response image 3.

      Total counts are the sum of all counts from transposons located in introns, genes, downstream (ds) or upstream (us) of genes (distance to gene < 25 kb) or in intergenic regions (distance to gene > 25 kb). Counts were defined as cumulative counts across all samples.

      3) Additionally, the correct control regions should be intronic regions other than the transposon, which overall contributed to the read counts of the intron.

      4) Furthermore, analysis of read spanning intron and partly transposons should more directly show this contribution.

      Thank you for this comment. To rephrase this, if we understand correctly, the concern is that an increase in transposon expression could bias the analysis of intron retention since transposons often make up a substantial portion of an intron. We would like to address this concern with the following three points:

      First, if the concern is the correlation between log fold-change of transposons vs log fold-change of their containing introns, we do not think that this kind of data is biased. While transposons make up much of the intron, a single transposon on average only accounts for less than 10% of an intron.

      Second, to address this more directly, we show here that even introns that do not contain expressed transposons are increased in aging fibroblasts and after induction of cellular senescence (Fig. S8). This shows that intron retention is universal and most likely not heavily biased by the presence or absence of expressed transposons.

      Author response image 4.

      We split the set of introns that significantly change with cellular aging (A) or cell senescence (B) into introns that contain at least one transposon (has_t) and those that do not contain any transposons (has_no_t). Intron retention is increased in both groups. In this analysis we included all transposons that passed minimal read filtering (n=63782 in A and n=124173 in B). Median log-fold change indicated with a dashed red line for the group of introns without transposons.

      Third, we provide an argument based on the distribution of transposons within introns (Fig. L3).

      Author response image 5.

      The 5’ and 3’ splice sites show the highest sequence conservation between introns, whereas the majority of the intronic sequence does not. This is because these sites contain binding sites for splicing factors such as U1, U2 and SF1 (A). Transposons could affect splicing and we present a biologically plausible mechanism and two ancillary hypotheses here (B). If transposons affect the splicing (retention) of introns the most likely mechanism would be via impairment of splice site recognition because a transposon close to the site forms a secondary structure, binds an effector protein or provides inadequate sequences for pairing. Hypothesis 1: Transposons impair splicing because they are close to the splice site. Hypothesis 2: Transposons do not impair splicing because they are located away from the splice junction. Retained introns should show a similar depletion of transposons around the junction. Image adapted from: Ren, Pingping, et al. "Alternative splicing: a new cause and potential therapeutic target in autoimmune disease." Frontiers in Immunology 12 (2021): 713540.

      Consistent with hypothesis 2 (“transposons do not impair splicing”), we show that the distribution of transposons within introns is similar for the set of all transposons and all significant transposons within significantly overexpressed introns (Fig. S7. A and B is similar in the case of aged fibroblasts; D and E is similar in the case of cellular senescence). If transposon expression was causally linked to changes in intron retention, the most likely mechanism would be via an impairment of splicing. We would expect transposons to be located close to the splice junction, which is not what we observed. Instead, the data is more consistent with intron retention as a driver of transposon expression.

      Author response image 6.

      Transposons are evenly distributed within introns except for the region close to splice junctions (A-E). Transposons appear to be excluded from the splice junction-adjacent region both in all introns (A, D) and in significantly retained introns (B, E). In addition, transposon density of all introns and significantly retained introns is comparable (C, F). We included only introns containing at least one transposon in this analysis. A) Distribution of 2292769 transposons within 163498 introns among all annotated transposons. B) Distribution of 195190 transposons within 14100 introns significantly retained with age. C) Density (transposon/1kb of intron) of transposons in all introns (n=163498) compared to significantly retained introns (n=14100). D) as in (A) E) Distribution of 428130 transposons within 13205 introns significantly retained with induced senescence. F) Density (transposon/1kb of intron) of transposons in all introns (n=163498) compared to significantly retained introns (n=13205).

      5) "This contrasts with the almost completely even distribution of randomly permuted transposons." How was random permutation of transposons performed? Why is this contract not trivial, and why is this a good control?

      Permutation was performed using the bedtools shuffle function (Quinlan et al. 2010). We use the set of all annotated transposons and all reshuffled transposons as a control. It is interesting to observe that these two show a very similar distribution with transposons evenly spread out relative to genes. In contrast, expressed transposons are found to cluster downstream of genes. This gave rise to our initial working hypothesis that readthrough should affect transposon expression.

      6) Fig 4: the choice to analyze only the 10kb-20kb region downstream to TSE for readthrough regions has probably reduced the number of regions substantially (there are only 200 left) and to what extent this faithfully represent the overall trend is unclear at this point.

      This is addressed in Suppl. Fig. 7, we repeated the analysis for every 10kb region between 0 and 100kb, showing similar results.

      Furthermore, we show below in a new figure that the results are comparable when we measure readthrough in the 0 to 10kb region, while the sample size of readthrough regions is increased.

      Finally, it is commonly accepted to remove readthrough regions overlapping genes, which while reducing sample size, increases accuracy for readthrough determination (Rosa-Mercado et al. 2021). Without filtering readthrough regions can overlap neighboring genes which is reflected in an elevated ratio of Readthrough_counts/Genic_counts (Fig. S9).

      Author response image 7.

      A) Readthrough was determined in a region 0 to 10 kb downstream of genes for a subset of genes that were at least 10 kb away from the nearest neighboring gene (n=684 regions). The log2 ratio of readthrough to gene expression is plotted across five age groups (adolescent n=32, young n=31, middle-aged n=22, old n=37 and very old n=21). B) As in (A) but data is plotted on a per sample basis. C) Readthrough was determined in a region 0 to 10 kb downstream of genes for a subset of genes that were at least 10 kb away from the nearest neighboring gene (n=1045 regions). The log2 ratio of readthrough to gene expression is plotted for the groups comprising senescence (n=12) and the non-senescent group (n=6). D) As in (D) but data is plotted on a per sample basis and for additional control datasets (serum-starved, immortalized, intermediate passage and early passage). N=3 per group.

      7) Fig. 5B shows the opposite of the authors claims: in the control samples there are more transposon reads than in the KCl samples.

      Thank you for pointing this out. During preparation of the manuscript the labels of Fig. 5B were switched (however, the color matching between Fig. 5A-C is correct). We apologize for this mistake, which we have now corrected.

      8) "induced readthrough led to preferential expression of gene proximal transposons (i.e. those within 25 kb of genes), when compared with senescence or aging". A convincing analysis would show if there is indeed preferential proximity of induced transposons to TSEs. Since readthrough transcription decays as a function of distance from TSEs, the expression of transposons should show the same trends if indeed simply caused by readthrough. Also, these should be compared to the extent of transposon expression (not induction) in intergenic regions without any readthrough, in these conditions.

      This is a very good suggestion. We now provide two new supplementary figures analyzing the distance-dependence of transposon expression.

      In the first figure (Fig. S13) we show that readthrough decreases with distance (A, B) and we show that transposon counts are higher for transposons close to genes, following a similar pattern to readthrough. This is true in fibroblasts isolated from aged donors (A) and with cellular senescence (B).

      Author response image 8.

      Readthrough counts (rt_counts) decrease exponentially downstream of genes, both in the aging dataset (A) and in the cellular senescence dataset (B). Although noisier, the pattern for transposon counts (transp_cum_counts) is similar with higher counts closer to gene terminals, both in the aging dataset (C) and in the cellular senescence dataset (D). Readthrough counts are the cumulative counts across all genes and samples. Readthrough was determined in 10 kb bins and the values are assigned to the midpoint of the bin for easier plotting. Transposon counts are the cumulative counts across all samples for each transposon that did not overlap a neighboring gene. n=801 in (C) and n=3479 in (D).

      In the second figure (Fig. S14) we show that transposons found downstream of genes with high readthrough show a more pronounced log-fold change (differential expression) than transposons downstream of genes with low readthrough (defined based on log-fold change). This is true in fibroblasts isolated from aged donors (A) and with cellular senescence (B). Furthermore, the difference between high and low readthrough region transposons is diminished for transposons that are more than 10 kb downstream of genes, as would be expected given that readthrough decreases with distance.

      Author response image 9.

      Transposons found downstream of genes with high readthrough (hi_RT) show a more pronounced log-fold change (transp_logfc) than transposons downstream of genes with low readthrough (low_RT). This is true in fibroblasts isolated from aged donors (A) and with cellular senescence (B). Furthermore, the difference between high and low readthrough region transposons is diminished for transposons that are more than 10 kb downstream of genes (“Transp > 10 kb”). Transposons in high readthrough regions were defined as those in the top 20% of readthrough log-fold change. Readthrough was measured between 0 and 10 kb downstream from genes. n=2124 transposons in (A) and n=6061 transposons in (B) included in the analysis.

      Reviewer #2 (Public Review):

      In this manuscript, the authors examined the role of transcription readout and intron retention in increasing transcription of transposable elements during aging in mammals. It is assumed that most transposable elements have lost the regulatory elements necessary for transcription activation. Using available RNA-seq datasets, the authors showed that an increase in intron retention and readthrough transcription during aging contributes to an increase in the number of transcripts containing transposable elements.

      Previously, it was assumed that the activation of transposable elements during aging is a consequence of a gradual imbalance of transcriptional repression and a decrease in the functionality of heterochromatin (de repression of transcription in heterochromatin). Therefore, this is an interesting study with important novel conclusion. However, there are many questions about bioinformatics analysis and the results obtained.

      Major comments:

      1) In Introduction the authors indicated that only small fraction of LINE-1 and SINE elements are expressed from functional promoters and most of LINE-1 are co-expressed with neighboring transcriptional units. What about other classes of mobile elements (LTR mobile element and transposons)?

      We thank the reviewer for this comment. Historically, most repetitive elements, e.g. DNA elements and retrotransposon-like elements, have been considered inactive, having accrued mutations which prevent them from transposition. On the other hand, based on recent data it is indeed very possible that certain LTR elements become active with aging as suggested in several manuscripts (Liu et al. 2023, Autio et al. 2020). However, these elements are not well annotated and our final analysis (Fig. 6) relies on a well-defined distinction between active and inactive elements. (See also question 2 for further discussion.)

      Finally, we would like to point out some of the difficulties with defining expression and re-activation of LTR/ERV elements based on RNAseq data that have been highlighted for the Liu manuscript and are concordant with several of our results: https://pubpeer.com/publications/364E785636ADF94732A977604E0256

      Liu, Xiaoqian, et al. "Resurrection of endogenous retroviruses during aging reinforces senescence." Cell 186.2 (2023): 287-304.

      Autio A, Nevalainen T, Mishra BH, Jylhä M, Flinck H, Hurme M. Effect of ageing on the transcriptomic changes associated with expression at the HERV-K (HML-2) provirus at 1q22. Immun Ageing. 2020;17(1):11.

      2) Results: Why authors considered all classes of mobile elements together? It is likely that most of the LTR containing mobile elements and transposons contain active promoters that are repressed in heterochromatin or by KRAB-C2H2 proteins.

      We do not consider LTR containing elements because there is uncertainty regarding their overall expression levels and their expression with aging (Nevalainen et al. 2018). Furthermore, we believe that substantial activity of LTR elements in human genomes should have been detectable through patterns of insertional mutagenesis. Yet studies generally show low to negligible levels of LTR (ERV) mutagenesis. Here, for example, at a 200-fold lower rate than for LINEs (Lee et al. 2012).

      Importantly, our analysis in Fig. 6 relies on well-annotated elements like LINEs, which is why we do not include LTR or SINE elements that could be potentially expressed. However, for other analyses we did consider element families independently as can be seen in Table S1, for example.

      Nevalainen, Tapio, et al. "Aging-associated patterns in the expression of human endogenous retroviruses." PLoS One 13.12 (2018): e0207407.

      Lee, Eunjung, et al. "Landscape of somatic retrotransposition in human cancers." Science 337.6097 (2012): 967-971.

      3) Fig. 2. A schematic model of transposon expression is not presented clearly. What is the purpose of showing three identical spliced transcripts?

      This is indeed confusing. There are three spliced transcripts to schematically indicate that the majority of transcripts will be correctly spliced and that intron retention is rare (estimated at 4% of all reads in our dataset). We have clarified the figure now, please see below:

      Author response image 10.

      A schematic model of transposon expression. In our model, represented in this schematic, transcription (A) can give rise to mRNAs and pre-mRNAs that contain retained introns when co-transcriptional splicing is impaired. This is often seen during aging and senescence, and these can contain transposon sequences (B). In addition, transcription can give rise to mRNAs and pre-mRNAs that contain transposon sequences towards the 3’-end of the mRNA when co-transcriptional termination at the polyadenylation signal (PAS) is impaired (C, D) as seen with aging and senescence. Some of these RNAs may be successfully polyadenylated (as depicted here) whereas others will be subject to nonsense mediated decay. Image created with Biorender.

      4) The study analyzed the levels of RNA from cell cultures of human fibroblasts of different ages. The annotation to the dataset indicated that the cells were cultured and maintained. (The cells were cultured in high-glucose (4.5mg/ml) DMEM (Gibco) supplemented with 15% (vol/vol) fetal bovine serum (Gibco), 1X glutamax (Gibco), 1X non-essential amino acids (Gibco) and 1% (vol/vol) penicillin-streptomycin (Gibco). How correct that gene expression levels in cell cultures are the same as in body cells? In cell cultures, transcription is optimized for efficient division and is very different from that of cells in the body. In order to correlate a result on cells with an organism, there must be rigorous evidence that the transcriptomes match.

      We agree and have updated the discussion to reflect this shortcoming. While we do not have human tissue data, we would like to draw the reviewer’s attention to Fig. S3 where we presented some liver data for mice. We now provide an additional supplementary figure (in a style similar to Fig. S2) showing how readthrough, transposon expression and intron retention changes in 26 vs 5-month-old mice (Fig. S4). Indeed, intron, readthrough and transposons increase with age in mice, although this is more pronounced for transposons and readthrough.

      Author response image 11.

      Intron, readthrough and transposon elements are elevated in the liver of aging mice (26 vs 5-month-old, n=6 per group). Readthrough and transposon expression is especially elevated even when compered to genic transcripts. The percentage of upregulated transcripts is indicated above each violin plot and the median log10-fold change for genic transcripts is indicated with a dashed red line.

      Finally, just to elaborate, we used the aging fibroblast dataset by Fleischer et al. for three reasons:

      1) Yes, aging fibroblasts could be a model of human aging, with important caveats as you correctly point out,

      2) it is one of the largest such datasets allowing us to draw conclusions with higher statistical confidence and do things such as partial correlations

      3) it has been analyzed using similar techniques before (LaRocca, Cavalier and Wahl 2020) and this dataset is often used to make strong statements about transposons and aging such as transposon expression in this dataset being “consistent with growing evidence that [repetitive element] transcripts contribute directly to aging and disease”. Our goal was to put these statements into perspective and to provide a more nuanced interpretation.

      LaRocca, Thomas J., Alyssa N. Cavalier, and Devin Wahl. "Repetitive elements as a transcriptomic marker of aging: evidence in multiple datasets and models." Aging Cell 19.7 (2020): e13167.

      5) The results obtained for isolated cultures of fibroblasts are transferred to the whole organism, which has not been verified. The conclusions should be more accurate.

      We agree and have updated the discussion accordingly.

      6) The full pipeline with all the configuration files IS NOT available on github (pabisk/aging_transposons).

      Thank you for pointing this out, we have now uploaded the full pipeline and configuration files.

      7) Analysis of transcripts passing through repeating regions is a complex matter. There is always a high probability of incorrect mapping of multi-reads to the genome. Things worsen if unpaired short reads are used, as in the study (L=51). Therefore, the authors used the Expectation maximization algorithm to quantify transposon reads. Such an option is possible. But it is necessary to indicate how statistically reliable the calculated levels are. It would be nice to make a similar comparison of TE levels using only unique reads. The density of reads would drop, but in this case it would be possible to avoid the artifacts of the EM algorithm.

      We thank the reviewer for this suggestion. We show here that mapping only unique alignments (outFilterMultimapNmax=1 in STAR) leads to similar results.

      For the aging fibroblast dataset:

      Author response image 12.

      For the induced senescence dataset:

      Author response image 13.

    1. Author Response

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      The regulation of motor autoinhibition and activation is essential for efficient intracellular transport. This manuscript used biochemical approaches to explore two members in the kinesin-3 family. They found that releasing UNC-104 autoinhibition triggered its dimerization whereas unlocking KLP-6 autoinhibition is insufficient to activate its processive movement, which suggests that KLP-6 requires additional factors for activation, highlighting the common and diverse mechanisms underlying motor activation. They also identified a coiled-coil domain crucial for the dimerization and processive movement of UNC-104. Overall, these biochemical and single-molecule assays were well performed, and their data support their statements. The manuscript is also clearly written, and these results will be valuable to the field.

      Thank you very much!

      Ideally, the authors can add some in vivo studies to test the physiological relevance of their in vitro findings, given that the lab is very good at worm genetic manipulations. Otherwise, the authors should speculate the in vivo phenotypes in their Discussion, including E412K mutation in UNC-104, CC2 deletion of UNC-104, D458A in KLP-6.

      1. We have shown the phenotypes unc-104(E412K) mutation in C. elegans (Niwa et al., Cell Rep, 2016) and described about it in discussion (p.14 line 3-4). The mutant worm showed overactivation of the UNC-104-dependent axonal transport, which is consistent with our biochemical data showing that UNC-104(1-653)(E412K) is prone to form a dimer and more active than wild type.

      2. It has been shown that L640F mutation induces a loss of function phenotype in C. elegans (Cong et al., 2021). The amount of axonal transport is reduced in unc-104(L640F) mutant worms. L640 is located within the CC2 domain. To show the importance of CC2-dependent dimerization in the axonal transport in vivo, we biochemically investigated the impact of L640F mutation.

      By introducing L640F into UNC-104(1-653)(E412K), we performed SEC analysis. The result shows that UNC-104(1-653)(E412K,L640F) failed to form stable dimers despite the release of their autoinhibition (new Figure S8). This result strongly suggests the importance of the CC2 domain in the axonal transport in vivo. Based on the result, we discussed it in the revised manuscript (p.13 line 6-8).

      1. Regarding KLP-6(D458A), we need a genetic analysis using genome editing and we would like to reserve it for a future study. We speculate that the D458A mutation could lead to an increase in transport activity in vivo similar to unc-104(E412K). This is because the previous study have shown that wild-type KLP-6 was largely localized in the cell body, while KLP-6(D458A) was enriched at the cell periphery in the N2A cells (Wang et al., 2022). We described it in discussion (p.14 line 13-14).

      While beyond the scope of this study, can the author speculate on the candidate for an additional regulator to activate KLP-6 in C. elegans?

      The heterodimeric mechanoreceptor complex, comprising LOV-1 and PKD-2, stands as potential candidates for regulating KLP-6 dimerization. We speculate the heterodimerization property is suitable for the enhancement of KLP-6 dimerization. On the other hand, it's noteworthy that KLP-6 can undergo activation in Neuro 2a cells upon the release of autoinhibition (Wang et al., 2022). This observation implies the involvement of additional factors which are not present in sf9 cells may be able to induce dimerization. Post-translational modifications would be one of the candidates. We discussed it in p14 line 7-14.

      The authors discussed the differences between their porcine brain MTs and chlamydonomas axonemes in UNC-104 assays. However, the authors did not really retest UNC-104 on axonemes after more than two decades, thereby not excluding other possibilities.

      We thought that comparing different conditions used in different studies is essential for the advancement of the field of molecular motors. Therefore, we newly performed single-molecule assay using Chlamydomonas axonemes and compared the results with brain MTs (Fig. S6). Just as observed in the study by Tomoshige et al., we were also unable to observe the processive runs of UNC-104(1-653) on Chlamydomonas axonemes (Fig. S6A). Furthermore, we found that the landing rate of UNC-104(1-653) on Chlamydomonas axonemes was markedly lower in comparison to that on purified porcine microtubules (Fig. S6B).

      Reviewer #1 (Recommendations For The Authors):

      More discussion as suggested above would improve the manuscript.

      We have improved our manuscript as described above.

      Reviewer #2 (Public Review):

      The Kinesin superfamily motors mediate the transport of a wide variety of cargos which are crucial for cells to develop into unique shapes and polarities. Kinesin-3 subfamily motors are among the most conserved and critical classes of kinesin motors which were shown to be self-inhibited in a monomeric state and dimerized to activate motility along microtubules. Recent studies have shown that different members of this family are uniquely activated to undergo a transition from monomers to dimers.

      Niwa and colleagues study two well-described members of the kinesin-3 superfamily, unc104 and KLP6, to uncover the mechanism of monomer to dimer transition upon activation. Their studies reveal that although both Unc104 and KLP6 are both self-inhibited monomers, their propensities for forming dimers are quite different. The authors relate this difference to a region in the molecules called CC2 which has a higher propensity for forming homodimers. Unc104 readily forms homodimers if its self-inhibited state is disabled while KLP6 does not.

      The work suggests that although mechanisms for self-inhibited monomeric states are similar, variations in the kinesin-3 dimerization may present a unique form of kinesin-3 motor regulation with implications on the forms of motility functions carried out by these unique kinesin-3 motors.

      Thank you very much!

      Reviewer #2 (Recommendations For The Authors):

      The work is interesting but the process of making constructs and following the transition from monomers to dimers seems to be less than logical and haphazard. Recent crystallographic studies for kinesin-3 have shown the fold and interactions for all domains of the motor leading to the self-inhibited state. The mutations described in the manuscript leading to disabling of the monomeric self-inhibited state are referenced but not logically explained in relation to the structures. Many of the deletion constructs could also present other defects that are not presented in the mutations. The above issues prevent wide audience access to understanding the studies carried out by the authors.

      We appreciate this comment. We improved it as described bellow.

      Suggestions: Authors should present schematic, or structural models for the self-inhibited and dimerized states. The conclusions of the papers should be related to those models. The mutations should be explained with regard to these models and that would allow the readers easier access. Improving access to the readers in and outside the motor field would truly improve the impact of the manuscript on the field.

      The structural models illustrating the autoinhibited state have been included in new Figure S4, accompanied by an explanation of the correlation between the mutations and these structures in the figure legend. Additionally, schematic models outlining the dimerization process of both UNC-104 and KLP-6 have been provided in Figure S9 to enhance reader comprehension of the process.

      Reviewer #3 (Public Review):

      In this work, Kita et al., aim to understand the activation mechanisms of the kinesin-3 motors KLP-6 and UNC-104 from C. elegans. As with many other motor proteins involved in intracellular transport processes, KLP-6 and UNC-104 motors suppress their ATPase activities in the absence of cargo molecules. Relieving the autoinhibition is thus a crucial step that initiates the directional transport of intracellular cargo. To investigate the activation mechanisms, the authors make use of mass photometry to determine the oligomeric states of the full-length KLP-6 and the truncated UNC-104(1-653) motors at sub-micromolar concentrations. While full-length KLP-6 remains monomeric, the truncated UNC-104(1-653) displays a sub-population of dimeric motors that is much more pronounced at high concentrations, suggesting a monomer-to-dimer conversion. The authors push this equilibrium towards dimeric UNC-104(1-653) motors solely by introducing a point mutation into the coiled-coil domain and ultimately unleashing a robust processivity of the UNC-104 dimer. The authors find that the same mechanistic concept does not apply to the KLP-6 kinesin-3 motor, suggesting an alternative activation mechanism of the KLP-6 that remains to be resolved. The present study encourages further dissection of the kinesin-3 motors with the goal of uncovering the main factors needed to overcome the 'self-inflicted' deactivation.

      Thank you very much!

      Reviewer #3 (Recommendations For The Authors):

      126-128: It is surprising that surface-attachment does not really activate the full-length KLP6 motor (v=48 {plus minus} 42 nm/s). Can the authors provide an example movie of the gliding assay for the FL KLP6 construct? Gliding assays are done by attaching motors via their sfGFP to the surface using anti-GFP antibodies. Did the authors try to attach the full-length KLP-6 motor directly to the surface? If the KLP-6 motor sticks to the surface via its (inhibitory) C-terminus, this attachment would be expected to activate the motor in the gliding assay, ideally approaching the in vivo velocities of the activated motor.

      We have included an example kymograph showing the gliding assay of KLP-6FL (Fig. S1A). When we directly attached KLP-6FL to the surface, the velocity was 0.15 ± 0.02 µm/sec (Fig. S1B), which is similar to the velocity of KLP-6(1-390). While the velocity observed in the direct-attachment condition is much better than those observed in GFP-mediated condition, the observed velocity remains considerably slower than in vivo velocities. Firstly, we think this is because dimerization of KLP-6 is not induced by the surface attachment. Previous studies have shown that monomeric proteins are generally slower than dimeric proteins in the gliding assay (Tomishige et al., 2002). These are consistent with our observation that KLP-6 remains to be monomeric even when autoinhibition is released. Secondly, in vitro velocity of motors is generally slower than in vivo velocity.

      156-157: It seems that the GCN4-mediated dimerization induces aggregation of the KLP6 motor domains as seen in the fractions under the void volume in Figure 3B (not seen with the Sf9 expressed full-length constructs, see Figure 1B). Also, the artificially dimerized motor construct does not fully recapitulate the in vivo velocity of UNC-104. Did the authors analyze the KLP-6(1-390)LZ with mass photometry and is it the only construct that is expressed in E. coli?

      KLP-6::LZ protein is not aggregating. We have noticed that DNA and RNA from E. coli exists in the void fraction and they occasionally trap recombinant kinesin-3 proteins in the void fraction. To effectively remove these nucleic acids from our protein samples, we employed streptomycin sulfate as a purification method (Liang et al., Electrophoresis, 2009). Please see Purification of recombinant proteins in Methods. In the size exclusion chromatography analysis, we observed that KLP-6(1-393)LZ predominantly eluted in the dimer fraction (New Figure 3). Subsequently, we reanalyzed the motor's motility using a total internal reflection fluorescence (TIRF) assay, as shown in the revised Figure 3. Even after these efforts, the velocity was not changed significantly. The velocity of KLP-6LZ is about 0.3 µm/sec while that of cellular KLP-6::GFP is 0.7 µm/sec (Morsci and Barr, 2011). Similar phenomena, "slower velocity in vitro", has been observed in other motor proteins.

      169: In Wang et al., (2022) the microtubule-activated ATPase activities of the mutants were measured in vitro as well, with the relative activities of the motor domain and the D458A mutant being very similar. The D458A mutation is introduced into the full-length motor in Wang et al., while in the present work, the mutation is introduced into the truncated KLP-6(1-587) construct. Can the authors explain their reasoning for the latter?

      (1) Kinesins are microtubule-stimulated ATPases. i.e. The ATPase activity is induced by the binding with a microtubule.

      (2) Previous studies have shown that the one-dimensional movement of the monomeric motor domain of kinesin-3 depends on the ATPase activity even when the movement does not show clear plus-end directionality (Okada et al., Science, 1998).

      (3) While KLP-6(1-587) does not bind to microtubules, both KLP-6(1-390) (= the monomeric motor domain) and KLP-6(1-587)(D458A) similarly bind to microtubules and show one dimensional diffusion on microtubules (Fig. 4E and S2B).

      Therefore, the similar ATPase activities of the motor domain(= KLP-6(1-390)) and KLP-6(D458A) observed by Wang et al. is because both proteins similarly associate with and hydrolyze ATP on microtubules, which is consistent with our observation. On the other hand, because KLP-6(wild type) cannot efficiently bind to microtubules, the ATPase activity is low.

      Can the authors compare the gliding velocities of the KLP-6(1-390)LZ vs KLP-6(1-587) vs KLP-6(1-587)(D458A) constructs to make sure that the motors are similarly active?

      We conducted a comparative analysis of gliding velocities involving KLP-6(1-390), KLP-6(1-587), and KLP-6(1-587)(D458A) (Fig. S1C). We used KLP-6(1-390) instead of KLP-6(1-390)LZ, aligning with the protein used by Wang et al.. We demonstrated that both KLP-6(1-587) and KLP-6(1-587) (D458A) exhibited activity levels comparable to that of KLP-6(1-390). The data suggests that the motor of all recombinant proteins are similarly active.

      Please note that, unlike full length condition (Fig. 1D and S1A and S1B), the attachment to the surface using the anti-GFP antibody can activates KLP-6(1-587). The data suggests that, due to the absence of coverage by the MBS and MATH domain (Wang et al., Nat. Commun., 2022), the motor domain of KLP-6(1-587) to some extent permits direct binding to microtubules under gliding assay conditions.

      Are the monomeric and dimeric UNC-104(1-653) fractions in Figure 5B in equilibrium? Did the authors do a re-run of the second peak of UNC-104(1-653) (i.e. the monomeric fraction with ~100 kDa) to assess if the monomeric fraction re-equilibrates into a dimer-monomer distribution?

      We conducted a re-run of the second peak of UNC-104(1-653) and verified its re-equilibration into a distribution of dimers and monomers after being incubated for 72 hours at 4°C (Fig. S5).

      UNC-104 appears to have another predicted coiled-coiled region around ~800 aa (e.g. by NCoils) that would correspond to the CC3 in the mammalian homolog KIF1A. This raises the question if the elongated UNC-104(1-800) would dimerize more efficiently than UNC-104(1-653) (authors highlight the sub-population of dimerized UNC-104(1-653) at low concentrations in Figure 5C) and if this dimerization alone would suffice to 'match' the UNC-104(1-653)E412K mutant (Figure 5D). Did the authors explore this possibility? This would mean that dimerization does not necessarily require the release of autoinhibition.

      We have tried to purify UNC-104(1-800) and full-length UNC-104 using the baculovirus system. However, unfortunately, the expression level of UNC-104(1-800) and full length UNC-104 was too low to perform in vitro assays even though codon optimized vectors were used. Instead, we have analyzed full-length human KIF1A. We found that full-length KIF1A is mostly monomeric, not dimeric (Please look at the Author response image 1). The property is similar to UNC-104(1-653) (Figure 5A-C). Therefore, we think CC3 does not strongly affect dimerization of KIF1A, and probably its ortholog UNC-104. Moreover, a recent study has shown that CC2 domain, but not other CC domains, form a stable dimer in the case of KIF1A (Hummel and Hoogenraad, JCB, 2021). Given the similarity in the sequence of KIF1A and UNC-104, we anticipate that the CC2 domain of UNC-104 significantly contributes to dimerization, potentially more than other CC domains. We explicitly describe it in the Discussion in the revised manuscript.

      Author response image 1.

      Upper left, A representative result of size exclusion chromatography obtained from the analysis of full-length human KIF1A fused with sfGFP. Upper right, A schematic drawing showing the structure of KIF1A fused with sfGFP and a result of SDS-PAGE recovered from SEC analysis. Presumable dimer and monomer peaks are indicated. Lower left, Presumable dimer fractions in SEC were collected and analyzed by mass photometry. The result confirms that the fraction contains considerable amount of dimer KIF1A. Lower right, Presumable monomer fractions were collected and analyzed by mass photometry. The result confirms that the fraction mainly consists of monomer KIF1A. Note that these results obtained from full-length KIF1A protein are similar to those of UNC-104(1-653) protein shown in Figure 5A-C.

    1. Author Response

      The following is the authors’ response to the original reviews.

      Response to reviewer’s comments

      Reviewer #1 (Public Review):

      In this study, the structural characteristics of plant AlaDC and SerDC were analyzed to understand the mechanism of functional differentiation, deepen the understanding of substrate specificity and catalytic activity evolution, and explore effective ways to improve the initial efficiency of theanine synthesis.

      On the basis of previous solid work, the authors successfully obtained the X-ray crystal structures of the precursors of theanine synthesis-CsAlaDC and AtSerDC, which are key proteins related to ethylamine synthesis, and found a unique zinc finger structure on these two crystal structures that are not found in other Group II PLP-dependent amino acid decarboxylases. Through a series of experiments, it is pointed out that this characteristic zinc finger motif may be the key to the folding of CsAlaDC and AtSerDC proteins, and this discovery is novel and prospective in the study of theine synthesis.

      In addition, the authors identified Phe106 of CsAlaDC and Tyr111 of AtSerDC as key sites of substrate specificity by comparing substrate binding regions and identified amino acids that inhibit catalytic activity through mutation screening based on protein structure. It was found that the catalytic activity of CsAlaDCL110F/P114A was 2.3 times higher than that of CsAlaDC. At the same time, CsAlaDC and AtSerDC substrate recognition key motifs were used to carry out evolutionary analysis of the protein sequences that are highly homologous to CsAlaDC in embryos, and 13 potential alanine decarboxylases were found, which laid a solid foundation for subsequent studies related to theanine synthesis.

      In general, this study has a solid foundation, the whole research idea is clear, the experimental design is reasonable, and the experimental results provide strong evidence for the author's point of view. Through a large number of experiments, the key links in the theanine synthesis pathway are deeply studied, and an effective way to improve the initial efficiency of theanine synthesis is found, and the molecular mechanism of this way is expounded. The whole study has good novelty and prospectivity, and sheds light on a new direction for the efficient industrial synthesis of theanine

      Response: Thank you very much for taking time to review this manuscript. We appreciate all your insightful comments and constructive suggestions.

      Reviewer #1 (Recommendations For The Authors):

      (1) If some test methods are not original, references or method basis should be indicated.

      Response: Thank you very much for your careful reading of the manuscript and valuable suggestions. We have added references for the enzymatic activity experiments performed to measure the synthesis of theanine in the revised manuscript.

      (2) The conclusion is a little lengthy, and the summary of the whole study is not well condensed.

      Response: Thank you very much for your valuable suggestions. We have refined the conclusion in the revised manuscript, and it is as follows:

      In conclusion, our structural and functional analyses have significantly advanced understanding of the substrate-specific activities of alanine and serine decarboxylases, typified by CsAlaDC and AtSerDC. Critical amino acid residues responsible for substrate selection were identified—Tyr111 in AtSerDC and Phe106 in CsAlaDC—highlighting pivotal roles in enzyme specificity. The engineered CsAlaDC mutant (L110F/P114A) not only displayed enhanced catalytic efficiency but also substantially improved L-theanine yield in a synthetic biosynthesis setup with PsGS or GMAS. Our research expanded the repertoire of potential alanine decarboxylases through the discovery of 13 homologous enzyme candidates across embryophytic species and uncovered a special motif present in serine protease-like proteins within Fabale, suggesting a potential divergence in substrate specificity and catalytic functions. These insights lay the groundwork for the development of industrial biocatalytic processes, promising to elevate the production of L-theanine and supporting innovation within the tea industry.

      Reviewer #2 (Public Review)

      Summary:

      The manuscript focuses on the comparison of two PLP-dependent enzyme classes that perform amino acyl decarboxylations. The goal of the work is to understand the substrate specificity and factors that influence the catalytic rate in an enzyme linked to theanine production in tea plants.

      Strengths:

      The work includes x-ray crystal structures of modest resolution of the enzymes of interest. These structures provide the basis for the design of mutagenesis experiments to test hypotheses about substrate specificity and the factors that control catalytic rate. These ideas are tested via mutagenesis and activity assays, in some cases both in vitro and in plants.

      Weaknesses:

      The manuscript could be more clear in explaining the contents of the x-ray structures and how the complexes studied relate to the reactant and product complexes. The structure and mechanism section would also be strengthened by including a diagram of the reaction mechanism and including context about reactivity. As it stands, much of the structural results section consists of lists of amino acids interacting with certain ligands without any explanation of why these interactions are important or the role they play in catalysis. The experiments testing the function of a novel Zn(II)-binding domain also have serious flaws. I don't think anything can be said at this point about the function of the Zn(II) due to a lack of key controls and problems with experimental design.

      Response: Thank you very much for your thoughtful comments and feedback on our manuscript. We are pleased to hear that the work's strengths, such as the X-ray crystal structures and the mutagenesis experiments tied to the catalytic rate and substrate specificity, align with the goals of our research.

      We recognize the areas identified for improvement and appreciate the suggestions provided. We have emphasized how we use the structural information obtained to infer the roles of key amino acid residues in the reaction. Additionally, we have added a diagram of the reaction mechanism in the Supplementary figure to provide clearer context on reactivity and improve the overall understanding of the catalytic process. Regarding the structural results section, we have included a discussion that contextualizes the list of amino acids and their interactions with the ligands by explaining their significance and roles in catalysis. We acknowledge the weaknesses you've pointed out in the experiments concerning the novel Zn(II)-binding domain, but we would like to clarify that the focus of our study was not primarily on the zinc structure. While we agree that there may be limitations in the experimental design and controls for the zinc binding domain, we believe that these flaws do not significantly impact the overall findings of the study. The experiment served as a preliminary exploration of the potential functionality of the domain, and further studies are required to fully understand its role and mechanism.

      Reviewer #2 (Recommendations For The Authors):

      (1) In addition to the points raised in the public review, it would be ideal to provide some context for the enzymatic characterization. Why are the differences in kinetic parameters for AlaDC and SerDC significant?

      Response: Thank you for your comments and suggestions. The Km values for CsAlaDC and SerDCs are comparable, suggesting similar substrate affinities. However, CsAlaDC exhibits a significantly lower Vmax compared to AtSerDC and CsSerDC. This discrepancy implies that CsAlaDC and SerDCs may differ in the rates at which they convert substrate to product when saturated with substrate. SerDCs may have a faster turnover rate, meaning they convert substrate to product and release the enzyme more quickly, resulting in a higher Vmax. Differences in the stability or correct folding of the enzymes under assay conditions can also affect their Vmax. If SerDCs are more stable, they might maintain their catalytic activity better at higher substrate concentrations, contributing to a higher Vmax. We have added these to the part of “Enzymatic properties of CsAlaDC, AtSerDC, and CsSerDC” in our revised manuscript.

      (2) Why is Phe106/Tyr111 pair critical for substrate specificity? Does the amino acid contact the side chain? It might be helpful to a reader to formulate a hypothesis for this interaction.

      Response: Thank you for the question and comments. We conducted a comparison between the active sites of CsAlaDC and AtSerDC and observed a distinct difference in only two amino acids: F106 in CsAlaDC and Y111 in AtSerDC. The remaining amino acids were found to be identical. Expanding on previous research concerning Group II PLP-dependent amino acid decarboxylases, it was postulated and subsequently confirmed that these specific amino acids play a crucial role in substrate recognition. However, since we lack the structure of the enzyme-substrate complex, we are unable to elucidate the precise interactions occurring between the substrate and the amino acids at this particular site based solely on structural information.

      (3) Line 55 - Define EA again.

      Response: Thank you very much for your careful reading of the manuscript and valuable suggestions. We have redefined “EA” as the abbreviation for ethylamine in the revised manuscript.

      (4) Line 58 - The meaning of "determined by the quality formation of tea" is not clear.

      Response: Thank you very much for your careful reading of the manuscript and valuable suggestions. We have modified it in the revised manuscript.

      (5) Line 65 - Missing words between "despite they".

      Response: Thank you very much for your careful reading of the manuscript. We have corrected it in the revised manuscript.

      (6) Line 67 - Need a reference for the statement about lower activity?

      Response: Thank you for the question and comments. We have provided the following reference to support this statement in the revised manuscript.

      Reference: Bai, P. et al. (2021) Biochemical characterization of specific Alanine Decarboxylase (ADC) and its ancestral enzyme Serine Decarboxylase (SDC) in tea plants (Camellia sinensis). BMC Biotechnol. 21,17.

      (7) Line 100-101 - The meaning of "its closer relationship was Dicots plants." is not clear.

      Response: We have revised the sentence in the revised manuscript, as follows: “Phylogenetic analysis indicated that CsAlaDC is homologous with SerDCs in Dicots plants.”

      (8) Line 139 - Missing a word between "as well as" and "of".

      Response: Thank you very much for your careful reading of the manuscript and valuable suggestions. We have corrected it in the revised manuscript.

      (9) Line 142 - The usage of comprised here is not correct. It would be more correct to say "The overall architecture of CsAlaDC and AtSerDC is homodimeric with the two subunits...".

      Response: Thank you very much for your careful reading of the manuscript and valuable suggestions. We have corrected it in the revised manuscript.

      (10) Line 148-149 - I didn't understand the statement about the "N-terminal structures" Are these structures obtained from protein samples that have a truncated N-terminus?

      Response: Group II PLP-dependent amino acid decarboxylases are comprised of three distinct structural domains: the N-terminal domain, the large domain, and the C-terminal domain. Each of these domains possesses unique structural features. Similarly, CsAlaDC and AtSerDC can also be classified into three structural domains based on their specific characteristics. To achieve more stable proteins for further experiments, we conducted truncation on both of these proteins. The truncated section pertains to a subsection of the N-terminal domain and is truncated from the protein's N-terminus.

      (11) Line 153 - Say "is composed of" instead of "composes of".

      Response: Thank you very much for your careful reading of the manuscript and valuable suggestions. We have corrected it in the revised manuscript.

      (12) Line 156 - I didn't understand the statement about the cofactor binding process. What is the cofactor observed? And how can we say anything about the binding process from a single static structure of the enzyme? It might be better to say that the cofactor binding site is located at the subunit junction - but the identity of the cofactor still needs to be defined first.

      Response: Thank you for your comments and suggestions. The cofactor mentioned here is PLP. We aim to elucidate the binding state of PLP at the active site, excluding the binding process. The description has been revised in the revised manuscript.

      (13) Lines 157-158 - I didn't understand the conclusion about the roles of each monomer. In the images in Figure 3 - both monomers appear to bind PLP but the substrate is not present - so it's not clear how conclusions can be drawn about differential substrate binding in the two subunits.

      Response: Thank you very much for your careful reading and valuable suggestions. The main idea we want to convey is that this protein possesses two active sites. At each active site, the two monomers carry out distinct functions. Of course, our previous conclusion is inaccurate due to the non-existence of the substrate. So, we have made the necessary amendments in the revised manuscript.

      (14) Line 161 - I would say loop instead of ring.

      Response: Thank you very much for your careful reading of the manuscript and valuable suggestions. We have corrected it in the revised manuscript.

      (15) Line 165 - Please provide some references for this statement. It would also be ideal to state the proximity of the Zn-binding motif to the active site or otherwise provide some information about the role of the motif based on its location.

      Response: Thank you for your comments and suggestions. We have provided the following references to support this statement in the revised manuscript.

      Author response image 1.

      (A) Structure of histidine decarboxylase. (B) Structure of glutamate decarboxylase.

      Reference:

      30 Komori, H. et al. (2012) Structural study reveals that Ser-354 determines substrate specificity on human Histidine Decarboxylase. J Biol Chem. 287, 29175-83.

      31 Huang, J. et al. (2018) Lactobacillus brevis CGMCC 1306 glutamate decarboxylase: Crystal structure and functional analysis. Biochem Biophys Res Co. 503, 1703-1709

      In CsAlaDC, the zinc is positioned at a distance of 29.6 Å from the active center, whereas in AtSerDC, the zinc is situated 29 Å away from the active center. Hence, we hypothesize that this structure does not impact the enzyme's catalytic activity but might be correlated with its stability.

      (16) Lines 166-178 - This paragraph appears to be a list of all of the interactions between the protein, PLP, and the EA product. It would be ideal to provide some text to explain why these interactions are important and what we can learn from them.

      Response: Thank you very much for your careful reading of the manuscript and valuable suggestions. We have been conducting additional analysis on the functional roles of amino acid residues involved in the interaction between the active site and PLP. This analysis focuses on aiding PLP binding, determining its orientation, and understanding enzyme catalytic mechanisms. These details are mentioned in the revised manuscript.

      (17) Line 192 - Bond not bound.

      Response: Thank you very much for your careful reading of the manuscript and valuable suggestions. We have made corrections in the revised manuscript.

      (18) Lines 201-207 - It would be ideal to verify that the inclusion of 5 mM DTT affects Zn binding. It's not clear to me that this reagent would necessarily disrupt Zn binding. Under certain circumstances, it could instead promote Zn association. For example, if the Cys ligands are oxidized initially but then become reduced? I don't think the current experiment really provides any insight into the role of the Zn.

      Response: Thank you for your valuable insights regarding the role of DTT and its potential effects on Zn binding in our experiments. The main function of DTT is to protect or restore the reduced state of proteins and other biological molecules, particularly by disrupting the crosslinking formed by thiol (-SH) groups and disulfide bonds to maintain the function and structure of proteins. Therefore, the reason for DTT's inhibition of enzyme activity is unknown, and we cannot provide a reasonable explanation for this phenomenon. As a result, we have removed the section discussing the inhibition of enzyme activity by DTT in our revised manuscript.

      Reviewer #3 (Public Review):

      In the manuscript titled "Structure and Evolution of Alanine/Serine Decarboxylases and the Engineering of Theanine Production," Wang et al. solved and compared the crystal structures of Alanine Decarboxylase (AlaDC) from Camellia sinensis and Serine Decarboxylase (SerDC) from Arabidopsis thaliana. Based on this structural information, the authors conducted both in vitro and in vivo functional studies to compare enzyme activities using site-directed mutagenesis and subsequent evolutionary analyses. This research has the potential to enhance our understanding of amino acid decarboxylase evolution and the biosynthetic pathway of the plant-specialized metabolite theanine, as well as to further its potential applications in the tea industry. Response: Thank you very much for taking the time to review this manuscript. We appreciate all your insightful comments.

      Reviewer #3 (Recommendations For The Authors):

      Page 6, Figure 2, Page 23 (Methods)

      "The supernatants were purified with a Ni-Agarose resin column followed by size-exclusion chromatography."

      What kind of SEC column did the authors use? Can the authors provide the SEC elution profile comparison results and size standard curve?

      Response: We use a Superdex 200 (Hiload 16/600) column for size exclusion chromatography. The comparison results of SEC elution profiles for AtSerDC and CsAlaDC, along with the standard curve of SEC column, are presented below.

      Author response image 2.

      (A) Comparison of elution profiles of CsAlaDC and AtSerDC. (B) Elution profile of Blue Dextron 2000. (C) Elution profile of mixed protein (Aldolase, 158000 Da,71.765ml; Conalbumin, 75000 Da,79.391ml; Ovalbumin, 44000 Da,83.767ml; Carbonic anhydrase, 29000 Da,90.019ml; Ribonuclease A, 13700 Da,98.145ml). (D) Size standard curves of Superdex 200 (Hiload 16/600) column.

      Page 6 & Page 24 (Methods)

      "The 100 μL reaction mixture, containing 20 mM substrate (Ala or Ser), 100 mM potassium phosphate, 0.1 mM PLP, and 0.025 mM purified enzyme, was prepared and incubated at standard conditions (45 ℃ and pH 8.0 for CsAlaDC, 40 ℃ and pH 8.0 for AtSerDC for 30 min)."

      (1) The enzymatic activities of CsAldDC and AtSerDC were measured at two different temperatures (45 and 40 ℃, but their activities were directly compared. Is there a reason for experimenting at different temperatures?

      Response: We determined that the optimal reaction temperature for AtSerDC is 40°C and for CsAlaDC is 45°C through our verification process. Consequently, all subsequent experiments were performed at these specific temperatures.

      Author response image 3.

      (A) Relative activity of CsAlaDC at different temperatures. (B) Relative activity of AtSerDC at different temperatures.

      (2) Enzyme activities were measured at temperatures above 40℃, which is not a physiologically relevant temperature and may affect the stability or activity of the proteins. At the very least, the authors should provide temperature-dependent protein stability data (e.g., CD spectra analysis) or, if possible, temperature-dependent enzyme activities, to show that their experimental conditions are suitable for studying the activities of these enzymes.

      Response: Thank you very much for your careful reading. We have already validated that the experimental temperature we used did not significantly affect the stability of the protein before experimenting. The results are shown in the figure below:

      Author response image 4.

      Place the two proteins individually into water baths set at temperatures of 25°C, 37°C, 45°C, 60°C, and 80°C for 15 minutes. Subsequently, carry out enzymatic reactions utilizing a standard reaction system, with untreated enzymes serving as the experimental control within the said system. The experimental results suggest that the temperature at which we experimented does not have a significant impact on the stability of the enzyme.

      (3) The authors used 20 mM of substrate. What are the physiological concentrations of alanine and serine typically found in plants?

      Response: The content of alanine in tea plant roots ranges from 0.28 to 4.18 mg/g DW (Yu et al., 2021; Cheng et al., 2017). Correspondingly, the physiological concentration of alanine is 3.14 mM to 46.92 mM, in tea plant roots. The content of serine in plants ranges from 0.014 to 17.6 mg/g DW (Kumar et al., 2017). Correspondingly, the physiological concentration of serine is 0.13 mM to 167.48 mM in plants. In this study, the substrate concentration of 20 mM was close to the actual concentrations of alanine and serine in plants.

      Yu, Y. et al. (2021) Glutamine synthetases play a vital role in high accumulation of theanine in tender shoots of albino tea germplasm "Huabai 1". J. Agric. Food Chem. 69 (46),13904-13915.

      Cheng, S. et al. (2017) Studies on the biochemical formation pathway of the amino acid L-theanine in tea (Camellia sinensis) and other plants.” J. Agric. Food Chem. 65 (33), 7210-7216.

      Kumar, V. et al. (2017) Differential distribution of amino acids in plants. Amino Acids. 49(5), 821-869.

      Pages 6-7 & Table 1

      (1) Use the correct notation for Km and Vmax. Also, the authors show kinetic parameters and use multiple units (e.g., mmol/L or mM for Km).

      Response: Thank you very much for your careful reading of the manuscript and valuable suggestions. We have corrected this in the revised manuscript.

      (2) When comparing the catalytic efficiency of enzymes, kcat/Km (or Vmax/Km) is generally used. The authors present a comparison of catalytic activity from results to conclusion. A clarification of what results are being compared is needed.

      Response: Thank you for your comments and suggestions. The catalytic activity is assessed by comparing reaction rates.

      Page 7 & Figure 3

      In Figure 3A, the authors describe the overall structure, but a simple explanation or labeling within the figure should be added.

      Response: Thank you very much for your suggestions, we have made modifications to Figure 3A as follows:

      Author response image 5.

      Crystal structures of CsAlaDC and AtSerDC. (A) Dimer structure of CsAlaDC. The color display of the N-terminal domain, large domain, and C-terminal domains of chain A is shown in light pink, khaki and sky blue, respectively. Chain B is shown in spring green. The PLP molecule is shown as a sphere model. The zinc finger structure at the C-terminus of CsAlaDC is indicated by the red box. The gray spheres represent zinc ions, while the red dotted line depicts the coordination bonds formed by zinc ions with cysteine and histidine.

      Figures 3F & 4A

      In these figures, the two structures are overlaid and compared, but the colors are very similar to see the differences. The authors should use a different color scheme.

      Response: Thank you very much for your suggestions, we have made modifications to the Figure 3F & 4A as follows:

      Author response image 6.

      (Figure 3F) - The monomers of CsAlaDC and AtSerDC are superimposed. CsAlaDC is depicted in spring green, while AtSerDC is shown in plum. The conserved amino acid catalytic ring is indicated by the red box. (Figure 4A) - Superposition of substrate binding pocket amino acid residues in CsAlaDC and AtSerDC. The amino acid residues of CsAlaDC are shown in spring green, the amino acid residues of AtSerDC are shown in plum, with the substrate specificity-related amino acid residue highlighted in a red ellipse.

      Pages 7 & 8

      Figures 3 and 4 do not include illustrations of what the authors describe in the text. The reader will not be able to understand the descriptions until they download and view the structures themselves. The authors should create additional figures to make it easier for readers to understand the structures.

      Response: Thank you very much for your suggestions, we have included supplementary figure 1 in the revised manuscript, which presents more elaborate structural depictions of the two proteins.

      Pages 9 & 10

      "This result suggested this Tyr is required for the catalytic activity of CsAlaDC and AtSerDC."

      The author's results are interesting, but it is recommended to perform the experiments in a specific order. First, experiments should determine whether mutagenesis affects the protein's stability (e.g., CD, as discussed earlier), and second, whether mutagenesis affects ligand binding (e.g., ITC, SPR, etc.), before describing how site-directed mutagenesis alters enzyme activity. In particular, the authors' hypothesis would be much more convincing if they could show that the ligand binding affinity is similar between WT and mutants.

      Response: Thank you for your insightful feedback on our manuscript, which we greatly appreciate. Your suggestion to methodically sequence the experiments provides a clear pathway to bolster the strength and conclusiveness of our results.

      We agree that it is crucial to first assess the stability of the mutant proteins, as changes therein could inadvertently affect catalytic activity. To this end, we have employed circular dichroism (CD) to study the potential structural alterations in the proteins induced by mutations. The experimental results are shown in the following figure:

      Author response image 7.

      (A) Circular Dichroism Spectra of CsAlaDC (WT). (B) Circular Dichroism Spectra of CsAlaDC (Y336F). (C) Circular Dichroism Spectra of CD of AtSerDC (WT). (D) Circular Dichroism Spectra of AtSerDC (Y341F).

      The experimental results indicate that the secondary structure of the mutant proteins remains unchanged, which means the mutations do not alter the protein's stability.

      The ligand PLP forms a Schiff base structure with the ε-amino group of a lysine residue in the protein, with maximum absorbance around 420-430 nm. Since we have already added PLP during the protein purification process, as long as the absorbance of mutant proteins and wild-type proteins is the same at 420-430 nm at equivalent concentrations, it indicates that the mutant proteins do not affect the binding of the ligand PLP. Therefore, we scanned the UV-visible absorption spectra of both the wild-type and mutant proteins, and the results are as presented in the following figure:

      Author response image 8.

      (A) UV-Visible Absorption Spectra of CsAlaDC (WT) compared to CsAlaDC (Y336F). (B) UV-Visible Absorption Spectra of AtSerDC (WT) compared to AtSerDC (Y341F).

      The mutant protein and the wild-type protein exhibit similar absorbance at 420-430 nm, indicating that the mutation does not affect the binding of PLP to the protein.

      The above experiments have confirmed that the mutations do not significantly affect the stability of the protein or the affinity for the ligand, so we can more confidently attribute changes in enzyme activity to the specific role of the tyrosine residue in question. We believe this comprehensive approach will substantiate our hypothesis and illustrate the necessity of this Tyr residue for the catalytic activity of CsAlaDC and AtSerDC enzymes.

      Figure 3

      In the 3D structure figure provided by the authors, the proposed reaction mechanism of the enzyme and the involved amino acids are not included. Can the authors add a supplementary figure with a schematic drawing that includes more information, such as distances?

      Response: Thank you for your valuable feedback on our manuscript. We completely agree that a schematic drawing with additional details, including distances, would enhance the clarity and understanding of the enzymatic mechanism. In response to your suggestion, we have added a supplementary figure 2 in the revised manuscript that accurately illustrates the proposed reaction pathway, highlighting the key amino acids involved.

      Page 10

      "The results showed that 5 mM L-DTT reduced the relative activity of CsAlaDC and AtSerDC to 22.0% and 35.2%, respectively"

      The authors primarily use relative activity to compare WT and mutants. Can the authors specify the exact experiments, units, and experimental conditions? Is it Vmax or catalytic efficiency? If so, under what specific experimental conditions?

      Response: Thank you for your attention and review of our research paper, we appreciate your suggestions and feedback. The experimental protocol employed to evaluate the influence of DTT on protein catalytic efficiency is outlined as follows:

      The 100 μL reaction mixture, containing 20 mM substrate (Ala or Ser), 100 mM potassium phosphate, 0.1 mM PLP, 5 mM L-DTT, and 0.025 mM purified enzyme, was prepared and incubated at standard conditions (45 °C and pH 8.0 for CsAlaDC for 5 min, 40 °C and pH 8.0 for AtSerDC for 2 min). DTT is absent as a control in the reaction system. Then the reaction was stopped with 20 μL of 10% trichloroacetic acid. The product was derivatized with 6-aminoquinolyl-N-hydroxy-succinimidyl carbamate (AQC) and subjected to analysis by UPLC. All enzymatic assays were performed in triplicate.

      However, due to the unknown mechanism of DTT inhibition on protein activity, we have removed this part of the content in the revised manuscript.

      Pages 10-12

      The identification of 'Phe106 in CsAlaDC' and 'Tyr111 in AtSerDC,' along with the subsequent mutagenesis and enzymatic activity assays, is intriguing. However, the current manuscript lacks an explanation and discussion of the underlying reasons for these results. As previously mentioned, it would be helpful to gain insights and analysis from WT-ligand and mutant-ligand binding studies (e.g., ITC, SPR, etc.). Furthermore, the authors' analysis would be more convincing with accompanying structural analysis, such as steric hindrance analysis.

      Response: Thank you for your insightful comments and constructive feedback on our manuscript. We appreciate the interest you have expressed in the identification of 'Phe106 in CsAlaDC' and 'Tyr111 in AtSerDC' and their functional implications based on mutagenesis and enzymatic assays.

      In order to investigate the binding status of the mutant protein and the ligand PLP,we scanned the UV-visible absorption spectra of both the wild-type and mutant proteins, and the results are as presented in the following figure:

      Author response image 9.

      (A) UV-Visible Absorption Spectra of CsAlaDC (WT) compared to CsAlaDC (F106Y). (B) UV-Visible Absorption Spectra of AtSerDC (WT) compared to AtSerDC (Y111F).

      The mutant protein and the wild-type protein exhibit similar absorbance at 420-430 nm, indicating that the mutation does not affect the binding of PLP to the protein. Therefore, we can conclude that the change in activity of the mutant protein is caused by the substitution of the amino acid at that site, i.e., the amino acid at that site affects substrate specificity. By combining the structure of the two proteins, we can see that the Lys at position 111 of AtSerDC is a hydrophilic amino acid, which increases the hydrophilicity of the active site, and thus the substrate is the hydrophilic amino acid Ser. In contrast, the amino acid at the corresponding site in CsAlaDC is Phe, which, lacking a hydroxyl group compared to Lys, increases the hydrophobicity of the active site, making the substrate lean towards the hydrophobic amino acid Ala. We have added a discussion of the potential reasons for this result to the revised manuscript's discussion section.

      Page 5 & Figure 1B

      "As expected, CsSerDC was most closed to AtSerDC, which implies that they shared similar functions. However, CsAlaDC is relatively distant from CsSerDC."

      In Figure 1B, CsSerDC and AtSerDC are in different clades, and this figure does not show that the two enzymes are closest. To provide another quantitative comparison, please provide a matrix table showing amino acid sequence similarities as a supplemental table.

      Response: Many thanks for your constructive suggestion. We added a matrix table showing amino acid sequence similarities in the supplemental materials. The results showed that the similarity of amino acid sequences between CsSerDC and AtSerDC is 86.21%, which is higher than that between CsAlaDC and CsSerDC (84.92%). This data exactly supports the description of Figure 1B. We added the description of the amino acid sequence similarities analysis in the revised manuscript. The description of "As expected, CsSerDC was most closed to AtSerDC, which implies that they shared similar functions. " is not accurate enough, so we revised it to "As expected, CsSerDC was closer to AtSerDC, which implies that they shared similar functions.", in the revised manuscript.

      Page 5 & Figure 1C

      Figure 1C, which shows a multiple sequence alignment with the amino acid sequences of the 6 SerDCs and CsAlaDC, clearly shows the differences between the sequences of AlaDC and other SerDCs. However, the authors' hypothesis would be more convincing if they showed that this difference is also conserved in AlaDCs from other plants. Can the authors show a new multiple-sequence alignment by adding more amino acid sequences of other AlaDCs?

      Response: Thank you for your comments and suggestions. We aim to discover additional alanine decarboxylase. However, at present, the only experimentally confirmed alanine decarboxylase is CsAlaDC. No experimentally verified alanine decarboxylases have been found in other plant species.

      Figure 5A

      Figure 5A is missing the error bar.

      Response: Figure 5A serves as a preliminary screening for these mutants, without conducting repeated experiments. Subsequently, only the L110F and P114A mutants, which exhibited significantly improved activity, underwent further experimental verification to confirm their enhanced functionality.

    1. Author Response

      The following is the authors’ response to the original reviews.

      First, the authors would like to thank the reviewers and editors for their thoughtful comments. The comments were used to guide our revision, which is substantially improved over our initial submission. We have addressed all comments in our responses below, through a combination of clarification, new analyses and new experimental data.

      Reviewer #1 (Public Review):

      In this manuscript, the authors identified and characterized the five C-terminus repeats and a 14aa acidic tail of the mouse Dux protein. They found that repeat 3&5, but not other repeats, contribute to transcriptional activation when combined with the 14aa tail. Importantly, they were able to narrow done to a 6 aa region that can distinguish "active" repeats from "inactive" repeats. Using proximal labeling proteomics, the authors identified candidate proteins that are implicated in Dux-mediated gene activation. They were able to showcase that the C-terminal repeat 3 binds to some proteins, including Smarcc1, a component of SWI/SNF (BAF) complex. In addition, by overexpressing different Dux variants, the authors characterized how repeats in different combinations, with or without the 14aa tail, contribute to Dux binding, H3K9ac, chromatin accessibility, and transcription. In general, the data is of high quality and convincing. The identification of the functionally important two C-terminal repeats and the 6 aa tail is enlightening. The work shined light on the mechanism of DUX function.

      A few major comments that the authors may want to address to further improve the work:

      We thank the reviewer for their efforts and constructive comments, which have guided our revisions.

      1) The summary table for the Dux domain construct characteristics in Fig. 6a could be more accurate. For example, C3+14 clearly showed moderate weaker Dux binding and H3K9ac enrichment in Fig 3c and 3e. However, this is not illustrated in Fig. 6a. The authors may consider applying statistical tests to more precisely determine how the different Dux constructs contribute to DNA binding (Fig. 3c), H3K9ac enrichment (Fig. 3e), Smarcc1 binding (Fig. 5e), and ATAC-seq signal (Fig. 5f).

      We thank the reviewer for this comment, and agree that there were some modest differences in construct characteristics that were not captured in the Summary Table (6a). To better reflect the differences between constructs, we added additional dynamic range to our depiction/scoring, and believe that the new scoring system provides sufficient qualitative range to capture the difference without imposing a statistical approach.

      2) Another concern is that exogenous overexpressed Dux was used throughout the experiments. The authors may consider validating some of the protein-protein interactions using spontaneous or induced 2CLCs (where Dux is expressed).

      We agree that it would be helpful to determine endogenous DUX interaction with our BioID candidates. Here, we attempted co-IPs for endogenous DUX protein with the DUX antibody and were unsuccessful, which indicated that the DUX antibody is useful for detection but not efficient in the primary IP. This is why we utilized the mCherry tag for DUX IP experiments, which worked exceptionally well.

      3) It could be technically challenging, but the authors may consider to validate Dux and Smarcc1 interaction in a biologically more relevant context such as mouse 2-cell embryos where both proteins are expressed. Whether Smarcc1 binding will be dramatically reduced at 4-cell embryos due to loss of Dux expression?

      While we agree that it would be interesting to validate the in vivo interaction of DUX and SMARCC1 in the early embryo, it is not technically feasible for us to conduct the experiment, as the IP would require thousands of two-cell embryos, and we have the issue of poor co-IP quality with the DUX antibody.

      Reviewer #2 (Public Review):

      In this manuscript, Smith et al. delineated novel mechanistic insights into the structure-function relationships of the C-terminal repeat domains within the mouse DUX protein. Specifically, they identified and characterised the transcriptionally active repeat domains, and narrowed down to a critical 6aa region that is required for interacting with key transcription and chromatin regulators. The authors further showed how the DUX active repeats collaborate with the C-terminal acidic tail to facilitate chromatin opening and transcriptional activation at DUX genomic targets.

      Although this study attempts to provide mechanistic insights into how DUX4 works, the authors will need to perform a number of additional experiments and controls to bolster their claims, as well as provide detailed analyses and clarifications.

      We thank this reviewer for their constructive comments, and have conducted several new analyses, additional experiments and clarifications – which have strengthened the manuscript in several locations. Highlights include a statistical approach to the similarity of mouse repeats to themselves and to orthologs (Figure S1d) and clarified interpretations, a wider dynamic range to better reflect changes in DUX construct behaviors (Figure 6a), and additional data on construct behavior, including ‘inactive’ constructs (e.g C1+14aa in Figure 1a,d, new ATAC-seq in Figure S1g), and active constructs such as C3+C5+14aa and C3+C514aa (in Figure S1b).

      Reviewer #3 (Public Review):

      Dux (or DUX4 in human) is a master transcription factor regulating early embryonic gene activation and has garnered much attention also for its involvement in reprogramming pluripotent embryonic stem cells to totipotent "2C-like" cells. The presented work starts with the recognition that DUX contains five conserved c. 100-amino acid carboxy-terminal repeats (called C1-C5) in the murine protein but not in that of other mammals (e.g. human DUX4). Using state-of-the-art techniques and cell models (BioID, Cut&Tag; rescue experiments and functional reporter assays in ESCs), the authors dissect the activity of each repeat, concluding that repeats C3 and C5 possess the strongest transactivation potential in synergy with a short C-terminal 14 AA acidic motif. In agreement with these findings, the authors find that full-length and active (C3) repeat containing Dux leads to increased chromatin accessibility and active histone mark (H3K9Ac) signals at genomic Dux binding sites. A further significant conclusion of this mutational analysis is the proposal that the weakly activating repeats C2 and C4 may function as attenuators of C3+C5-driven activity.

      By next pulling down and identifying proteins bound to Dux (or its repeat-deleted derivatives) using BioID-LC/MS/MS, the authors find a significant number of interactors, notably chromatin remodellers (SMARCC1), a histone chaperone (CHAF1A/p150) and transcription factors previously (ZSCAN4D) implicated in embryonic gene activation.

      The experiments are of high quality, with appropriate controls, thus providing a rich compendium of Dux interactors for future study. Indeed, a number of these (SMARCC1, SMCHD1, ZSCAN4) make biological sense, both for embryonic genome activation and for FSHD (SMCHD1).

      A critical question raised by this study, however, concerns the function of the Dux repeats, apparently unique to mice. While it is possible, as the authors propose, that the weak activating C1, C2 C4 repeats may exert an attenuating function on activation (and thus may have been selected for under an "adaptationist" paradigm), it is also possible that they are simply the result of Jacobian evolutionary bricolage (tinkering) that happens to work in mice. The finding that Dux itself is not essential, in fact appears to be redundant (or cooperates with) the OBOX4 factor, in addition to the absence of these repeats in the DUX protein of all other mammals (as pointed out by the authors), might indeed argue for the second, perhaps less attractive possibility.

      In summary, while the present work provides a valuable resource for future study of Dux and its interactors, it fails, however, to tell a compelling story that could link the obtained data together.

      We appreciated the reviewer’s views regarding the high quality of the work and our generation of an important dataset of DUX interactors. We also appreciate the comments provided to improve the work, and have performed and included in the revised version a set of clarifications, additional analyses and additional experiments that have served to reinforce our main points and provide additional mechanistic links. We also agree that more remains to be done to understand the function and evolution of repeats C1, C2 and C4.

      Reviewer #1 (Recommendations For The Authors):

      1) For immuno-blots, authors may indicate the expected bands to help readers better understand the results.

      Agreed, and we have included the predicted molecular weight of proteins in the Figure Legends. We note that our work shows that the C-terminal domains confer anomalous migration in SDS-PAGE.

      2) Fig. 5b, a blot missing for the mCherry group?

      Figure 5b is a volcano blot, so we believe the reviewer is referring to Figure 5d, which is a coimmunoprecipitation experiment between SMARCC1 and mCherry-tagged DUX constructs. However, we are unsure of the comment as an anti mCherry sample is present in that panel.

      3) Line 99-100, Fig. S1d, it seems that repeat2, but not repeat3, is more similar to human DUX4 C-terminal region.

      This comment and one by another reviewer have prompted us to re-examine the similarities of the DUX repeats, and we have new analyses (Figure S1d) and an alternative framing in the manuscript as a result. We have expanded on this in our response to Reviewer #2, point #1 – and direct the reviewer there for our expanded treatment.

      4) There are a few references are misplaced. For example, line 48, the studies that reported the role of Dux in inducing 2CLCs should be from Hendrickson et al., 2017, De Iaco et al., 2017, and Whiddon et al., 2017. The authors may want to double check all references.

      Thanks for pointing these out. These issues have been corrected in the manuscript.

      5) In the materials & methods section, a few potential errors are noticed. For example, concentrations of PD0325901 and CHIR99021 in mESC medium appear ~1000-fold higher than standards.

      Thanks – corrected.

      Reviewer #2 (Recommendations For The Authors):

      Major Points

      1) Line 99 - The authors claimed that the "human DUX4 C-terminal region is most similar to the 3rd repeat of mouse DUX", but based on Supp. Fig. 1d, the human DUX4 C-term should be most similar to the 2nd repeat of mouse DUX. If this is indeed the case, it will undermine the rest of this study, since the authors claim that the 3rd repeat is transcriptionally active, whereas the 2nd repeat is transcriptionally inactive, and the bulk of this study largely focused on how the active repeats, not the inactive repeats, are critical in recruiting key transcriptional and chromatin regulators to induce the embryonic gene expression program.

      We thank the reviewer for their comments here. Since submission,and as mentioned above for reviewer #1 we have revisited the issue of similarity of the DUX4 C-terminal region to the mouse C-terminal repeats, with a BLAST-based approach that is more rigorous and informed by statistics – which is in Author response table 1 and now in the manuscript as Figure S1d, and has affected our interpretation. Our prior work involved a simple % identity comparison table and we now appreciate that some of the similarity analyses did not meet statistical significance, and therefore we are unable to draw certain conclusions. We make the appropriate modifications in the text. For example, we no longer state that the DUX4 C-terminus appears to be most similar to mouse repeats 3 and 5. This does not affect the main conclusions of the paper regarding interactions of the C-terminus with chromatin-related proteins, only our speculation on which repeat might have represented the original single repeat in the mouse – an issue we think of some interest, but did not rise to the level of mentioning in the original or current abstract.

      Author response table 1.

      Parameters: PAM250 matrix. Gap costs of existence: 15 and extension: 3. Numbers represent e-value of each pairwise comparison

      *No significant similarities found (>0.05).

      2) In Supp Fig 1d, it seems that the rat DUX4 C-terminal region is most similar to the 4th repeat of mouse DUX, which according to the author is supposedly transcriptionally inactive. This weakens the authors justification that the 3rd or 5th repeat is likely the "parental repeat for the other four", and further echoes my concern in point 1 where the human DUX4 C-term is most similar to the 2nd (inactive) repeat of mouse DUX.

      The reviewer’s point is well taken and is addressed in point #1 above.

      3) In Fig. 1d, the authors showed that DUX4-containing C3 and C5, but lacking acidic tail, can promote MERVL::GFP expression, albeit to a slightly lower extent compared to FL. However, in Fig. 2b, C3 or C5 alone (lacking acidic tail) completely failed to promote MERVL::GFP expression. However, in the presence of the acidic tail, both versions were able to promote MERVL::GFP expression, similar to that of FL. The latter would suggest that it is the acidic tail that is crucial for MERVL::GFP expression, and this does not quite agree with Fig 1b, where C12345 (lacking acidic tail) was able to promote MERVL::GFP expression. Although C12345 did not activate MERVL to a similar level as FL, it is clearly proficient, compared to C3 or C5 alone (lacking acidic tail) where there is no increase in MERVL at all. Additional constructs will be helpful to clarify these points. For example, 'C3+C5 minus acidic tail' and 'HD1+HD2+acidic tail only' constructs.

      We agree that constructs such as those mentioned would add to the work. First, we have done the additional construct HD1+HD2+14aa tail, which is presented as ΔC12345+14aa in Figure 2a and in S2a. Additionally, we performed experiments on the requested C3+C5+14aa and C3+C5Δ14aa (see samples 6 and 7 in Author response image 1, which are now included in Supplemental Figure 2b). The results reinforce our hypothesis of an additive effect toward DUX target gene activation by increasing C-terminal repeats and including the 14aa tail.

      Author response image 1.

      4) Related to the above, the flow cytometry data for the MERVL::GFP reporter as presented in Figures 1 and 2, as well as in Supp. Fig. 2, show a considerably large difference in the %GFP|mCherry for the FL construct, ranging from ~6-26%. This makes it difficult to convince the reader which of the different DUX domain constructs cannot or can partially induce GFP|mCherry signal when compared to FL, and hence it is tough to definitively ascertain the exact contribution of each of the 5 C-terminal repeats with high confidence, as it appears that there exists a significant amount of variability in this MERVL::GFP reporter system. The authors need to address this issue since this is their primary method to elucidate the transcriptional activity of each of the mouse DUX repeat domains.

      We note that with the Dux-/- cell lines we used throughout the timeline of the study, the percent of %GFP|mCherry expression progressively and slowly decreased – possibly due to slow/modest epigenetic silencing of the reporter. However, we always used the full-length DUX construct to establish the dynamic range. We emphasize that the relative differences between constructs over multiple cell line replicates remained relatively consistent. However, we elected to show absolute values in each experiment, rather than simply normalizing the full-length to 100% and showing relative.

      5) Lines 140-142 - The authors claimed that the functional difference between the transcriptionally active and inactive repeats could be narrowed down to a "6aa region which is conserved between repeats C3 and C5, but not conserved in C1, C2 and C4". Assuming the 6aa sequence is DPLELF, why does C1C3a elicit almost twice the intensity of GFP|mCherry signal compared to C3C1c, despite both constructs having the exact same 6aa sequence?

      Indeed, C1C3a and C3C1c both containing the ‘active’ DPL sequence but having different relative levels of %GFP|mCherry. This is consistent with these sequences having a positive role in DUX target gene regulation – but likely in combination with other other regions which potentiate its affect, possibly through interacting proteins or post-translational modifications.

      Why does DPLEPL (the intermediate C3C1b construct) induce a similar extent of GFP|mCherry signal as the FL construct, even though the former includes 3aa from a transcriptionally inactive repeat? In contrast, GSLELF (the other intermediate C1C3b construct) that also includes 3aa from a transcriptionally inactive repeat is almost completely deficient in inducing any GFP|mCherry signal. Why is that so? Is DPL the most crucial sequence? It will be important to mutate these 3 (or the above 6) residues on FL DUX4 to examine if its transcriptional activity is abolished.

      These are interesting points. DPL does appear to be the most important region in the mouse DUX repeats. However, DPL is not shared in the C-terminus of human DUX4. Notably, the DUX4 C-terminus is sufficient to activate the mouse MERVL::GFP reporter when cloned to mouse homeodomains (see Author response image 2, second sample) and other DUX target genes (initially published in Whiddon et al. 2017). One clear possibility is that the DPL region is helping to coordinate the additive effects of multiple DUX repeats, which only exist in the mouse protein.

      Author response image 2.

      6) Line 154 - The intermediate DUX domain construct C1C3b occupied a different position on the PCA plot from the C1C3c construct that does not contain any of the critical 6aa sequence, as shown in Fig. 2e. However, both these constructs appear to be similarly deficient in inducing any GFP|mCherry signal, as seen in Fig. 2c. Why is that so?

      The PCA plot assesses the impact on the whole transcriptome and not just the MERVL::GFP reporter, suggesting the 3aa region has transcriptional effects on the genome beyond what is detected in the MERVL::GFP reporter.

      7) To strengthen the claim that "Chromatin alterations at DUX bindings sites require a transcriptionally active DUX repeat", the authors should also perform CUT&Tag for constructs containing transcriptionally inactive DUX repeats (e.g. C1+14aa), and show that such constructs fail to occupy DUX binding sites, as well as are deficient in H3K9ac accumulation.

      This is a good comment. We elected to control this with constructs containing or lacking an active repeat. Although we have not pursued this by CUT&TAG, we have examined the impact of DUX constructs with inactive repeats (including the requested C1+14aa, new Figure S1g) by ATAC-seq (see #12, ATAC-seq section, below), and observe no chromatin opening, suggesting that the lack of transcriptional activity is rooted in the inability to open chromatin.

      8) It would be good if the authors could also include CUT&Tag data for some of the C1C3 chimeric constructs that were used in Fig. 2, since the authors argued that the minimal 6aa region is sufficient to activate many of the DUX target genes. This would also strengthen the authors’ case that the transcriptionally active, not inactive, repeats are critical for binding at DUX binding sites and ensuring H3K9ac occupancy.

      We agree that these would be helpful, and have examined the inactive repeats in transcription and ATAC-seq formats during revision (new data in Figures 1d and S1g), but not yet the CUT&TAG format.

      9) Line 213 - "SMARCA4" should have been "SMARCA5"? Based on Fig. 4d, SMARCA5 is picked up in the BirA*-DUX interactome, not SMARCA4.

      Thanks – corrected.

      10) Lines 250-252 - The authors compared the active BirA-C3 against the inactive BirA-C1 to elucidate the interactome of the transcriptionally active C3 repeat, as illustrated in Fig. 5c. They found 12 proteins more enriched in C1 and 154 proteins in C3. This information should be presented clearly as a separate tab in Supp Table 2. What are the proteins common to both constructs, i.e. enriched to a similar extent? Do they include chromatin remodellers too? Although the authors sought to identify differential interactors between the 2 constructs, it is also meaningful to perform 2 separate comparisons - active BirA-C3 against BirA alone control, and inactive BirA-C1 against BirA alone control - like in Fig. 4d, so as to more accurately define whether the active C3 repeat, and not the inactive C1 repeat, interacts with proteins involved in chromatin remodeling.

      We thank the reviewer for this comment, and we have modified the manuscript by adding a second sheet in Supplementary Table 2 including the results for enriched proteins in BirA-C1 vs. C3. Additionally, due to limitations of annotation between BirA alone and BirA*-C3 being sequenced in different mass spectrometry experiments, it is difficult to quantitatively compare the two datasets with pairwise comparisons.

      11) Fig 5d: The authors mentioned in the legend that endogenous IP was performed for SMARCC1. However, in line 266, they stated Flag-tagged SMARCC1. Is SMARCC1 overexpressed? The reciprocal IP should also be presented. More importantly, C1 constructs (e.g. C1+14aa and C1Δ14aa) should also be included.

      To clarify, Figure 4e used exogenously overexpressed FLAG-SMARCC1 in HEK-293T cells to confirm the results of the full-length DUX BioID experiment. Figure 5d was performed with overexpressed DUX construct, but involved endogenous SMARCC1 in mESCs. This has now been made clearer in the revised manuscript.

      12) For both the SMARCC1 CUT&Tag and ATAC-seq experiments shown in Figures 5e and 5f respectively, the authors need to include DUX derivatives that contain transcriptionally inactive repeats with and without the 14aa acidic tail, i.e. C1+14aa and C1Δ14aa, and show that these constructs prevent the binding/recruitment of SMARCC1 to DUX genomic targets, and correspondingly display a decrease in chromatin accessibility. Only then can they assert the requirement of the transcriptionally active repeat domains for proper DUX protein interaction, occupancy and target activation.

      We agree that examination of an inactive repeat in certain approaches would improve the manuscript. Importantly, we have now included C1+14 in our ATAC-seq experiments, and in Author response image 3 two individual replicates, which constitute a new Figure S1g. Compared to the transcriptionally active DUX constructs, which see opening at DUX binding sites, we do not see chromatin opening at DUX binding sites with transcriptionally inactive C1+14.

      Author response image 3.

      13) To prove that DUX-interactors are important for embryonic gene expression, it will be important to perform loss of function studies. For instance, will the knockdown/knockout of SMARCC1 in cells expressing the active DUX repeat(s) lead to a loss of DUX target gene occupancy and activation?

      We agree that it would be interesting to better understand SMARCC1 cooperation with DUX function in the embryo, but we believe this is beyond the scope of this paper.

      Minor Points

      1) Lines 124-126 - What is the reason/rationale for why the authors used one linker (GGGGS2) for constructs with a single internal deletion, but 2 different linkers (GGGGS2 and GAGAS2) for constructs with 2 internal deletions?

      With Gibson cloning, there are homology overhang arms for each PCR amplicon that are required to be specific for each overlap. Additionally, each PCR amplicon needs to be specific enough from one another so that all inserts (up to 5 in this manuscript) are included and oriented in the right order. The linker sequences were included in the homology arm overlaps, so the nucleotide sequences for each linker needed to be specific enough to include all inserts. This is a general rule to Gibson cloning. Additionally, both GGGGS2 and GAGAS2 are common linker sequences used in molecular biology and the amino acids structures are similar to one another, suggesting there is no functional difference between linkers.

      2) Line 704 - 705: In the figure legend, the authors stated that 'Constructs with a single black line have the linker GGGGS2 and constructs with two black lines have linkers with GGGGS2 and GAGAS2, respectively.'. This was not obvious in the figures.

      Constructs used for flow and genomics experiments that are depicted in Figure 2, Supplementary Figure 2, Figure 3, Figure 4, and Figure 5 have depicted black lines where deletions are present. Where these deletions are present, there are linkers in order to preserve spacing and mobility for the protein.

      3) Line 160 - Clusters #1 and #2 are likely written in the wrong order. It should have been "activating the majority of DUX targets in cluster #2, not cluster #1" and "failed to activate those in cluster #1, not cluster #2", based on the RNA-seq heatmap in Fig. 2f.

      We thank the reviewer for this comment, and the error has been corrected in the manuscript.

      4) Line 188 - Delete the word "of" in the following sentence fragment: "DUX binding sites correlating with the of transcriptional".

      Thanks – corrected.

      5) Line 191 - Delete the word "aids" in the following sentence fragment: "important for conferring H3K9ac aids at bound".

      Thanks – corrected.

      6) Line 711 - "C1-C3 a,b,d" should be "C1-C3 a,b,c".

      Thanks – corrected.

      7) Lines 711-712 - The colors "pink to blue" and "blue to pink" are likely written in the wrong order. Based on Fig. 2c, the blue to pink bar graphs should represent C1-C3 a,b,c in that order, and likewise the pink to blue bar graphs should represent C3-C1 a,b,c in that order.

      Thanks – corrected.

      8) There is an overload of data presented in Fig. 2c, such that it is difficult to follow which part of the figure represents each data segment as written in the figure legend. It is recommended that the data presented here is split into 2 sub-figures.

      Figure 2c has a supporting figure in Supplementary Figure 2b. While there is both a graphical depiction of the constructions and the data both in the main panel of Figure 2C, we have depicted it as so to be as clear as possible for the reader to interpret the complexity and presentence of amino acids in each of the constructs.

      9) Line 717 - "following" is misspelt.

      Thanks – corrected.

      10) Lines 720-721 - "(Top)" and "(Bottom)" should be replaced with "(Left)" and "(Right)", as the 2 bar graphs presented in Fig. 2d are placed side by side to each other, not on the top and bottom.

      Thanks – corrected.

      11) Lines 725 and 839 - "Principle" is misspelt. It should be "Principal".

      Thanks – corrected.

      12) In Figures 3d and 3e, the sample labeled "C3+14_1" should be re-labeled to "C3+14", in accordance with the other sub-figures. Additionally, for the sake of consistency, "aa" should be appended to the relevant constructs, e.g. "C3+14aa" and "C3Δ14aa".

      Thanks – corrected.

      13) Line 773 - Were the DUX domain constructs over-expressed for 12hr (as written in the figure legend) or 18hr (as labeled in Fig. 5d)?

      Thanks – corrected.

      14) Related to minor point 19 above, is there a reason/rationale for why some of the experiments used 12hr over-expression of DUX domain constructs (e.g. for CUT&TAG in Fig. 3), whereas in other experiments 18hr over-expression was chosen instead (e.g. flow cytometry for MERVL::GFP reporter in Figures 1 and 2, and co-IP validations of BirA*-DUX interactions in Fig. 4)?

      Thanks for the opportunity to explain. In this work, experiments that reported on proteins that are translated following DUX gene activation (e.g. MERVL:GFP via flow) were done at 18hr to allow for enough time for transcription and translation of GFP (or other DUX target genes). For experiments that report on the impact of DUX on chromatin and transcription, such as RNA-seq, CUT&Tag, and ATAC-seq, we induced DUX domain constructs for 12 hours.

      15) Line 804 - "ΔHDs" is missing between "C2345+14aa" and "ΔHD1".

      Thanks – corrected.

      16) In Fig. 5c, "Chromatin remodelers" is misspelt.

      Thanks – corrected.

      17) There is no reference in the manuscript to the proposed model that is presented in Fig. 6b.

      Thanks – corrected.

      Reviewer #3 (Recommendations For The Authors):

      Given the uncertainty of the function of the Dux peptide repeats in mice, could it not also be possible that the underlying repeated nature of the (coding) DNA? That is, could these DNA repeats exert a regulatory function on Dux transcription itself (also given the dire consequences of misregulated DUX4 expression as seen in FSHD, for example).

      Yes, it remains possible that the internal coding repeats within Dux are playing a role in locus regulation, and might be interesting to examine. However, we consider this question as being outside the scope of the current paper.

      Finally, it would be interesting to know whether these repeats are, in fact, present in all mouse species. Already no longer present in rat, do they exist, or not, in more "distant" mice, e.g. M. caroli?

      Determining whether all mouse strains contain C-terminal repeats in DUX is a question we also considered. However, Dux and its orthologs are present in long and very complex repeat arrays that are not present in the sequencing data or annotation in other mouse strains. Therefore, we are not unable to answer this question from existing sequencing data. Answering would require a considerable genome sequencing and bioinformatics effort, or alternatively a considerable effort aimed at cloning ortholog cDNAs from 2-cell embryos.

      Minor points:

      line 169: here it seems, in fact, that the 'inactive' C2, C4 repeats are more similar to each other (my calculation: 91 and 96% identity at the protein and DNA level, respectively) than the active C3 and C5 repeats (82 and 89% identity, resp.), the outlier being C1.

      Thanks for this comment, which was mentioned by other reviewers as well and has been addressed through new statistical analyses and interpretation (see new Figure S1d).

      line 191: I'm not sure this sentence parses correctly ("...14AA tail is important for conferring H3K9Ac aids at bound sites...")

      We thank the reviewer for this comment, and we have corrected the sentence in the manuscript.

    1. Author Response

      The following is the authors’ response to the original reviews.

      eLife assessment

      The authors have developed a compelling coarse-grained simulation approach for nucleosome-nucleosome interactions within a chromatin array. The data presented are solid and provide new insights that allow for predictions of how chromatin interactions might occur in vivo, but some of the claims should be tempered. The tools will be valuable for the chromosome biology field.

      Response: We want to thank the editors and all the reviewers for their insightful comments. We have made substantial changes to the manuscript to improve its clarity and temper necessary claims, as detailed in the responses, and we performed additional analyses to address the reviewers’ concerns. We believe that we have successfully addressed all the comments, and the quality of our paper has improved significantly.

      In the following, we provide point-to-point responses to all the reviewer comments. 

      RESPONSE TO REFEREE 1:

      Comment 0: This study develops and applies a coarse-grained model for nucleosomes with explicit ions. The authors perform several measurements to explore the utility of a coarse-grained simulation method to model nucleosomes and nucleosome arrays with explicit ions and implicit water. ’Explicit ions’ means that the charged ions are modeled as particles in simulation, allowing the distributions and dynamics of ions to be measured. Since nucleosomes are highly charged and modulated by charge modifications, this innovation is particularly relevant for chromatin simulation.

      Response: We thank the reviewer’s excellent summary of the work.

      Comment 1: Strengths: This simulation method produces accurate predictions when compared to experiments for the binding affinity of histones to DNA, counterion interactions, nucleosome DNA unwinding, nucleosome binding free energies, and sedimentation coefficients of arrays. The variety of measured quantities makes both this work and the impact of this coarse-grained methodology compelling. The comparison between the contributions of sodium and magnesium ions to nucleosome array compaction, presented in Figure 3, was exciting and a novel result that this simulation methodology can assess.

      Response: We appreciate the reviewer’s strong assessment of the paper’s significance, novelty, and broad interest, and we thank him/her for the detailed suggestions and comments.

      Comment 2: Weaknesses: The presentation of experimental data as representing in vivo systems is a simplification that may misrepresent the results of the simulation work. In vivo, in this context, typically means experimental data from whole cells. What one could expect for in vivo experimental data is measurements on nucleosomes from cell lysates where various and numerous chemical modifications are present. On the contrary, some of the experimental data used as a comparison are from in vitro studies. In vitro in this context means nucleosomes were formed ’in a test tube’ or under controlled conditions that do not represent the complexity of an in vivo system. The simulations performed here are more directly compared to in vitro conditions. This distinction likely impacts to what extent these simulation results are biologically relevant. In vivo and in vitro differences could be clarified throughout and discussed.

      Response: As detailed in Response to Comment 3, we have made numerous modifications in the Introduction, Results, and Discussion Section to emphasize the differences between reconstituted and native nucleosomes. The newly added texts also delve into the utilization of the interaction strength measured for reconstituted nucleosomes as a reference point for conceptualizing the interactions among native nucleosomes.

      Comment 3: In the introduction (pg. 3), the authors discuss the uncertainty of nucleosome-tonucleosome interaction strengths in vivo. For example, the authors discuss works such as Funke et al. However, Funke et al. used reconstituted nucleosomes from recombinant histones with one controlled modification (H4 acetylation). Therefore, this study that the authors discuss is measuring nucleosome’s in vitro affinity, and there could be significant differences in vivo due to various posttranslational modifications. Please revise the introduction, results section ”Close contacts drive nucleosome binding free energy,” and discussion to reflect and clarify the difference between in vitro and in vivo measurements. Please also discuss how biological variability could impact your findings in vivo. The works of Alexey Onufriev’s lab on the sensitivity of nucleosomes to charge changes (10.1016/j.bpj.2010.06.046, 10.1186/s13072-018-0181-5), such as some PTMs, are one potential starting place to consider how modifications alter nucleosome stability in vivo.

      Response: We thank the reviewer for the insightful comments and agree that native nucleosomes can differ from reconstituted nucleosomes due to the presence of histone modifications.

      We have revised the introduction to emphasize the differences between in vitro and in vivo nucleosomes. The new text now reads

      "The relevance of physicochemical interactions between nucleosomes to chromatin organization in vivo has been constantly debated, partly due to the uncertainty in their strength [cite]. Examining the interactions between native nucleosomes poses challenges due to the intricate chemical modifications that histone proteins undergo within the nucleus and the variations in their underlying DNA sequences [cite]. Many in vitro experiments have opted for reconstituted nucleosomes that lack histone modifications and feature wellpositioned 601-sequence DNA to simplify the chemical complexity. These experiments aim to establish a fundamental reference point for understanding the strength of interactions within native nucleosomes. Nevertheless, even with reconstituted nucleosomes, a consensus regarding the significance of their interactions remains elusive. For example, using force-measuring magnetic tweezers, Kruithof et al. estimated the inter-nucleosome binding energy to be ∼ 14 kBT [cite]. On the other hand, Funke et al. introduced a DNA origamibased force spectrometer to directly probe the interaction between a pair of nucleosomes [cite], circumventing any potential complications from interpretations of single molecule traces of nucleosome arrays. Their measurement reported a much weaker binding free energy of approximately 2 kBT. This large discrepancy in the reported reference values complicates a further assessment of the interactions between native nucleosomes and their contribution to chromatin organization in vivo."

      We modified the first paragraph of the results section to read

      "Encouraged by the explicit ion model’s accuracy in reproducing experimental measurements of single nucleosomes and nucleosome arrays, we moved to directly quantify the strength of inter-nucleosomes interactions. We once again focus on reconstituted nucleosomes for a direct comparison with in vitro experiments. These experiments have yielded a wide range of values, ranging from 2 to 14 kBT [cite]. Accurate quantification will offer a reference value for conceptualizing the significance of physicochemical interactions among native nucleosomes in chromatin organization in vivo."

      New text was added to the Discussion Section to emphasize the implications of simulation results for interactions among native nucleosomes.

      "One significant finding from our study is the predicted strong inter-nucleosome interactions under the physiological salt environment, reaching approximately 9 kBT. We showed that the much lower value reported in a previous DNA origami experiment is due to the restricted nucleosomal orientation inherent to the device design. Unrestricted nucleosomes allow more close contacts to stabilize binding. A significant nucleosome binding free energy also agrees with the high forces found in single-molecule pulling experiments that are needed for chromatin unfolding [cite]. We also demonstrate that this strong inter-nucleosomal interaction is largely preserved at longer nucleosome repeat lengths (NRL) in the presence of linker histone proteins. While posttranslational modifications of histone proteins may influence inter-nucleosomal interactions, their effects are limited, as indicated by Ding et al. [cite], and are unlikely to completely abolish the significant interactions reported here. Therefore, we anticipate that, in addition to molecular motors, chromatin regulators, and other molecules inside the nucleus, intrinsic inter-nucleosome interactions are important players in chromatin organization in vivo."

      The suggested references (10.1016/j.bpj.2010.06.046, 10.1186/s13072-018-0181-5) are now included as citations # 44 and 45.

      Comment 4: Due to the implicit water model, do you know if ions can penetrate the nucleosome more? For example, does the lack of explicit water potentially cause sodium to cluster in the DNA grooves more than is biologically relevant, as shown in Figure 1?

      Response: We thank the reviewer for the insightful comments. The parameters of the explicit-ion model were deduced from all-atom simulations and fine-tuned to replicate crucial aspects of the local ion arrangements around DNA (1). The model’s efficacy was demonstrated in reproducing the radial distribution function of Na+ and Mg2+ ion distributions in the proximity of DNA (see Author response image 1). Consequently, the number of ions near DNA in the coarse-grained models aligns with that observed in all-atom simulations, and we do not anticipate any significant, unphysical clustering. It is worth noting that previous atomistic simulations have also reported the presence of a substantial quantity of Na+ ions in close proximity to nucleosomal DNA (refer to Author response image 2).

      Author response image 1.

      Comparison between the radial distribution functions of Na+ (left) and Mg2+ (right) ions around the DNA phosphate groups computed from all-atom (black) and coarse-grained (red) simulations. Figure adapted from Figure 4 of Ref. 1. The coarse-grained explicit ion model used in producing the red curves is identical to the one presented in the current manuscript. (© 2011, AIP Publishing. This figure is reproduced with permission from Figure 4 in Freeman GS, Hinckley DM, de Pablo JJ (2011) A coarse-grain three-site-pernucleotide model for DNA with explicit ions. The Journal of Chemical Physics 135:165104. It is not covered by the CC-BY 4.0 license and further reproduction of this figure would need permission from the copyright holder.)

      Author response image 2.

      Three-dimensional distribution of sodium ions around the nucleosome determined from all-atom explicit solvent simulations. Darker blue colors indicate higher sodium density and high density of sodium ions around the DNA is clearly visible. The crystallographically identified acidic patch has been highlighted as spheres on the surface of the histone core and a high level of sodium condensation is observed around these residues. Figure adapted from Ref. 2. (© 2009, American Chemical Society. This figure is reproduced with permission from Figure 7 in Materese CK, Savelyev A, Papoian GA (2009) Counterion Atmosphere and Hydration Patterns near a Nucleosome Core Particle. J. Am. Chem. Soc. 131:15005–15013.. It is not covered by the CC-BY 4.0 license and further reproduction of this figure would need permission from the copyright holder.)

      Comment 5: Histone side chain to DNA interactions, such as histone arginines to DNA, are essential for nucleosome stability. Therefore, can the authors provide validation or references supporting your model of the nucleosome with one bead per amino acid? I would like to see if the nucleosomes are stable in an extended simulation or if similar dynamic motions to all-atom simulations are observed.

      Response: The nucleosome model, which employs one bead per amino acid and lacks explicit ions, has undergone extensive calibration and has found application in numerous prior studies. For instance, the de Pablo group utilized a similar model to showcase its ability to accurately replicate the experimentally measured nucleosome unwinding free energy penalty (3), sequence-dependent nucleosome sliding (4), and the interaction between two nucleosomes (5). Similarly, the Takada group employed a comparable model to investigate acetylation-modulated tri-nucleosome structures (6), chromatin structures influenced by chromatin factors (7), and nucleosome sliding (8). Our group also employed this model to study the structural rearrangement of a tetranucleosome (9) and the folding of larger chromatin systems (10). In cases where data were available, simulations frequently achieved quantitative reproduction of experimental results.

      We added the following text to the manuscript to emphasize previous studies that validate the model accuracy.

      "We observe that residue-level coarse-grained models have been extensively utilized in prior studies to examine the free energy penalty associated with nucleosomal DNA unwinding [cite], sequence-dependent nucleosome sliding [cite], binding free energy between two nucleosomes [cite], chromatin folding [cite], the impact of histone modifications on tri-nucleosome structures [cite], and protein-chromatin interactions [cite]. The frequent quantitative agreement between simulation and experimental results supports the utility of such models in chromatin studies. Our introduction of explicit ions, as detailed below, further extends the applicability of these models to explore the dependence of chromatin conformations on salt concentrations."

      We agree that arginines are important for nucleosome stability. Since we assign positive charges to these residues, their contribution to DNA binding can be effectively captured. The model’s ability in reproducing nucleosome stability is supported by the good agreement between the simulated free energy penalty associated with nucleosomal DNA unwinding and experimental value estimated from single molecule experiments (Figure 1).

      To further evaluate nucleosome stability in our simulations, we conducted a 200-ns-long simulation of a nucleosome featuring the 601-sequence under physiological salt conditions– 100 mM NaCl and 0.5 mM MgCl2, consistent with the conditions in Figure 1 of the main text. We found that the nucleosome maintains its overall structure during this simulation. The nucleosome’s radius of gyration (Rg) remained proximate to the value corresponding to the PDB structure (3.95 nm) throughout the entire simulation period (see Author response image 3).

      Author response image 3.

      Time trace of the radius of gyration (Rg) of a nucleosome with the 601-sequence along an unbiased, equilibrium trajectory. It is evident the Rg fluctuates around the value found in the PDB structure (3.95 nm), supporting the stability of the nucleosome in our simulation.

      Occasional fluctuations in Rg corresponded to momentary, partial unwrapping of the nucleosomal DNA, a phenomenon observed in single-molecule experiments. However, we advise caution due to the coarse-grained nature of our simulations, which prevents a direct mapping of simulation timescale to real time. Importantly, the rate of DNA unwrapping in our simulations is notably overestimated.

      It’s plausible that coarse-grained models, lacking side chains, might underestimate the barrier for DNA sliding along the nucleosome. Specifically, our model, without differentiation between interactions among various amino acids and nucleotides, accurately reproduces the average nucleosomal DNA binding affinity but may not capture the energetic variations among binding interfaces. Since sliding’s contribution to chromatin organization is minimal due to the use of strongly positioning 601 sequences, we imposed rigidity on the two nucleotides situated at the dyad axis to prevent nucleosomal DNA sliding. In future studies, enhancing the calibration of protein-DNA interactions to achieve improved sequence specificity would be an intriguing avenue. To underscore this limitation of the model, we have included the following text in the discussion section of the main text.

      "Several aspects of the coarse-grained model presented here can be further improved. For instance, the introduction of specific protein-DNA interactions could help address the differences in non-bonded interactions between amino acids and nucleotides beyond electrostatics [cite]. Such a modification would enhance the model’s accuracy in predicting interactions between chromatin and chromatin-proteins. Additionally, the single-bead-per-amino-acid representation used in this study encounters challenges when attempting to capture the influence of histone modifications, which are known to be prevalent in native nucleosomes. Multiscale simulation approaches may be necessary [cite]. One could first assess the impact of these modifications on the conformation of disordered histone tails using atomistic simulations. By incorporating these conformational changes into the coarse-grained model, systematic investigations of histone modifications on nucleosome interactions and chromatin organization can be conducted. Such a strategy may eventually enable the direct quantification of interactions among native nucleosomes and even the prediction of chromatin organization in vivo."

      Comment 6: The solvent salt conditions vary in the experimental reference data for internucleosomal interaction energies. The authors note, for example, that the in vitro data from Funke et al. differs the most from other measurements, but the solvent conditions are 35 mM NaCl and 11 mM MgCl2. Since this simulation method allows for this investigation, could the authors speak to or investigate if solvent conditions are responsible for the variability in experimental reference data? The authors conclude on pg. 8-9 and Figure 4 that orientational restraints in the DNA origami methodology are responsible for differences in interaction energy. Can the authors rule out ion concentration contributions?

      Response: We thank the reviewer for the insightful comment. We would like to clarify that the black curve presented in Figure 4B of the main text was computed using the salt concentration specified by Funke et al. (35 mM NaCl and 11 mM MgCl2). Furthermore, there were no restraints placed on nucleosome orientations during these calculations. Consequently, the results in Figure 4B can be directly compared with the black curve in Figure 5C. The data in Figure 5C were calculated under physiological salt conditions (150 mM NaCl and 2 mM MgCl2), which are the standard solvent salt conditions used in most studies. It is worth noting that the free energy of nucleosome binding is significantly higher at the salt concentration employed by Funke et al. (14 kBT) than the value at the physiological salt condition (9 kBT). Therefore, comparing the results in Figure 4B and 5C eliminates ion concentration conditions as a potential cause for the the almost negligible result reported by Funke et al.

      Comment 7: In the discussion on pg. 12 residual-level should be residue-level.

      Response: We apologize for the oversight and have corrected the grammatical error in our manuscript.

      RESPONSE TO REFEREE 2:

      Comment 0: In this manuscript, the authors introduced an explicit ion model using the coarse-grained modelling approach to model the interactions between nucleosomes and evaluate their effects on chromatin organization. The strength of this method lies in the explicit representation of counterions, especially divalent ions, which are notoriously difficult to model. To achieve their aims and validate the accuracy of the model, the authors conducted coarse-grained molecular dynamics simulations and compared predicted values to the experimental values of the binding energies of protein-DNA complexes and the free energy profile of nucleosomal DNA unwinding and inter-nucleosome binding. Additionally, the authors employed umbrella sampling simulations to further validate their model, reproducing experimentally measured sedimentation coefficients of chromatin under varying salt concentrations of monovalent and divalent ions.

      Response: We thank the reviewer’s excellent summary of the work.

      Comment 1: The significance of this study lies in the authors’ coarse-grained model which can efficiently capture the conformational sampling of molecules while maintaining a low computational cost. The model reproduces the scale and, in some cases, the shape of the experimental free energy profile for specific molecule interactions, particularly inter-nucleosome interactions. Additionally, the authors’ method resolves certain experimental discrepancies related to determining the strength of inter-nucleosomal interactions. Furthermore, the results from this study support the crucial role of intrinsic physicochemical interactions in governing chromatin organization within the nucleus.

      Response: We appreciate the reviewer’s strong assessment of the paper’s significance, novelty, and broad interest, and we thank him/her for the detailed suggestions and comments.

      Comment 2: The method is simple but can be useful, given the authors can provide more details on their ion parameterization. The paper says that parameters in their ”potentials were tuned to reproduce the radial distribution functions and the potential of mean force between ion pairs determined from all-atom simulations.” However, no details on their all-atom simulations were provided; at some point, the authors refer to Reference 67 which uses all-atom simulations but does not employ the divalent ions. Also, no explanation is given for their modelling of protein-DNA complexes.

      Response: We appreciate the reviewer’s suggestion on clarifying the parameterization of the explicition model. The parameterization was not carried out in reference 67 nor by us, but by the de Pablo group in citation 53. Specifically, ion potentials were parameterized to fit the potential of mean force between both monovalent and divalent ion pairs, calculated either from all-atom simulations or from the literature. The authors carried out extensive validations of the model parameters by comparing the radial distribution functions of ions computed using the coarse-grained model with those from all-atom simulations. Good agreements between coarse-grained and all-atom results ensure that the parameters’ accuracy in reproducing the local structures of ion interactions.

      To avoid confusion, we have revised the text from:

      "Parameters in these potentials were tuned to reproduce the radial distribution functions and the potential of mean force between ion pairs determined from all-atom simulations."

      to

      "Parameters in these potentials were tuned by Freeman et al. [cite] to reproduce the radial distribution functions and the potential of mean force between ion pairs determined from all-atom simulations."

      We modified the Supporting Information at several places to clarify the setup and interpretation of protein-DNA complex simulations.

      For example, we clarified the force fields used in these simulation with the following text

      "All simulations were carried out using the software Lammps [cite] with the force fields defined in the previous two sections."

      We added details on the preparation of these simulations as follows

      "We carried out a series of umbrella-sampling simulations to compute the binding free energies of a set of nine protein-DNA complexes with experimentally documented binding dissociation constants [cite]. Initial configurations of these simulations were prepared using the crystal structures with the corresponding PDB IDs listed in Fig. S1."

      We further revised the caption of Figure S1 (included as Author response image 4) to facilitate the interpretation of simulation results.

      Author response image 4.

      The explicit-ion model predicts the binding affinities of protein-DNA complexes well, related to Fig. 1 of the main text. Experimental and simulated binding free energies are compared for nine protein-DNA complexes [cite], with a Pearson Correlation coefficient of 0.6. The PDB ID for each complex is indicated in red, and the diagonal line is drawn in blue. The significant correlation between simulated and experimental values supports the accuracy of the model. To further enhance the agreement between the two, it will be necessary to implement specific non-bonded interactions that can resolve differences among amino acids and nucleotides beyond simple electrostatics. Such modifications will be interesting avenues for future research. See text Section: Binding free energy of protein-DNA complexes for simulation details.

      Comment 3: Overall, the paper is well-written, concise and easy to follow but some statements are rather blunt. For example, the linker histone contribution (Figure 5D) is not clear and could be potentially removed. The result on inter-nucleosomal interactions and comparison to experimental values from Ref#44 is the most compelling. It would be nice to see if the detailed shape of the profile for restrained inter-nucleosomal interactions in Figure 4B corresponds to the experimental profile. Including the dependence of free energy on a vertex angle would also be beneficial.

      Response: We thank the reviewer for the comments and agree that the discussion on linker histone results was brief. However, we believe the results are important and demonstrate our model’s advantage over mesoscopic approaches in capturing the impact of chromatin regulators on chromatin organization.

      Therefore, instead of removing the result, we expanded the text to better highlight its significance, to help its comprehension, and to emphasize its biological implications. The image in Figure 5D was also redesigned to better visualize the cross contacts between nucleosomes mediated by histone H1. The added texts are quoted as below, and the new Figure 5 is included.

      Author response image 5.

      Revised main text Figure 5, with Figure 5D modified for improved visual clarity.

      "Importantly, we found that the weakened interactions upon extending linker DNA can be more than compensated for by the presence of histone H1 proteins. This is demonstrated in Fig. 5C and Fig. S8, where the free energy cost for tearing part two nucleosomes with 167 bp DNA in the presence of linker histones (blue) is significantly higher than the curve for bare nucleosomes (red). Notably, at larger inter-nucleosome distances, the values even exceed those for 147 bp nucleosomes (black). A closer examination of the simulation configurations suggests that the disordered C-terminal tail of linker histones can extend and bind the DNA from the second nucleosome, thereby stabilizing the internucleosomal contacts (as shown in Fig. 5D). Our results are consistent with prior studies that underscore the importance of linker histones in chromatin compaction [cite], particularly in eukaryotic cells with longer linker DNA [cite]."

      We further compared the simulated free energy profile, depicting the center of mass distance between nucleosomes, with the experimental profile, as depicted in Author response image 6. The agreement between the simulated and experimental results is evident. The nuanced features observed between 60 to 80 Ain the simulated profile stem from DNA unwinding˚ to accommodate the incoming nucleosome, creating a small energy barrier. It’s worth noting that such unwinding is unlikely to occur in the experimental setup due to the hybridization method used to anchor nucleosomes onto the DNA origami. Moreover, our simulation did not encompass configurations below 60 A, resulting in a lack of data in˚ that region within the simulated profile.

      We projected the free energy profile onto the vertex angle of the DNA origami device, utilizing the angle between two nucleosome faces as a proxy. Once more, the simulated profile demonstrates reasonable agreement with the experimental data (Author response image 6). Author response image 6 has been incorporated as Figure S4 in the Supporting Information.

      Author response image 6.

      Explicit ion modeling reproduces the experimental free energy profiles of nucleosome binding. (A) Comparison between the simulated (black) and experimental (red) free energy profile as a function of the inter-nucleosome distance. Error bars were computed as the standard deviation of three independent estimates. The barrier observed between 60A and 80˚ A arises from the unwinding of nucleosomal DNA when the two nu-˚ cleosomes are in close proximity, as highlighted in the orange circle. (B) Comparison between the simulated (black) and experimental (red) free energy profile as a function of the vertex angle. Error bars were computed as the standard deviation of three independent estimates. (C) Illustration of the vertex angle Φ used in panel (B).

      Comment 4: Another limitation of this study is that the authors’ model sacrifices certain atomic details and thermodynamic properties of the modelled systems. The potential parameters of the counter ions were derived solely by reproducing the radial distribution functions (RDFs) and potential of mean force (PMF) based on all-atom simulations (see Methods), without considering other biophysical and thermodynamic properties from experiments. Lastly, the authors did not provide any examples or tutorials for other researchers to utilize their model, thus limiting its application.

      Response: We agree that residue-level coarse-grained modeling indeed sacrifices certain atomistic details. This sacrifice can be potentially limiting when studying the impact of chemical modifications, especially on histone and DNA methylations. We added a new paragraph in the Discussion Section to point out such limitations and the relevant text is quoted below.

      "Several aspects of the coarse-grained model presented here can be further improved. For instance, the introduction of specific protein-DNA interactions could help address the differences in non-bonded interactions between amino acids and nucleotides beyond electrostatics [cite]. Such a modification would enhance the model’s accuracy in predicting interactions between chromatin and chromatin-proteins. Additionally, the single-bead-per-amino-acid representation used in this study encounters challenges when attempting to capture the influence of histone modifications, which are known to be prevalent in native nucleosomes. Multiscale simulation approaches may be necessary [cite]. One could first assess the impact of these modifications on the conformation of disordered histone tails using atomistic simulations. By incorporating these conformational changes into the coarse-grained model, systematic investigations of histone modifications on nucleosome interactions and chromatin organization can be conducted. Such a strategy may eventually enable the direct quantification of interactions among native nucleosomes and even the prediction of chromatin organization in vivo."

      Nevertheless, it’s important to note that while the model sacrifices accuracy, it compensates with superior efficiency. Atomistic simulations face significant challenges in conducting extensive free energy calculations required for a quantitative evaluation of ion impacts on chromatin structures.

      The explicit ion model, introduced by the de Pablo group, follows a standard approach adopted by other research groups, such as the parameterization of ion models using the potential of mean force from atomistic simulations (11; 12). According to multiscale coarse-graining theory, reproducing potential mean force (PMF) enables the coarsegrained model to achieve thermodynamic consistency with the atomistic model, ensuring identical statistical properties derived from them. However, it’s crucial to recognize that an inherent limitation of such approaches is their dependence on the accuracy of atomistic force fields in reproducing thermodynamic properties from experiments, as any inaccuracies in the atomistic force fields will similarly affect the resulting coarse-grained (CG) model.

      We have provided the implementation of CG model and detailed instructions on setting up and performing simulations GitHub repository. Examples include simulation setup for a protein-DNA complex and for a nucleosome with the 601-sequence.

      References [1] Freeman GS, Hinckley DM, de Pablo JJ (2011) A coarse-grain three-site-pernucleotide model for DNA with explicit ions. The Journal of Chemical Physics 135:165104.

      [2] Materese CK, Savelyev A, Papoian GA (2009) Counterion Atmosphere and Hydration Patterns near a Nucleosome Core Particle. J. Am. Chem. Soc. 131:15005–15013.

      [3] Lequieu J, Cordoba A, Schwartz DC, de Pablo JJ´ (2016) Tension-Dependent Free Energies of Nucleosome Unwrapping. ACS Cent. Sci. 2:660–666.

      [4] Lequieu J, Schwartz DC, De Pablo JJ (2017) In silico evidence for sequence-dependent nucleosome sliding. Proc. Natl. Acad. Sci. U.S.A. 114.

      [5] Moller J, Lequieu J, de Pablo JJ (2019) The Free Energy Landscape of Internucleosome Interactions and Its Relation to Chromatin Fiber Structure. ACS Cent. Sci. 5:341–348.

      [6] Chang L, Takada S (2016) Histone acetylation dependent energy landscapes in trinucleosome revealed by residue-resolved molecular simulations. Sci Rep 6:34441.

      [7] Watanabe S, Mishima Y, Shimizu M, Suetake I, Takada S (2018) Interactions of HP1 Bound to H3K9me3 Dinucleosome by Molecular Simulations and Biochemical Assays. Biophysical Journal 114:2336–2351.

      [8] Brandani GB, Niina T, Tan C, Takada S (2018) DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations. Nucleic Acids Research 46:2788–2801.

      [9] Ding X, Lin X, Zhang B (2021) Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface. Nat Commun 12:1091.

      [10] Liu S, Lin X, Zhang B (2022) Chromatin fiber breaks into clutches under tension and crowding. Nucleic Acids Research 50:9738–9747.

      [11] Savelyev A, Papoian GA (2010) Chemically accurate coarse graining of doublestranded DNA. Proc. Natl. Acad. Sci. U.S.A. 107:20340–20345.

      [12] Noid WG (2013) Perspective: Coarse-grained models for biomolecular systems. The Journal of Chemical Physics 139:090901.

    1. Author response:

      The following is the authors’ response to the original reviews

      List of major changes

      (1) We have emphasized the assumptions underlying our modeling approach in the third paragraph of the Introduction section.

      (2) We have included a new paragraph in the Discussion section to compare our model with a molecular mechanism-oriented model.

      (3) We have included a new paragraph at the end of the Introduction section to outline the main content of each subsection in Results and the logical connections between them. Correspondingly, the chapter hierarchy and section titles have been adjusted.

      (4) The Supplementary Material includes an additional table (Table S2) that provides detailed explanations of the symbols used in the model.

      (5) We have included a new paragraph in the Introduction section to explicitly emphasize the phenomenological nature of our model and its broad applicability.

      (6) In the Osmoregulation subsection, we have added a discussion on how our model can be directly generalized to scenarios involving the environmental uptake of osmolytes.

      (7) We have included a more detailed examination of the limitations inherent in our modeling approach in the second last paragraph of the Discussion section.

      (8) In the third last paragraph of the Discussion section, we have explicitly demonstrated that our model does not conflict with the observation that, in E. coli, cell wall synthesis is not directly regulated by the turgor pressure.

      Reviewer #1 (Public review):

      Summary:

      A theoretical model for microbial osmoresponse was proposed. The model assumes simple phenomenological rules: (i) the change of free water volume in the cell due to osmotic imbalance based on pressure balance, (ii) osmoregulation that assumes change of the proteome partitioning depending on the osmotic pressure that affects the osmolyte-producing protein production, (iii) the cell-wall synthesis regulation where the change of the turgor pressure to the cell-wall synthesis efficiency to go back to the target turgor pressure, (iv) effect of Intracellular crowding assuming that the biochemical reactions slow down for more crowding and stops when the protein density (protein mass divided by free water volume) reaches a critical value. The parameter values were found in the literature or obtained by fitting to the experimental data. The authors compare the model behavior with various microorganisms (E. coli, B. subtils, S. Cerevisiae, S. pombe), and successfully reproduced the overall trend (steady state behavior for many of them, dynamics for S. pombe). In addition, the model predicts non-trivial behavior such as the fast cell growth just after the hypoosmotic shock, which is consistent with experimental observation. The authors further make experimentally testable predictions regarding mutant behavior and transient dynamics.

      Strength:

      The theory assumes simple mechanistic dependence between core variables without going into specific molecular mechanisms of regulations. The simplicity allows the theory to apply to different organisms by adjusting the time scales with parameters, and the model successfully explains broad classes of observed behaviors. Mathematically, the model provides analytical expressions of the parameter dependences and an understanding of the dynamics through the phase space without being buried in the detail. This theory can serve as a base to discuss the universality and diversity of microbial osmoresponse.

      We would like to thank Reviewer 1 for thoroughly reading our work and appreciating our theoretical approach to investigating microbial osmotic response.

      Weakness:

      The core part of this model is that everything is coupled with growth physiology, and, as far as I understand, the assumption (iv) (Eq. 8) that imposes the global reaction rate dependence on crowding plays a crucial role. I would think this is a strong and interesting assumption. However, the abstract or discussion does not discuss the importance of this assumption. In addition, the paper does not discuss gene regulation explicitly, and some comparison with a molecular mechanismoriented model may be beneficial to highlight the pros and cons of the current approach

      We thank Reviewer 1 for their very helpful feedback. We have significantly revised the manuscript as suggested by Reviewer 1. See the detailed answers in the following.

      Reviewer #1 (Recommendations for the authors)

      (1) Explicitly stating the assumption (iv) in the abstract and discussing its role would help readers understand.

      In the revised manuscript, we have significantly rewritten the third paragraph of the Introduction section to emphasize our key assumptions as suggested by Reviewer 1, including the relationship between global reaction rate and crowding:

      “Our model assumes the following phenomenological rules: (1) the change in free water volume within the cell is driven by osmotic imbalance (Cadart et al., Nature Physics, 2019; Rollin et al., Elife, 2023), while the remaining volume changes in proportion to protein production; (2) osmoregulation influences the production of osmolyte-producing protein, governed by intracellular protein density (Scott et al., Science, 2010); (3) cell-wall synthesis is regulated through a feedback mechanism, wherein turgor pressure modulates the efficiency of cell-wall synthesis, enabling the cell to maintain a relatively stable turgor pressure; and (4) intracellular crowding slows down biochemical reactions as cytoplasmic density increases, with reactions ceasing entirely when protein density reaches a critical threshold.”

      We have also modified the abstract to mention the crowding effects explicitly. Additionally, we have added a few sentences in the first and second paragraphs of the Discussion section to emphasize the importance of crowding effects to our conclusions regarding the growth rate reduction in steady states and the non-monotonic dependence of the growth rate peak on the shock amplitude after a hyperosmotic shock.

      (2) I found [Shen W , Gao Z, Chen K, Zhao A, Ouyang Q, Luo C. The regulatory mechanism of the yeast osmoresponse under different glucose concentrations. Iscience. 2023 Jan 20;26(1)], which discusses the medium glucose concentration dependence of the response, focused on the gene regulatory circuit and the metabolic flux. As far as I understood, this paper considers the effect of the reallocation of resources but not the mechanical part of the osmoresponse such as pressure explicitly. It will be interesting to discuss the pros and cons in comparison with such a model. In principle, I will not be surprised if the current model does not differentiate the different glucose concentrations much since it is a more coarse-grained model, and I don't think it is a problem, but it will be good to have an explicit discussion.

      We appreciate Reviewer 1's insightful comment regarding the work by Shen et al. (iScience, 2023), which elucidates the two distinct osmoresponse strategies in yeast. By quantifying Hog1 nuclear translocation dynamics and downstream protein expression, the study reveals that in a rich medium, cells can leverage surplus glycolytic products as defensive reserves, reallocating metabolic flux to facilitate rapid adaptation to osmotic changes. Conversely, limited glycolytic intermediates in low-glucose environments necessitate increased enzyme synthesis for osmotic adaptation. 

      The paper highlighted by Reviewer 1 studies yeast's adaptive strategies under two stresses— nutrient limitation and osmotic pressure and provides an important complement to our study.

      In our simplified model, we did not include the interaction between cell growth and osmolyte production, assuming a constant fraction of ribosomes translating ribosomal proteins, supported by the experiments of E. coli (Dai et al., mBio, 2018). We remark that incorporating competitive dynamics for translational resources into our framework can be achieved by modifying the proportion of ribosomes translating themselves (X<sub>r</sub>), from a constant to a function related to the translation strategy of the osmolyte-producing enzyme ((X<sub>a</sub>).

      In the revised manuscript, we have included a new discussion in the third paragraph of the Discussion section to compare our approach with the molecular mechanism-oriented model:

      “We remark that our model is intrinsically a coarse-grained model with many molecular details regarding gene expression regulation neglected, which allows us to gain more analytical insights. In [Shen et al., iScience, 2023], the authors studied the responses to osmotic stress in glucose-limited environments and found that cells exhibited stronger osmotic gene expression response under glucose-limited conditions than under glucose-rich conditions. Using a computational model based on molecular mechanisms combined with experimental measurements, the authors demonstrated that in a glucose-limited environment, glycolysis intermediates were limited, which required cells to express more glycerol-production enzymes for stress adaptation. In the current version of our model, we do not account for the interaction between cell growth and osmolyte production; instead, we assume a constant fraction of ribosomes dedicated to translating ribosomal proteins. Our model can be further generalized to include the more complex interactions, including the coupling between biomass and osmolyte production, e.g., by allowing the fraction of ribosomes translating ((X<sub>r</sub>) to depend on the translation strategy of the osmolyte-producing enzyme ((X<sub>a</sub>).”

      (3) A minor comment: The authors call assumption (iii) (eq. 7) "positive feedback from turgor pressure to the cell-wall synthesis efficiency" (line 204). I have a hard time seeing this as positive feedback. It regulates the cell wall synthesis so that turgor pressure returns to the desired value; hence, isn't it negative feedback?

      We apologize for this confusion. We have removed the term "positive feedback" in the revised manuscript.

      Reviewer #2 (Public review):

      Summary:

      In this study, Ye et al. have developed a theoretical model of osmotic pressure adaptation by osmolyte production and wall synthesis.

      Strengths:

      They validate their model predictions of a rapid increase in growth rate on osmotic shock experimentally using fission yeast. The study has several interesting insights which are of interest to the wider community of cell size and mechanics.

      Weaknesses:

      Multiple aspects of this manuscript require addressing, in terms of clarity and consistency with previous literature. The specifics are listed as major and minor comments.

      Major comments:

      (1) The motivation for the work is weak and needs more clarity.

      We thank Reviewer 2 for this very helpful comment, which we believe has significantly improved our manuscript. We would like to clarify the two major motivations of our study. 

      First, we aim to construct a systems-level and coarse-grained model capable of elucidating the complex processes underlying microbial osmoresponse. By leveraging the separation of timescales associated with mechanical equilibrium, cell-wall synthesis regulation, and osmoregulation, our model facilitates in-depth analytical and numerical analysis of how these various processes interact during cellular adaptation. In particular, we demonstrate the key physiological functions of osmoregulation and cell-wall synthesis regulation.

      Second, we seek to apply this model to interpret the phenomenon of supergrowth observed in fission yeast Schizosaccharomyces pombe (Knapp et al., Cell Systems, 2019). This application addresses an essential challenge in experimental studies: exclusive knockout experiments can be difficult, and mechanistic interpretations of experimental observations are often lacking. Our theoretical framework offers a valuable tool for understanding such phenomena, contributing to the fundamental knowledge of microbial physiology and developing predictive models for microbial behavior under osmotic stress.

      In the revised manuscript, we have included a new paragraph at the end of the Discussion section to emphasize our motivations better:

      “In this work, we construct a systems-level and coarse-grained model capable of elucidating the complex processes underlying microbial osmoresponse. By leveraging the separation of timescales associated with mechanical equilibrium, cell-wall synthesis regulation, and osmoregulation, our model facilitates in-depth analytical and numerical analysis of how these various processes interact during cellular adaptation. In particular, we demonstrate the key physiological functions of osmoregulation and cell-wall synthesis regulation. We then apply this model to interpret the unusual phenomenon of supergrowth observed in fission yeast. This application addresses an essential challenge in experimental studies: exclusive knockout experiments can be difficult, and mechanistic interpretations of experimental observations are often lacking. Our theoretical framework offers a valuable tool for understanding such phenomena, contributing to the fundamental knowledge of microbial physiology and developing predictive models for microbial behavior under osmotic stress.”

      (2) The link between sections is very frequently missing. The authors directly address the problem that they are trying to solve without any motivation in the results section.

      We are grateful to Reviewer 2 for their valuable feedback. In the revised manuscript, we have included a new paragraph at the end of the Introduction section to outline the main content of each subsection in Results and the logical connections between them:

      “In the following “Results” section, we begin by outlining the primary assumptions and equations of our model in the subsection "Model Description," which includes four parts, each addressing one of the four phenomenological rules. Additional details can be found in Methods. We then proceed to the subsection “Steady states in constant environments”, where we employ our theoretical framework to analyze steady-state growth and examine how the growth rate varies with external osmolarity. In the “Transient dynamics after a constant osmotic shock” subsection, we investigate the time-dependent osmoresponse after a constant hyperosmotic and hypoosmotic shock. Finally, in “Comparison with experiments: supergrowth phenomena after osmotic oscillation”, we address the supergrowth phenomena observed in S. pombe, utilizing our model to elucidate these experimental observations.”

      (3) The parameters used in the models (symbols) need to be explained better to make the paper more readable.

      We apologize for this confusion. In the revised Supplementary Material, we have included an additional table (Table S2) to explain the meanings of the symbols employed in the model to help the reader better understand.

      (4) Throughout the paper, the authors keep switching between organisms that they are modelling. There needs to be some consistency in this aspect where they mention what organism they are trying to model, since some assumptions that they make may not be valid for both yeast as well as bacteria.

      We thank Reviewer 2 for this very helpful comment. We would like to clarify that our model is coarse-grained without including detailed molecular mechanisms; therefore, it presumably applies to various species of microorganisms. Indeed, the predicted steady-state growth curves derived from our model and the experimental data obtained from various organisms agree reasonably well (Figure 2A of the main text). 

      In the revised manuscript, we have explicitly emphasized the nature of our phenomenological model and its broad applicability in the fourth paragraph of the Introduction section:

      “We remark that our model is coarse-grained, without including detailed molecular mechanisms, and is therefore applicable across diverse microbial species. Notably, the predicted steady-state growth rate as a function of internal osmotic pressure from our model aligns well with experimental data from diverse organisms. This alignment allows us to quantify the sensitivities of translation speed and regulation of osmolyte-producing protein in response to intracellular density. Additionally, we demonstrate that osmoregulation and cellwall synthesis regulation enable cells to adapt to a wide range of external osmolarities and prevent plasmolysis. Our model also predicts a non-monotonic time dependence of growth rate and protein density as they approach steady-state values following a constant osmotic shock, in concert with experimental observations (Rojas et al., PNAS, 2014; Rojas et al., Cell systems, 2017). Moreover, we show that a supergrowth phase can arise following a sudden decrease in external osmolarity, driven by cell-wall synthesis regulation, either through the direct application of a hypoosmotic shock or the withdrawal of an oscillatory stimulus. Remarkably, the predicted amplitudes of supergrowth (i.e., growth rate peaks) quantitatively agree with multiple independent experimental measurements.”

      Furthermore, we have also included a comparison with a detailed molecular mechanism model in the third paragraph of the Discussion section:

      “We remark that our model is intrinsically a coarse-grained model with many molecular details regarding gene expression regulation neglected, which allows us to gain more analytical insights. In [Shen et al., iScience, 2023], the authors studied the responses to osmotic stress in glucose-limited environments and found that cells exhibited stronger osmotic gene expression response under glucose-limited conditions than under glucose-rich conditions. Using a computational model based on molecular mechanisms combined with experimental measurements, the authors demonstrated that in a glucose-limited environment, glycolysis intermediates were limited, which required cells to express more glycerol-production enzymes for stress adaptation. In the current version of our model, we do not account for the interaction between cell growth and osmolyte production; instead, we assume a constant fraction of ribosomes dedicated to translating ribosomal proteins. Our model can be further generalized to include the more complex interactions, including the coupling between biomass and osmolyte production, e.g., by allowing the fraction of ribosomes translating ((X<sub>r</supb) to depend on the translation strategy of the osmolyte-producing enzyme ((X<sub>a</sub>).”

      (5) The extent of universality of osmoregulation i.e the limitations are not very well highlighted.

      The osmoregulation mechanism described in our model primarily addresses changes in cytoplasmic osmolarity through the de-novo synthesis of compatible solutes, widely observed across bacteria, archaea, and eukaryotic microorganisms. This review article (GundeCimerman et al., FEMS microbiology reviews, 2018) provides an extensive summary and exploration of the primary compatible solutes utilized by organisms from all three domains of life, underscoring the prevalence of this osmoregulatory strategy. Furthermore, our model can be directly generalized to scenarios involving the direct uptake of osmolytes from the environment. One only needs to change the interpretation of the parameter, 𝑘<sub>𝑎</sub> in the production of osmolyte molecule, , from the synthesis rate to the uptake rate, and all the results are equally applicable. In the revised manuscript, we have briefly discussed this point in the subsection “Osmoregulation.”

      We agree with Reviewer 2 that our model's coarse-grained nature makes it broadly applicable to diverse microbial taxa; however, more specialized adaptations are beyond our model. In the revised manuscript, we have included a more detailed examination of the limitations inherent in our modeling approach in the second last paragraph of the Discussion section:

      “We remark several limitations of our current coarse-grained model. First, the high membrane tension that inhibits transmembrane flux of peptidoglycan precursors, leading to a growth inhibition before the supergrowth peak (Rojas et al., Cell systems 2017) is beyond our model. Second, in our current framework, the osmoregulation and cell-wall synthesis regulation rely on the instantaneous cellular states. However, microorganisms can exhibit memory effects to external stimuli by adapting to their temporal order of appearance (Mitchell et al., Nature 2009). Notably, in the osmoregulation of yeast, a short-term memory, facilitated by post-translational regulation of the trehalose metabolism pathway, and a long-term memory, orchestrated by transcription factors and mRNP granules, have been identified (Jiang et al., Science signaling 2020). Besides, our model does not account for the role of osmolyte export in osmoregulation (Tamas et al., Molecular microbiology, 1999) and the interaction between biomass and osmolyte production (Shen et al., Iscience 2023). Extending our model to include more realistic biological processes will be interesting.”

      (6) Line 198-200: It is not clear in the text what organisms the authors are writing about here. "Experiments suggested that the turgor pressure induce cell-wall synthesis, e.g., through mechanosensors on cell membrane [45, 46], by increasing the pore size of the peptidoglycan network [5], and by accelerating the moving velocity of the cell-wall synthesis machinery [31]". This however is untrue for bacteria as shown by the study (reference 22 is this paper: E. Rojas, J. A. Theriot, and K. C. Huang, Response of escherichia coli growth rate to osmotic shock, Proceedings of the National Academy of Sciences 111, 7807 (2014).

      We thank Reviewer 2 for pointing out this very important issue and apologize for the confusion. References 45 and 46 (Dupres et al., Nature Chemical Biology 2009; Neeli-Venkata et al., Developmental Cell 2021) discuss how Wsc1 acts as a mechanosensor in S. pombe, detecting turgor pressure and activating pathways that reinforce the cell wall. Reference 5 (Typas et al., Cell 2010) explains the role of LpoA and LpoB, the two outer membrane lipoprotein regulators in E. coli, which modulate peptidoglycan synthesis in an extracellular manner. Reference 31 (Amir and Nelson, PNAS 2012) is a theoretical paper showing that turgor pressure may accelerate the moving velocity of the cell wall synthesis machinery in E. coli. In the revised manuscript, we have been more explicit about the organisms we refer to in the subsection “Cell-wall synthesis regulation.”

      Meanwhile, we agree with Reviewer 2 that cell wall synthesis may not be directly regulated by turgor pressure in E. coli (Rojas et al., PNAS 2014). We would like to clarify that this scenario is also included in our model corresponding to H<sub>cw</sub> = 0 (Eq. (7) in the main text): the turgor pressure does not affect the cell-wall synthesis. Therefore, the supergrowth phenomenon observed in S. pombe does not manifest under hypotonic stimulation in E. coli.

      In the revised manuscript, we have emphasized this point more explicitly in the third last paragraph of the Discussion section:

      “Reference 22 (Rojas et al., PNAS, 2014) showed that the expansion of E. coli cell wall is not directly regulated by turgor pressure, and this scenario is also included in our model as the case of H<sub>cw</sub> \= 0. According to our model, the supergrowth phase is absent if H<sub>cw</sub> = 0 (Figure S8), consistent with the absence of a growth rate peak after a hypoosmotic shock in the experiments of E. coli (Rojas et al., PNAS, 2014). Meanwhile, our predictions are consistent with the growth rate peak after a hypoosmotic shock observed for B. subtilis (Rojas et al., Cell systems, 2017).”

      (7) The time scale of reactions to hyperosmotic shocks does not agree with previous literature (reference 22). Therefore defining which organism you are looking at is important. Hence the statement " Because the timescale of the osmoresponse process, which is around hours (Figure 3B), is much longer than the timescale of the supergrowth phase, which is about 20 minutes, the turgor pressure at the growth rate peak can be well approximated by its immediate value after the shock." from line 447 does not seem to make sense. The authors need to address this.

      We apologize for this confusion. In the revised manuscript, we have clarified that the cited time scales are for the fission yeast S. pombe after Eq. (13) in the main text.

      Reviewer #2 (Recommendations for the authors):

      (1) Inconsistency in nomenclature: On line 117, the equation reads V<sub>b</sub> = αm<sub>p where V<sub>b</sub> is the bound volume. Whereas bound volume has been referred to as V<sub>bd</sub> previously and in Figure 1.

      Answer: We apologize for this confusion. In our model, the total bound volumeV<sub>b</sub> comprises the volume of dry mass and bound water, V<sub>b</sub> \= V<sub>bd</sub> + V<sub>bw</sub>, where V<sub>bd</sub> is the volume occupied by dry mass and V<sub>bw</sub> is the volume of bound water. In the revised manuscript, we have added a brief discussion of this point in the caption of Figure 1.

      (2) Line 180: Please define 𝜌𝜌 for equation 4.

      We apologize for this confusion. In the text, the symbol 𝜌<sub>p</sub> denotes the mass of a given substance per unit volume of free water, and its unit is g/ml. The specific substance in consideration is indicated by a subscript. For example, 𝜌<sub>p</sub> in Eq. (4) represents the protein density, and 𝜌<sub>c</sub> stands for the critical protein density, above which intracellular chemical reactions cease according to Eq. (8) of the main text. In the revised manuscript, we have clarified the meaning of 𝜌<sub>c</sub> after Eq. (4).

      (3) Line 187: Equation 5 also needs to be explained better. Hence there is a need to be more specific while stating the assumptions.

      The elastic modulus 𝐺 defined in Eq. (5) of the main text is a measure of the cell wall's resistance to volume expansion. We assume a constant 𝐺 for simplicity, which is reasonable when the cell wall deformation is mild. In the revised manuscript, we have been more explicit about our assumptions regarding the turgor pressure in the subsection “Cell-wall synthesis regulation.”

      (4) Line 225: For a biological audience some elaboration on "glass transition" may be required- either as a reference to a review or to a 1 sentence statement of relevance.

      We appreciate Reviewer 2’s helpful comment. In the revised manuscript, we have added a brief introduction to the glass transition and a citation to a review paper (Hunter and Weeks, Rep. Prog. Phys. 2012) at the beginning of the subsection “Intracellular crowding.”

      (5) Line 247: "All growth rates in steady states of cell growth are the same: 𝜇<sub>𝑓</sub> \= 𝜇<sub>r</sub> \= 𝜇<sub>cw</sub>". The authors need to explain in a line or two why this is true. Since the processes are independent, it is safe to assume that all 𝜇's are constant, but it is not obvious why they should all be equal.

      We apologize for the lack of a clear explanation regarding the equality of steady-state growth rates in our previous manuscript. In the revised manuscript, we have added a brief explanation of the equality of the three growth rates at the beginning of the subsection “Steady states in constant environments”:

      “When cell growth reaches a steady state, the proportions of all components, including free water volume, cell mass, and cell wall volume, must be constant relative to the total cell volume to ensure homeostasis. Therefore, all growth rates in steady states of cell growth must be the same: 𝜇<sub>𝑓</sub> \= 𝜇<sub>r</sub> \= 𝜇<sub>cw</sub>.”

      (6) Line 264: "Because the typical doubling times of microorganisms are around hours, we can estimate 𝜇<sub>𝑓</sub>/k<sub>w</sub> ∼ 10 Pa [51, 52] ..." since the authors are generalizing for yeast and bacteria, specifically E. coli, this is not a valid assumption to make. There is also a need to explain the basis of "𝜇<sub>𝑓</sub>/k<sub>w</sub> ∼ 10 Pa".  

      We appreciate the need for clarity in the estimation and its implications. The rough estimation of 𝜇<sub>𝑓</sub>/k<sub>w</sub> ~ 10 Pa in the main text is given by:

      Here, the typical value of 𝜇<sub>𝑓</sub> (which equals to 𝜇<sub>r</sub> in steady state) is approximated by the inverse of the cell cycle, which is around hours. The estimation above is employed to justify the assumption that 𝜇<sub>𝑓</sub>/k<sub>w</sub> is much smaller than the cytoplasmic osmotic and turgor pressures, which can be several atmospheric pressures.

      For the case of E. coli, based on the experimental results from Boer et al. (Boer et al., Biochemistry 2011), an 800mM hypoosmotic shock leads to a rapid expansion of cell volume accomplished within a time scale of 0.1s, from which we obtain:

      .

      Therefore, our assumption that 𝜇<sub>𝑓</sub>/k<sub>w</sub> is much smaller than the cytoplasmic osmotic and turgor pressures is still valid. 

      In the revised manuscript, we have increased the estimation ranges to include the case of E. coli in the first paragraph of the subsection “Steady states in constant environments.”

      (7) Lines 279-283 need to be explained better.  

      We apologize for the confusion. In the revised manuscript, we have explained more explicitly the meaning of the growth curve in the second paragraph of the subsection “Steady states in constant environments”:

      “Intriguingly, the relationship between the normalized growth rate () and the normalized cytoplasmic osmotic pressure (), which we refer to as the growth curve in the following, has only one parameter 𝐻<sub>r</sub>/(𝐻<sub>𝑎</sub>) . Therefore, the growth curves of different organisms can be unified by a single formula, Eq. (10b), and different organisms may have different values of 𝐻<sub>r</sub>/(𝐻<sub>𝑎</sub> + 1).”

      (8) In Figure 3, an arrow representing the onset of osmotic shock would make the figure more intuitive to understand.

      We appreciate Reviewer 2 for this helpful suggestion. We have modified Figure 3 as suggested.

      (9) It is unclear to me if the growth rate 𝜇𝜇𝑟𝑟 is representative of the growth of total protein. This can be motivated better.

      We would like to clarify that the growth rate 𝜇𝜇𝑟𝑟 is defined as the changing rate of total protein mass divided by the total protein mass:

      Here, 𝑚<sub>𝑝,𝑟</sub> is the total mass of ribosomal proteins and 𝑘𝑘𝑟𝑟 is a constant proportional to the elongation speed of ribosome. The expression of 𝜇<sub>𝑟</sub> is a direct consequence of ribosomes being responsible for producing all proteins. In the revised manuscript, we have added more details in the introduction of the variable 𝜇<sub>𝑟</sub> in the last paragraph of the subsection “Cell growth”:

      “In this work, we assume that the dry-mass growth rate is proportional to the fraction of ribosomal proteins within the total proteome for simplicity, 𝜇<sub>𝑟</sub> \= 𝑘<sub>r</sub>𝑚<sub>𝑝,𝑟</sub>/𝑚<sub>𝑝</sub> \= 𝑘<sub>r</sub>𝜙<sub>𝑟</sub>. This assumption leverages the fact that ribosomes are responsible for producing all proteins. The proportionality coefficient 𝑘<sub>𝑟</sub> encapsulates the efficiency of ribosomal activity, being proportional to the elongation speed of the ribosome. We remark that 𝑘𝑘𝑟𝑟 is influenced by the crowding effect, which we address later.”

    1. Author response:

      The following is the authors’ response to the original reviews

      We again thank the reviewers for their comments and recommendations. In response to the reviewer’s suggestions, we have performed several additional experiments, added additional discussion, and updated our conclusions to reflect the additional work. Specifically, we have performed additional analyses in female WT and Marco-deficient animals, demonstrating that the Marco-associated phonotypes observed in male mice (reduced adrenal weight, increased lung Ace mRNA and protein expression, unchanged expression of adrenal corticosteroid biosynthetic enzymes) are not present in female mice. We also report new data on the physiological consequences of increased aldosterone levels observed in male mice, namely plasma sodium and potassium titres, and blood pressure alterations in WT vs Marco-deficient male mice. In an attempt to address the reviewer’s comments relating to our proposed mechanism on the regulation of lung Ace expression, we additionally performed a co-culture experiment using an alveolar macrophage cell line and an endothelial cell line. In light of the additional evidence presented herein, we have updated our conclusions from this study and changed the title of our work to acknowledge that the mechanism underlying the reported phenotype remains incompletely understood. Specific responses to reviewers can be seen below.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      The investigators sought to determine whether Marco regulates the levels of aldosterone by limiting uptake of its parent molecule cholesterol in the adrenal gland. Instead, they identify an unexpected role for Marco on alveolar macrophages in lowering the levels of angiotensin-converting enzyme in the lung. This suggests an unexpected role of alveolar macrophages and lung ACE in the production of aldosterone.

      Strengths:

      The investigators suggest an unexpected role for ACE in the lung in the regulation of systemic aldosterone levels.

      The investigators suggest important sex-related differences in the regulation of aldosterone by alveolar macrophages and ACE in the lung.

      Studies to exclude a role for Marco in the adrenal gland are strong, suggesting an extra-adrenal source for the excess Marco observed in male Marco knockout mice.

      Weaknesses:

      While the investigators have identified important sex differences in the regulation of extrapulmonary ACE in the regulation of aldosterone levels, the mechanisms underlying these differences are not explored.

      The physiologic impact of the increased aldosterone levels observed in Marco -/- male mice on blood pressure or response to injury is not clear.

      The intracellular signaling mechanism linking lung macrophage levels with the expression of ACE in the lung is not supported by direct evidence.

      Reviewer #2 (Public Review):

      Summary:

      Tissue-resident macrophages are more and more thought to exert key homeostatic functions and contribute to physiological responses. In the report of O'Brien and Colleagues, the idea that the macrophage-expressed scavenger receptor MARCO could regulate adrenal corticosteroid output at steady-state was explored. The authors found that male MARCO-deficient mice exhibited higher plasma aldosterone levels and higher lung ACE expression as compared to wild-type mice, while the availability of cholesterol and the machinery required to produce aldosterone in the adrenal gland were not affected by MARCO deficiency. The authors take these data to conclude that MARCO in alveolar macrophages can negatively regulate ACE expression and aldosterone production at steady-state and that MARCO-deficient mice suffer from secondary hyperaldosteronism.

      Strengths:

      If properly demonstrated and validated, the fact that tissue-resident macrophages can exert physiological functions and influence endocrine systems would be highly significant and could be amenable to novel therapies.

      Weaknesses:

      The data provided by the authors currently do not support the major claim of the authors that alveolar macrophages, via MARCO, are involved in the regulation of a hormonal output in vivo at steady-state. At this point, there are two interesting but descriptive observations in male, but not female, MARCO-deficient animals, and overall, the study lacks key controls and validation experiments, as detailed below.

      Major weaknesses:

      (1) According to the reviewer's own experience, the comparison between C57BL/6J wild-type mice and knock-out mice for which precise information about the genetic background and the history of breedings and crossings is lacking, can lead to misinterpretations of the results obtained. Hence, MARCO-deficient mice should be compared with true littermate controls.

      (2) The use of mice globally deficient for MARCO combined with the fact that alveolar macrophages produce high levels of MARCO is not sufficient to prove that the phenotype observed is linked to alveolar macrophage-expressed MARCO (see below for suggestions of experiments).

      (3) If the hypothesis of the authors is correct, then additional read-outs could be performed to reinforce their claims: levels of Angiotensin I would be lower in MARCO-deficient mice, levels of Antiotensin II would be higher in MARCO-deficient mice, Arterial blood pressure would be higher in MARCO-deficient mice, natremia would be higher in MARCO-deficient mice, while kaliemia would be lower in MARCO-deficient mice. In addition, co-culture experiments between MARCO-sufficient or deficient alveolar macrophages and lung endothelial cells, combined with the assessment of ACE expression, would allow the authors to evaluate whether the AM-expressed MARCO can directly regulate ACE expression.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) Corticosterone levels in male Marco -/- mice are not significantly different, but there is (by eye) substantially more variability in the knockout compared to the wild type. A power analysis should be performed to determine the number of mice needed to detect a similar % difference in corticosterone to the difference observed in aldosterone between male Marco knockout and wild-type mice. If necessary the experiments should be repeated with an adequately powered cohort.

      Using a power calculator (www.gigacalculator.com) it was determined that our sample size of 13 was one less than sufficient to detect a similar % difference in corticosterone as was detected in corticosterone. We regret that we unable to perform additional measurements as the author suggested in the available timeframe.

      (2) All of the data throughout the MS (particularly data in the lung) should be presented in male and female mice. For example, the induction of ACE in the lungs of Marco-/- female mice should be absent. Similar concerns relate to the dexamethasone suppression studies. Also would be useful if the single cell data could be examined by sex--should be possible even post hoc using Xist etc.

      Given the limitations outlined in our previous response to reviewers it was not possible to repeat every experiment from the original manuscript. We were able to measure the expression of lung Ace mRNA, ACE protein, adrenal weights, adrenal expression of steroid biosynthetic enzymes, presence of myeloid cells, and levels of serum electrolytes in female animals. These are presented in figures 1G, 3B, 4A, 4E, 4F, 4I, and 4J. We have elected to not present single cell seq data according to sex as it did not indicate substantial differences between males and females in Marco or Ace expression and so does not substantively change our approach.

      (3) IF is notoriously unreliable in the lung, which has high levels of autofluorescence. This is the only method used to show ACE levels are increased in the absence of Marco. Orthogonal methods (e.g. immunoblots of flow-sorted cells, or ideally CITE-seq that includes both male and female mice) should be used.

      We used negative controls to guide our settings during acquisition of immunofluorescent images. Additionally, we also used qPCR to show an increase in Ace mRNA expression in the lung in addition to the protein level. This data was presented in the original manuscript and is further bolstered by our additional presentation of expression data for Ace mRNA and protein in female animals in this revised manuscript.

      (4) Given the central importance of ACE staining to the conclusions, validation of the antibody should be included in the supplement.

      We don’t have ACE-deficient mice so cannot do KO validation of the antibody. We did perform secondary stain controls which confirmed the signal observed is primary antibody-derived. Moreover, we specifically chose an anti-ACE antibody (Invitrogen catalogue # MA5-32741) that has undergone advanced verification with the manufacturer. We additionally tested the antibody in the brain and liver and observed no significant levels of staining.

      Author response image 1.

      (5) The link between alveolar macrophage Marco and ACE is poorly explored.

      We carried out a co-culture experiments of alveolar macrophages and endothelial cells and measure ACE/Ace expression as a consequence. This is presented in figure 5D and the discussion.

      (6) Mechanisms explaining the substantial sex difference in the primary outcome are not explored.

      This is outside the scope if this project, though we would consider exploring such experiments in future studies.

      (7) Are there physiologic consequences either in homeostasis or under stress to the increased aldosterone (or lung ACE levels) observed in Marco-/- male mice?

      We measured blood electrolytes and blood pressure in Marco-deficient and Marco-sufficient mice. The results from these experiments are presented in 4G-4M.

      Reviewer #2 (Recommendations For The Authors):

      Below is a suggestion of important control or validation experiments to be performed in order to support the authors' claims.

      (1) It is imperative to validate that the phenotype observed in MARCO-deficient mice is indeed caused by the deficiency in MARCO. To this end, littermate mice issued from the crossing between heterozygous MARCO +/- mice should be compared to each other. C57BL/6J mice can first be crossed with MARCO-deficient mice in F0, and F1 heterozygous MARCO +/- mice should be crossed together to produce F2 MARCO +/+, MARCO +/- and MARCO -/- littermate mice that can be used for experiments.

      We thank the reviewer for their comments. We recognise the concern of the reviewer but due to limited experimenter availability we are unable to undertake such a breeding programme to address this particular concern.

      (2) The use of mice in which AM, but not other cells, lack MARCO expression would demonstrate that the effect is indeed linked to AM. To this end, AM-deficient Csf2rb-deficient mice could be adoptively transferred with MARCO-deficient AM. In addition, the phenotype of MARCO-deficient mice should be restored by the adoptive transfer of wild-type, MARCO-expressing AM. Alternatively, bone marrow chimeras in which only the hematopoietic compartment is deficient in MARCO would be another option, albeit less specific for AM.

      We recognise the concern of the reviewer. We carried out a co-culture experiments of alveolar macrophages and endothelial cells and measure ACE/Ace expression as a consequence. This is presented in figure 5D and the implications explored in the discussion.

      (3) If the hypothesis of the authors is correct, then additional read-outs could be performed to reinforce their claims: levels of Angiotensin I would be lower in MARCO-deficient mice, levels of Antiotensin II would be higher in MARCO-deficient mice, Arterial blood pressure would be higher in MARCO-deficient mice, natremia would be higher in MARCO-deficient mice, while kaliemia would be lower in MARCO-deficient mice. Similar read-outs could also be performed in the models proposed in point 2).

      We measured blood electrolytes and blood pressure in Marco-deficient and Marco-sufficient mice. The results from these experiments are presented in 4G-4M.

      (4) Co-culture experiments between MARCO-sufficient or deficient alveolar macrophages and lung endothelial cells, combined with the assessment of ACE expression, would allow the authors to evaluate whether the AM-expressed MARCO can directly regulate ACE expression.

      To address this concern we carried out a co-culture experiment as described above.

    1. Author response:

      The following is the authors’ response to the original reviews

      We thank the reviewers for their very constructive and helpful comments on the previous version of this manuscript. They have focused on some important issues and have raised many valuable questions that we expect to answer as research begins on these markings. As has been often the case with preprints, a number of experts beyond the four reviewers and editor have provided comments, questions, and suggestions, and we have taken these on board in our revision of the manuscript. In particular, Martinón-Torres et al. (2024) focused several comments upon this manuscript and raise some points that were not considered by the reviewers, and so we discuss those points here in addition to the reviewer comments.

      Some of us have been engaged in other aspects of the possible cultural activities of Homo naledi. After the discovery of these markings we considered it indefensible to publish further research on the activity of H. naledi within this part of the cave system without making readers aware that the H. naledi skeletal remains occur in a spatial context near markings on cave walls. Of course, the presence of markings leaves many questions open. A spatial context does not answer all questions about the temporal context. The situation of the Dinaledi Subsystem does entail some constraints that would not apply to markings within a more open cave or rock wall, and we discuss those in the text.

      We find ourselves in agreement with most of the reviewers on many points. As reflected by several of the reviewers, and most pointedly in the remarks by reviewer 1, the purpose of this preprint is a preliminary report on the observation of the markings in a very distinctive location. This initial report is an essential step to enable further research to move forward. That research requires careful planning due to the difficulty of working within the Dinaledi Subsystem where the markings are located. This pattern of initial publication followed by more detailed study is common with observations of rock art and other markings identified in South Africa and elsewhere. We appreciate that the reviewers have understood the role of this initial study in that process of research.

      Because of this, the revised manuscript represents relatively minimal changes, and all those at the advice of reviewers. Many thanks to all the reviewers for noting various typographic errors, missed references and other issues that we have done our best to fix in the revised manuscript.

      Expertise of authors. Reviewer 4 mentions that the expertise of the authors does not include previous publication history on the identification of rock art, and other reviewers briefly comment that experts in this area would enhance the description. AF does have several publications on ancient engravings and other markings; LRB has geological training and field experience with rock art. Notwithstanding this, we do take on board the advice to include a wider array of subject experts in this research, and this is already underway.

      Image enhancement. We appreciate the suggestions of some reviewers for possible strategies to use software filters to bring out details that may not be obvious even with our cross-polarization lighting and filtering. These are great ideas to try. In this manuscript we thought that going very far into software editing or image enhancement might be perceived by some readers as excessive manipulation, particularly in an age of AI. In future work we will experiment with the suggested approaches. 

      Natural weathering. In the process of review and commentary by experts and the public there has been broad acceptance that many of the markings illustrated in this paper are artificial and not a product of natural weathering of the dolomite rock. We deeply appreciate this. At the same time, we accept the comments from reviewers that some markings may be difficult to differentiate from natural weathering, and that some natural features that were elaborated or altered may be among the markings we recognize. On pages 3 and 4 we present a description of the process of natural subaerial weathering of dolomite, which we have rooted in several references as well as our own observations of the natural weathering visible on dolomite cave walls in the Rising Star cave system. This includes other cave walls within the Dinaledi Subsystem. We discuss the “elephant skin” patterning of natural dolomite surface weathering, how that patterning emerges, and how that differs from the markings that are the subject of this manuscript.

      Animal claw marks. Martinón-Torres et al. 2024 accept that some of the markings illustrated on Panel A are artificial, but they offer the hypothesis that some of those markings may be consistent with claw marks from carnivores or other mammals. They provide a photo of claw marks within a limestone cave in Europe to illustrate this point. On pages 5 and 6 of the revised manuscript we discuss the hypothesis of claw marks. We discuss the presence of animals in southern Africa that may dig in caves or mark surfaces. However the key aspect of the Malmani dolomite caves is that the hardness of dolomitic limestone rock is much greater than many of the limestone caves in other regions such as Europe and Australia, where claw marks have been noted in rock walls. As we discuss, we have not been able to find evidence of claw marks within the dolomite host bedrock of caves in this region, although carnivores, porcupines, and other animals dig into the soft sediments within and around caves. The form of the markings themselves also counter-indicates the hypothesis that they are claw marks. 

      Recent manufacture. One comment that occurs within the reviews and from other readers of the preprint is that recent human visitors to the cave, either in historic or recent prehistoric times, may have made these marks. We discuss this hypothesis on page 6 of the revised manuscript. The simple answer is that no evidence suggests that any human groups were in the Dinaledi Subsystem between the presence of H. naledi and the entry of explorers within the last 25 years. The list of all explorers and scientific visitors to have entered this portion of the cave system is presented in a table. We can attest that these people did not make the marks. More generally, such marks have not been known to be made by cavers in other contexts within southern Africa.

      Panels B and C. We have limited the text related to these areas, other than indicating that we have observed them. The analysis of these areas and quantification of artificial lines does not match what we have done for the Panel A area and we leave these for future work. 

      Presence of modern humans. We have observed no evidence of modern humans or other hominin populations within the Dinaledi Subsystem, other than H. naledi. Several reviewers raise the question of whether the absence of evidence is evidence of absence of modern humans in this area. This is connected by two of the reviewers to the observation that the investigation of other caves in recent years has shown that markings or paintings were sometimes made by different groups over tens of thousands of years, in some cases including both Neanderthals and modern humans. We have decided it is best for us not to attempt to prove a negative. It is simple enough to say that there is no evidence for modern humans in this area, while there is abundant evidence of H. naledi there.

      Association with H. naledi. Reviewer 2 made an incisive point that the previous version contained some text that appeared contradictory: on the one hand we argued that modern humans were not present in the subsystem due to the absence of evidence of them, yet we accepted that H. naledi may have been present for a longer time than currently established by geochronological methods.

      We appreciate this comment because it helped us to think through the way to describe the context and spatial association of these markings and the skeletal remains, and how it may relate to their timeline. Other reviewers also raised similar questions, whether the context by itself demonstrates an association with H. naledi. We have revised the text, in particular on pages 5 and 7, to simply state that we accept as the most parsimonious alternative at present the hypothesis that the engravings were made by H. naledi, which is the only hominin known to be present in this space.

      Age of H. naledi in the system. At one place in the previous manuscript we indicated that we cannot establish that H. naledi was only active in the cave system within the constraints of the maximum and minimum ages for the Dinaledi Subsystem skeletal remains (viz., 335 ka – 241 ka), because some localities with skeletal material are undated. We have adjusted this paragraph on page 7 to be clear that we are discussing this only to acknowledge uncertainty about the full range of H. naledi use of the cave system.

      Geochronological methods. Several reviewers discuss the issue of geochronology as applied to these markings. This is an area of future investigation for us after the publication of this initial report. As some reviewers note, the prospects for successful placement of these engraved features and other markings with geochronological methods depends on factors that we cannot predict without very high-resolution investigation of the surfaces. We have included greater discussion of the challenges of geochronological placement of engravings on page 6, including more references to previous work on this topic. We also briefly note the ethical problems that may arise as we go further with potentially  invasive, destructive or contact studies of these engravings, which must be carefully considered by not just us, but the entire academy.

      Title. Some reviewers suggested that the title should be rephrased because this paper does not use chronological methods to derive date constraints for the markings. We have rephrased the title to reflect less certainty while hopefully retaining the clear hypothesis discussed in the paper.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1 (Public review):

      Summary:

      The present study aims to associate reproduction with age-related disease as support of the antagonistic pleiotropy hypothesis of ageing predominantly using Mendelian Randomization. The authors found evidence that early-life reproductive success is associated with advanced ageing.

      Strengths:

      Large sample size. Many analyses.

      Weaknesses:

      Still a number of doubts with regard to some of the results and their interpretation.

      Reviewer #1 (Recommendations for the authors):

      Thank you for the opportunity to review a revised version.

      I still have serious doubts with regard to a number of datasets presented. For example, the results on essential hypertension and cervical cancer show very small effect sizes, but according to the authors still reach the level of statistical significance. This is unlikely to be accurate. For MR analyses, this is nearly impossible. The analyses of these data and the statistical analysis need to be checked for errors and repeated. While BOLT-LLM might not be relevant here, there might be other things happening here. The authors should therefore always interpret the results also with regard to the observed effect sizes instead of only looking at the p-values (0.999 means that there is a 0.1% lower risk).

      Thank you for your suggestions. We have updated the results for essential hypertension, GAD, and cervical cancer in results, figures, and supplemental tables (lines 65-89, Figure 1, Tables S3-S4).

      Reviewer #2 (Public review):

      Summary:

      The authors present an interesting paper where they test the antagonistic pleiotropy theory. Based on this theory they hypothesize that genetic variants associated with later onset of age at menarche and age at first birth may have a positive effect on a multitude of health outcomes later in life, such as epigenetic aging and prevalence of chronic diseases. Using a mendelian randomization and colocalization approach, the authors show that SNPs associated with later age at menarche are associated with delayed aging measurements, such as slower epigenetic aging and reduced facial aging and a lower risk of chronic diseases, such as type 2 diabetes and hypertension. Moreover, they identify 128 fertility-related SNPs that associate with age-related outcomes and they identified BMI as a mediating factor for disease risk, discussing this finding in the context of evolutionary theory.

      Strengths:

      The major strength of this manuscript is that it addresses the antagonistic pleiotropy theory in aging. Aging theories are not frequently empirically tested although this is highly necessary. The work is therefore relevant for the aging field as well as beyond this field, as the antagonistic pleiotropy theory addresses the link between fitness (early life health and reproduction) and aging.

      The authors addressed the remarks on the previous version very well. Addressing the two points below would further increase the quality of the manuscript.

      (1) In the previous version the authors mentioned that their results are also consistent with the disposable soma theory: "These results are also consistent with the disposable soma theory that suggests aging as an outcome tradeoff between an organism's investment in reproduction and somatic maintenance and repair."

      Although the antagonistic pleiotropy and disposable soma theories describe different mechanisms, both provide frameworks for understanding how genes linked to fertility influence health. The antagonistic pleiotropy theory posits that genes enhancing fertility early in life may have detrimental effects later. In contrast, the disposable soma theory suggests that energy allocation involves a trade-off, where investment in fertility comes at the expense of somatic maintenance, potentially leading to poorer health in later life.

      To strengthen the manuscript, a discussion section should be added to clarify the overlap and distinctions between these two evolutionary theories and suggest directions for future research in disentangling their specific mechanisms.

      Thank you for your suggestions to clarify the overlap and distinctions between the antagonistic pleiotropy and disposable soma theories. While our primary focus is on the antagonistic pleiotropy framework, we acknowledge that the disposable soma theory also provides a relevant perspective on the trade-offs between reproduction and somatic maintenance.

      To address this, we have expanded the discussion section to highlight how both theories contribute to our understanding of the relationship between fertility-related traits and aging-related health outcomes. We also suggested potential future research directions, such as integrating genetic data with biomarkers of somatic to further explore the mechanisms underlying these trade-offs (lines 213-223).

      (2) In response to the question why the authors did not include age at menopause in addition to the already included age at first child and age at menarche the following explanation was provided: "Our manuscript focuses on the antagonistic pleiotropy theory, which posits that inherent trade-off in natural selection, where genes beneficial for early survival and reproduction (like menarche and childbirth) may have costly consequences later. So, we only included age at menarche and age at first childbirth as exposures in our research."

      It remains, however, unclear why genes beneficial for early survival and reproduction would be reflected only in age at menarche and age at first childbirth, but not in age at menopause. While age at menarche marks the onset of fertility, age at menopause signifies its end. Since evolutionary selection acts directly until reproduction is no longer possible (though indirect evolutionary pressures persist beyond this point), the inclusion of additional fertility-related measures could have strengthened the analysis. A more detailed justification for focusing exclusively on age at menarche and first childbirth would enhance the clarity and rigor of the manuscript.

      Thank you for your question regarding the age at menopause in our analysis. Our decision was based on the theoretical framework of antagonistic pleiotropy, which emphasizes early-life reproductive advantages that may have trade-offs later in life. Age at menarche and age at first childbirth are direct markers of early reproductive investment, which align closely with this framework.

      While age at menopause marks the cessation of reproductive capability, its evolutionary role is distinct. The selective pressures acting on menopause are complex and may involve post-reproductive contributions rather than direct reproductive fitness benefits. Moreover, the genetic architecture of menopause may be influenced by different biological pathways compared to early reproductive traits.

      Nonetheless, we acknowledge that including age at menopause could provide additional insights into reproductive aging. Several papers1,2 were already published regarding age at menopause and age-related outcomes, including diabetes, AD, osteoporosis, cancers, and cardiovascular diseases.

      Reviewing Editor (Recommendations for the authors):

      Above/below you will find the remaining comments from the reviewers. One of the main issues remaining is that some of the data seems to be incorrectly analysed and some of the findings may not be correct. To clarify this a lot more, I asked the reviewer for some details and received the following:

      - In Figure 1B one of their main outcomes is "age of menopause", but they report the data as an odds ratio. This is not correct and should be fixed (it seems the authors can run the right analysis, but just reported it with the wrong heading in the figure). This likely also applies to the outcome "facial aging". Also the heading in Figure 1A should be Beta instead of OR.

      We have updated the figures to ensure that the beta values of continuous outcomes and odds ratio values of categorical outcomes are presented in Figure 1.

      - With essential hypertension, GAD and cervical cancer, the estimates are so small that they need to re-review their results. The current MR analysis is not sufficiently powered to have such small confidence intervals. Essential hypertension was based on data from UK biobank, although I was also unable to find what program was used to generate the GWAS results, I have strong thoughts this was also BOLT-LLM. Same for cervical cancer. Both datasets used familial-related samples, so they are very likely derived with BOLT-LLM.

      I hope this will help to solve this issue.

      Based on published paper, gastrointestinal or abdominal disease (GAD) (GWAS ID: ebi-a-GCST90038597) is after BOLT-LLM. Based on MRC IEU UK Biobank GWAS pipeline, version 1 and 2, essential hypertension (GWAS ID: ukb-b-12493) and cervical cancer (GWAS ID: ukb-b-8777) are after BOLT-LLM. We have updated the MR analysis results and figures (lines 65-89, Figure 1, Tables S3-S4) as well as the following IPA analysis (lines 106-162 and 255-280, Figures 2-3).

      (1) Magnus, M. C., Borges, M. C., Fraser, A. & Lawlor, D. A. Identifying potential causal effects of age at menopause: a Mendelian randomization phenome-wide association study. Eur J Epidemiol 37, 971-982 (2022). https://doi.org:10.1007/s10654-022-00903-3

      (2) Zhang, X., Huangfu, Z. & Wang, S. Review of mendelian randomization studies on age at natural menopause. Front Endocrinol (Lausanne) 14, 1234324 (2023). https://doi.org:10.3389/fendo.2023.1234324

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      This work employs both in vitro and in vivo/transplant methods to investigate the contribution of BDNF/TrkB signaling to enhancing differentiation and dentin-repair capabilities of dental pulp stem cells in the context of exposure to a variety of inflammatory cytokines. A particular emphasis of the approach is the employment of dental pulp stem cells in which BDNF expression has been enhanced using CRISPR technology. Transplantation of such cells is said to improve dentin regeneration in a mouse model of tooth decay.

      The study provides several interesting findings, including demonstrating that exposure to several cytokines/inflammatory agents increases the quantity of (activated) phospho-Trk B in dental pulp stem cells.

      However, a variety of technical issues weaken support for the major conclusions offered by the authors. These technical issues include the following:

      Thank you for your keen observation and evaluation, which helped us significantly improve our manuscript. We have addressed the concerns and comments point by point in detail and substantially revised the manuscript and Figures. We hope that the manuscript is acceptable in the current improvised version.

      Detailed response to your comments/concerns is as follows:

      (1) It remains unclear exactly how the cytokines tested affect BDNF/TrkB signaling. For example, in Figure 1C, TNF-alpha increases TrkB and phospho-TrkB immunoreactivity to the same degree, suggesting that the cytokine promotes TrkB abundance without stimulating pathways that activate TrkB, whereas in Figure 2D, TNF-alpha has little effect on the abundance of TrkB, while increasing phospho-TrkB, suggesting that it affects TrkB activation and not TrkB abundance.

      Thank you for your kind concern. Recently, we have demonstrated the effect and interaction of TNF-alpha and Ca2+/calmodulin-dependent protein kinase II on the regulation of the inflammatory hDPSCs dentino-differentiation via BDNF/TrkB receptor signaling using TrkB inhibitor (Ref. below, and Figure 9). Moreover, we agree with your concern, and we have re-analyzed our replicates and found a better trend and significant abundance of TrkB as well (please refer to revised Figure 2D).

      Ref.: Kim, Ji Hyun, et al. (2025) "Ca 2+/calmodulin-dependent protein kinase II regulates the inflammatory hDPSCs dentino-differentiation via BDNF/TrkB receptor signaling." Frontiers in Cell and Developmental Biology 13: 1558736.

      (2) I find the histological images in Figure 3 to be difficult to interpret. I would have imagined that DAPI nuclear stains would reveal the odontoblast layer, but this is not apparent. An adjacent section labeled with conventional histological stains would be helpful here. Others have described Stro-1 as a stem cell marker that is expressed on a minority of cells associated with vasculature in the dental pulp, but in the images in Figure 3, Stro-l label is essentially co-distributed with DAPI, in both control and injured teeth, indicating that it is expressed in nearly all cells. Although the authors state that the Stro-1-positive cells are associated with vasculature, but I see no evidence that is true.

      Thank you for your concern. STRO-1 is a mesenchymal stem cell marker also expressed in dental pulp stem cells; both populations are distributed in the pulp. DPSCs can contribute to tissue repair and regeneration in inflamed pulp by differentiating into odontoblasts and forming reparative dentin. Moreover, in the case of carious and inflamed pulp, they are disorganized depending on the extent of infection/injury. Our purpose here was to point out DPSCs presence, not vasculature, which will differentiate into odontoblasts in such a scenario. We have revised Figure 3 by adding magnified images and dotted lines to indicate the boundary between the pulp and dentin.

      Ref. Volponi A. A., Pang Y., Sharpe P. T. Stem cell-based biological tooth repair and regeneration. Trends in Cell Biology. 2010;20(12):715–722.

      (3) The data presented convincingly demonstrate that they have elevated BDNF expression in their dental pulp stem cells using a CRISPR-based approach I have a number of questions about these findings. Firstly, nowhere in the paper do they describe the nature of the CRISPR plasmid they are transiently transfecting. Some published methods delete segments of the BDNF 3'-UTR while others use an inactivated Cas9 to position an active transactivator to sequences in the BDNF promoter. If it is the latter approach, transient transfection will yield transient increases in BDNF expression. Also, as BDNF employs multiple promoters, it would be helpful to know which promoter sequence is targeted, and finally, knowing the identity of the guide RNAs would allow assessment for the potential of off-target effects I am guessing that the investigators employ a commercially obtained system from Santa Cruz, but nowhere is this mentioned. Please provide this information.

      Dear Reviewer, yes, you are right. We have used a commercially obtained system from Santa Cruz, i.e., BDNF CRISPR Activation Plasmid (h): sc-400029-ACT and UltraCruz® Transfection Reagent (sc-395739), and they have been mentioned in Chemicals and Reagents section of Materials and Methods as follows.

      “BDNF CRISPR Activation Plasmid (h) is a synergistic activation mediator (SAM) transcription activation system designed to upregulate gene expression specifically BDNF CRISPR Activation Plasmid (h) consists of three plasmids at a 1:1:1 mass ratio: a plasmid encoding the deactivated Cas9 (dCas9) nuclease (D10A and N863A) fused to the transactivation domain VP64, and a blasticidin resistance gene; a plasmid encoding the MS2-p65-HSF1 fusion protein, and a hygromycin resistance gene; a plasmid encoding a target-specific 20 nt guide RNA fused to two MS2 RNA aptamers, and a puromycin resistance gene.”

      The resulting SAM complex binds to a site-specific region approximately 200-250 nt upstream of the transcriptional start site and provides robust recruitment of transcription factors for highly efficient gene activation

      Following transfection, gene activation efficiency could be assayed by WB, IF, or IHC using antibody: pro-BDNF Antibody (5H8): sc-65514

      Author response image 1.

      (4) Another question left unresolved is whether their approach elevated BDNF, proBDNF, or both. Their 28 kDa western blot band apparently represents proBDNF exclusively, with no mature BDNF apparent, yet only mature BDNF effectively activates TrkB receptors. On the other hand, proBDNF preferentially activates p75NTR receptors. The present paper never mentions p75NTR, which is a significant omission, since other investigators have demonstrated that p75NTR controls odontoblast differentiation.

      Dear reviewer, thank you for your noticing the error.

      Pro-BDNF is produced as a 32-kDa precursor that undergoes N-glycosylation and glycosulfation on residues located within the pro-domain of the precursor. N-terminal cleavage of the precursor generates mature BDNF as well as a minor truncated form of the precursor (28 kDa) that arises by a different processing mechanism than mature BDNF. The precursor undergoes N-terminal cleavage within the trans-Golgi network and/or immature secretory vesicles to generate mature BDNF (14 kDa).

      We checked our data and band size, and it shows a little mistake (Thank you for your keen observation and pointing out). The CRISPR protocol required verification of gene activation by checking pro-BDNF, as mentioned in the methodology. The labeling has been revised in the figure as pro-BDNF, and the actual blot with a ladder has been shown below for clarification.

      (5) In any case, no evidence is presented to support the conclusion that the artificially elevated BDNF expression has any effect on the capability of the dental pulp stem cells to promote dentin regeneration. The results shown in Figures 4 and 5 compare dentin regeneration with BDNF-over-expressing stem cells with results lacking any stem cell transplantation. A suitable control is required to allow any conclusion about the benefit of over-expressing BDNF.

      We have tested the presence of BDNF overexpressing cells by the higher expression of GFP here. Moreover, a significant increment in the dentin mineralization volume indicates the advantage of BDNF-over-expressing stem cells. Recently, we published the in vitro effects of BDNF/TrkB on DPSCs odontoblastic differentiation strongly supporting our in vivo data. Currently, we are in a difficult position to conduct the animal study within a short period of time. We would definitely consider using positive control in our future studies.

      Ref.: Kim, Ji Hyun, et al. (2025) "Ca 2+/calmodulin-dependent protein kinase II regulates the inflammatory hDPSCs dentino-differentiation via BDNF/TrkB receptor signaling." Frontiers in Cell and Developmental Biology 13: 1558736.

      (6) Whether increased BDNF expression is beneficial or not, the evidence that the BDNF-overexpressing dental pulp stem cells promote dentin regeneration is somewhat weak. The data presented indicate that the cells increase dentin density by only 6%. The text and figure legend disagree on whether the p-value for this effect is 0.05 or 0.01. In either case, nowhere is the value of N for this statistic mentioned, leaving uncertainty about whether the effect is real.

      A significant increment in the dentin mineralization volume by about 7.76% indicates the advantage of BDNF-over-expressing stem cells, and we believe this could be a breakthrough to advance stem cell engineering and therapy further to get this percentage higher in the future. The text in the result section shows that the p-value for this effect is 0.05. While N was 3 previously, we analyzed two more samples by CT scan and revised results, taking N = 5, which improved the results a little more to about 8.53%. Thank you for noticing; the figure legend has been corrected to 0.05.

      Similarly, our in vitro data in the current study supports the notion that it adds up to mineralization and odontoblastic differentiation. We recently published that BDNF/TrkB significantly enhances calcium deposits and mineralization using a battery of in vitro experiments.

      Ref.: Kim, Ji Hyun, et al. (2025) "Ca 2+/calmodulin-dependent protein kinase II regulates the inflammatory hDPSCs dentino-differentiation via BDNF/TrkB receptor signaling." Frontiers in Cell and Developmental Biology 13: 1558736.

      (7) The final set of experiments applies transcriptomic analysis to address the mechanisms mediating function differences in dental pulp stem cell behavior. Unfortunately, while the Abstract indicates " we conducted transcriptomic profiling of TNFα-treated DPSCs, both with and without TrkB antagonist CTX-B" that does not describe the experiment described, which compared the transcriptome of control cells with cells simultaneously exposed to TNF-alpha and CTX-B. Since CTX-B blocks the functional response of cells to TNF-alpha, I don't understand how any useful interpretation can be attached to the data without controls for the effect of TNF alone and CTX-B alone.

      Dear reviewer, yes, we did it alone and together as well. Earlier, we showed only the combined results and mentioned the interaction between TNFα and TrkB. We have included the results from TNFα alone and combined them with CTX-B for better comparison (Please refer to Figure 8). Figure 8C1 clearly shows the reversal of certain factors with the treatment of TrkB inhibitor compared to figure 8C with TNFα alone treated group.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, the authors investigate the potential for overexpressing BDNF in dental pulp stem cells to enhance dentin regeneration. They suggest that in the inflammatory environment of injured teeth, there is increased signaling of TrkB in response to elevated levels of inflammatory molecules.

      Strengths:

      The potential application to dentin regeneration is interesting.

      Weaknesses:

      There are a number of concerns with this manuscript to be addressed.

      Thank you for your compliments, keen observation, and evaluation, which helped us significantly improve our manuscript. We have addressed the concerns and comments point by point in detail and substantially revised the manuscript and Figures. We hope that the manuscript is acceptable in the current improvised version.

      Detailed response to your comments/concerns is as follows:

      (1) Insufficient citation of the literature. There is a vast literature on BDNF-TrkB regulating survival, development, and function of neurons, yet there is only one citation (Zhang et al 2012) which is on Alzheimer's disease.

      More references have been cited accordingly.

      (2) There are several incorrect statements. For example, in the introduction (line 80) TrkA is not a BDNF receptor.

      Thank you for noticing the typo; the sentence has been corrected.

      (3) Most important - Specific antibodies must be identified by their RRID numbers. To state that "Various antibodies were procured:... from BioLegend" is unacceptable, and calls into question the entire analysis. Specifically, their Western blot in Figure 4B indicates a band at 28 kDa that they say is BDNF, however the size of BDNF is 14 kDa, and the size of proBDNF is 32 and 37 kDa, therefore it is not clear what they are indicating at 28 kDa. The validation is critical to their analysis of BDNF-expressing cells.

      Dear reviewer, thank you for your kind concern. Sorry for the inconvenience; we have added RRID numbers of antibodies.

      Pro-BDNF is produced as a 32-kDa precursor that undergoes N-glycosylation and glycosulfation on residues located within the pro-domain of the precursor. N-terminal cleavage of the precursor generates mature BDNF as well as a minor truncated form of the precursor (28 kDa) that arises by a different processing mechanism than mature BDNF. The precursor undergoes N-terminal cleavage within the trans-Golgi network and/or immature secretory vesicles to generate mature BDNF (14 kDa).

      We checked our data and band size, and it shows a mistake in recognizing ladder size. It is actually a 14kDa band which has been shown. The labeling has been revised in the figure, and the actual blot with a ladder has been shown below for clarification. Similarly, our data focused on the fact that the observed cellular effects are more consistent with BDNF/TrkB-mediated pathways, which are known to promote survival and differentiation.

      (4) Figure 2 indicates increased expression of TrkB and TrkA, as well as their phosphorylated forms in response to inflammatory stimuli. Do these treatments elicit increased secretion of the ligands for these receptors, BDNF and NGF, respectively, to activate their phosphorylation? Or are they suggesting that the inflammatory molecules directly activate the Trk receptors? If so, further validation is necessary to demonstrate that.

      Thank you for your kind concern. TNF-α increases the number of TrkB receptors. The enhanced TrkB activation may result from a greater number of receptors and/or increased activation of individual receptors. In either case, inflammatory agents enhance the TrkB receptor signaling pathway.

      Recently, we have demonstrated the effect and interaction of TNF-alpha and Ca2+/calmodulin-dependent protein kinase II on the regulation of the inflammatory hDPSCs dentino-differentiation via BDNF/TrkB receptor signaling using TrkB inhibitor (Ref. below, and Figure 9). For now, we have added figure 9 for the proposed mechanism of action based on our recent and current study.

      Ref.: Kim, Ji Hyun, et al. (2025) "Ca 2+/calmodulin-dependent protein kinase II regulates the inflammatory hDPSCs dentino-differentiation via BDNF/TrkB receptor signaling." Frontiers in Cell and Developmental Biology 13: 1558736.

      (5) Figure 7 - RNA-Seq data, what is the rationale for treatment with TNF+ CTX-B? How does this identify any role for TrkB signaling? They never define their abbreviations, but if CTX-B refers to cholera toxin subunit B, which is what it usually refers to, then it is certainly not a TrkB antagonist.

      Thank you for your concern. Cyclotraxin-B (CTX-B) is a TrkB antagonist (mentioned in the revised manuscript). In order to identify the underlying mechanism, we ought to locate certain transcriptional factors interacting with the TrkB/BDNF signaling, leading to differentiation and dentinogenesis. Therefore, we treated it with a TrkB inhibitor.

      Earlier, we showed only the combined results and mentioned the interaction between TNFα and TrkB. We have included the results from TNFα alone and combined them with CTX-B for better comparison (Please refer to Figure 8). Figure 8C1 clearly shows the reversal of certain factors with the treatment of TrkB inhibitor compared to figure 8C with TNFα alone treated group. We agree that the precise role of CTX-B in modulating TrkB signaling requires further clarification and have now included this point in the revised discussion while we are currently working on this aspect.

      Reviewer #3 (Public review):

      In general, although the authors interpret their results as pointing towards a possible role of BDNF in dentin regeneration, the results are over-interpreted due to the lack of proper controls and focus on TrkB expression, but not its isoforms in inflammatory processes. Surprisingly, the authors do not study the possible role of p75 in this process, which could be one of the mechanisms intervening under inflammatory conditions.

      Thank you for your compliments, keen observation, and evaluation, which helped us significantly improve our manuscript. We have addressed the concerns and comments point by point in detail and substantially revised the manuscript and Figures. We hope that the manuscript is acceptable in the current improvised version.

      Detailed response to your comments/concerns is as follows:

      (1) The authors claim that there are two Trk receptors for BDNF, TrkA and TrkB. To date, I am unaware of any evidence that BDNF binds to TrkA to activate it. It is true that two receptors have been described in the literature, TrkB and p75 or NGFR, but the latter is not TrkA despite its name and capacity to bind NGF along with other neurotrophins. It is crucial for the authors to provide a reference stating that TrkA is a receptor for BDNF or, alternatively, to correct this paragraph.

      Dear reviewer, we apologize for the inconvenience; it was an error. BDNF binds to TrkB, and the sentence has been corrected.

      (2) The authors discuss BDNF/TrkB in inflammation. Is there any possibility of p75 involvement in this process?

      Mature BDNF binds to the high-affinity receptor tyrosine kinase B (TrkB), activating signaling cascades, while pro-BDNF binds to the p75 neurotrophin receptor (p75NTR). So, we don’t think there’s a possibility, as our data shows mature BDNF production. Here, we initially screened the TrkA and TrkB involvement in dentinogenesis and chose to work with BDNF and its receptor TrkB. Future studies can be directed to elucidate its mechanism of action in the context of dentinogenesis.

      (3) The authors present immunofluorescence (IF) images against TrkB and pTrkB in the first figure. While they mention in the materials and methods section that these antibodies were generated for this study, there is no proof of their specificity. It should be noted that most commercial antibodies labeled as anti-TrkB recognize the extracellular domain of all TrkB isoforms. There are indications in the literature that pathological and excitotoxic conditions change the expression levels of TrkB-Fl and TrkB-T1. Therefore, it is necessary to demonstrate which isoform of TrkB the authors are showing as increased under their conditions. Similarly, it is essential to prove that the new anti-p-TrkB antibody is specific to this Trk receptor and, unlike other commercial antibodies, does not act as an anti-phospho-pan-Trk antibody.

      Thank you for your kind concern.

      Human TrkB has 7 isoforms and predicted Mw ranges from 35 to 93kDa. It has 11 potential N-glycosylation sites. The given antibody (isotype: Mouse IgG2a, κ) has been shown to interact with SHC1, PLCG1 and/or PLCG2, SH2B1 and SH2B2, NGFR, SH2D1A, SQSTM1 and KIDINS220, FRS2.

      And, sorry for the misunderstanding and text mistake. We procured all the antibodies from the market using proven products, and didn’t check any specific isoform. We have mentioned the details of antibodies and reagents in the chemicals section of the methodology.

      (4) I believe this initial conclusion could be significantly strengthened, without opening up other interpretations of the results, by demonstrating the specificity of the antibodies via Western blot (WB), both in the presence and absence of BDNF and other neurotrophins, NGF, and NT-3. Additionally, using WB could help reinforce the quantification of fluorescence intensity presented by the authors in Figure 1. It's worth noting that the authors fixed the cells with 4% PFA for 2 hours, which can significantly increase cellular autofluorescence due to the extended fixation time, favoring PFA autofluorescence. They have not performed negative controls without primary antibodies to determine the level of autofluorescence and nonspecific background. Nor have they indicated optimizing the concentration of primary antibodies to find the optimal point where the signal is strong without a significant increase in background. The authors also do not mention using reference markers to normalize specific fluorescence or indicating that they normalized fluorescence intensity against a standard control, which can indeed be done using specific signal quantification techniques in immunocytochemistry with a slide graded in black-and-white intensity controls. From my experience, I recommend caution with interpretations from fluorescence quantification assays without considering the aforementioned controls.

      Thank you for your insightful comments. We have now included a negative control image in the revised Figures. This control confirms that the observed fluorescence signal is specific and not due to autofluorescence or nonspecific background. In our lab, we have been using these antibodies and already optimized the concentration to use in certain cell types. Additionally, we followed the manufacturer’s recommended antibody concentration and protocol throughout our experiments to ensure an optimal signal-to-noise ratio.

      We agree that extended fixation with 4% PFA may increase autofluorescence; however, including negative controls helps account for this effect. We also ensured consistent imaging parameters and applied the same exposure settings across all samples to allow for a valid comparison of fluorescence intensity. We appreciate your emphasis on careful quantification and have clarified these methodological details in the revised Methods section.

      (5) In Figure 2, the authors determine the expression levels of TrkA and TrkB using qPCR. Although they specify the primers used for GAPDH as a control in materials and methods, they do not indicate which primers they used to detect TrkA and TrkB transcripts, which is essential for determining which isoform of these receptors they are detecting under different stimulations. Similarly, I recommend following the MIQE guidelines (Minimum Information for Publication of Quantitative Real-Time PCR experiments), so they should indicate the amplification efficiency of their primers, the use of negative and positive controls to validate both the primer concentration used, and the reaction, the use of several stable reference genes, not just one.

      We appreciate the reviewer’s suggestion regarding the specificity of primers and the amplification efficiency. In response, we have now included the primer sequences used for detecting TrkA and TrkB transcripts in the revised Materials and Methods section (Quantitative real-time PCR analysis of odontogenic differentiation marker gene expression in dental pulp stem cells). This ensures clarity on which isoforms of these receptors were assessed under different conditions. We also acknowledge the importance of following MIQE guidelines, and we got the primer provided by Integrated DNA Technologies with standard desalting purification and guaranteed yield.

      (6) Moreover, the authors claim they are using the same amounts of cDNA for qPCRs since they have quantified the amounts using a Nanodrop. Given that dNTPs are used during cDNA synthesis, and high levels remain after cDNA synthesis from mRNA, it is not possible to accurately measure cDNA levels without first cleaning it from the residual dNTPs. Therefore, I recommend that the authors clarify this point to determine how they actually performed the qPCRs. I also recommend using two other reference genes like 18S and TATA Binding Protein alongside GAPDH, calculating the geometric mean of the three to correctly apply the 2^-ΔΔCt formula.

      Thank you for your kind concern. We agree that residual dNTPs from cDNA synthesis could impact the accuracy of cDNA quantification. To address this, we have used the commercially available and guaranteed kit. The kit used is mentioned in Materials and Methods. We will definitely consider using 18S and TATA Binding Protein alongside GAPDH in our future studies. For now, we request you consider the results generated against GAPDH control.

      (7) Similarly, given that the newly generated antibodies have not been validated, I recommend introducing appropriate controls for the validation of in-cell Western assays.

      We apologize for the text mistake. Antibodies were procured commercially and not generated. We have corrected the sentence.

      (8) The authors' conclusion that TrkB levels are minimal (Figure 2E) raises questions about what they are actually detecting in the previous experiments might not be the TrkB-Fl form. Therefore, it is essential to demonstrate beyond any doubt that both the antibodies used to detect TrkB and the primers used for qPCR are correct, and in the latter case, specify at which cycle (Ct) the basal detection of TrkB transcripts occurs. Treatment with TNF-alpha for 14 days could lead to increased cell proliferation or differentiation, potentially increasing overall TrkB transcript levels due to the number of cells in culture, not necessarily an increase in TrkB transcripts per cell.

      Thank you for your comments. We appreciate your kind concerns. Here, we are trying to demonstrate that TrkB gets activated in inflammatory conditions. We have also provided the details on primers and antibodies. We have used commercial antibodies and qPCR primers, and they have been extensively validated with previous publications. The efficiency and validation of qPCR primers were provided by a company.

      Moreover, we used the minimal concentration of TNF-alpha twice a week, and before using it, we did preliminary experiments to determine whether it affected any experimental condition.

      (9) Overall, there are reasonable doubts about whether the authors are actually detecting TrkB in the first three images, as well as the phosphorylation levels and localization of this receptor in the cells. For example, in Figure 3 A to J, it is not clear where TrkB is expressed, necessitating better resolution images and a magnified image to show in which cellular structure TrkB is expressed.

      Thank you for your comment. Here, we aimed to show the expression of TrkB receptors in inflamed/infected pulp, especially in minority-distributed DPSCs. TrkB is present on the cell membrane and perinuclear region. We have provided a single-cell (magnified) image in the figure for better clarification.

      (10) In Figure 4, the authors indicate they have generated cells overexpressing BDNF after recombination using CRISPR technology. However, the WB they show in Figure 4B, performed under denaturing conditions, displays a band at approximately 28kDa. This WB is absolutely incorrect with all published data on BDNF detection via this technique. I believe the authors should demonstrate BDNF presence by showing a WB with appropriate controls and BDNF appearing at 14kDa to assume they are indeed detecting BDNF and that the cells are producing and secreting it. What antibodies have been used by the authors to detect BDNF? Have the authors validated it? There are some studies reporting the lack of specificity of certain commercial BDNF antibodies, therefore it is necessary to show that the authors are convincingly detecting BDNF.

      Dear reviewer, thank you for your kind concern. Firstly, we apologize for the inconvenience.

      Pro-BDNF is produced as a 32-kDa precursor that undergoes N-glycosylation and glycosulfation on residues located within the pro-domain of the precursor. N-terminal cleavage of the precursor generates mature BDNF and a minor truncated form of the precursor (28 kDa) that arises by a different processing mechanism than mature BDNF. The precursor undergoes N-terminal cleavage within the trans-Golgi network and/or immature secretory vesicles to generate mature BDNF (14 kDa).

      We checked our data and band size, and it shows a mistake in recognizing ladder size. It is actually a 14kDa band which has been shown. The labeling has been revised in the figure, and the actual blot with a ladder has been shown below for clarification. Similarly, our data focused on the fact that the observed cellular effects are more consistent with BDNF/TrkB-mediated pathways, which are known to promote survival and differentiation.

      (11) While the RNA sequencing data indicate changes in gene expression in cells treated with TNFalpha+CTX-B compared to control, the authors do not show a direct relationship between these genetic modifications with the rest of their manuscript's argument. I believe the results from these RNA sequencing assays should be put into the context of BDNF and TrkB, indicating which genes in this signaling pathway are or are not regulated, and their importance in this context.

      Thank you for your concern. In order to identify the underlying mechanism, we ought to locate certain transcriptional factors interacting with the TrkB/BDNF signaling, leading to differentiation and dentinogenesis. Therefore, we treated it with a TrkB inhibitor.

      Earlier, we showed only the combined results and mentioned the interaction between TNFα and TrkB. We have included the results from TNFα alone and combined them with CTX-B for better comparison (Please refer to Figure 8). Figure 8C1 clearly shows the reversal of certain factors with the treatment of TrkB inhibitor compared to figure 8C with TNFα alone treated group. We agree that the precise role of CTX-B in modulating TrkB signaling requires further clarification. We have now included this point in the revised discussion while working on this aspect. In a parallel study, we are trying to dig deep, especially the TCF family, as they have been documented to interact indirectly with BDNF and TrkB.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Some minor textual issues

      Line 120: It is obvious that TNFα stimulation caused significant phosphorylation of TrkB (p < 0.01) compared to TrkA (p < 0.05).

      Thank you for noticing the typo. The sentence has been corrected.

      The authors should consider rewording this sentence - I do not understand the intended meaning.

      Line 126: pronounced peak at 10 ng/mL. I am not convinced there is a peak. Looks like a plateau to me. To call it a peak one would have to show that the values at 10 ng/ml and 20 ng/ml are statistically different.

      We meant here the peak compared to 0.1 and 1ng/mL concentration and not compared to 20 ng/mL. The sentence has been elaborated accordingly.

      Reviewer #3 (Recommendations for the authors):

      The authors should show how they have validated the specificity of all the used antibodies as well as the efficiency and specificity of their qPCR data.

      We procured the commercially available antibodies (all of them have been extensively validated with previous publications) and also performed negative controls (provided in revised figures). We frequently used Western blot and validate it with band size. Primer sequences are also provided in the revised manuscript. We checked its specificity with R<sup>2</sup> of Standard Curve ≥ 0.98 and the single peak of melting curves. We edited accordingly in line 263.

      Once again, we thank all of you for your efforts in evaluating our study. It really helped us improve the quality of the manuscript. We hope all the queries have been answered and the revised manuscript is acceptable.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews: 

      Reviewer #1 (Public Review): 

      This manuscript presents insights into biased signaling in GPCRs, namely cannabinoid receptors. Biased signaling is of broad interest in general, and cannabinoid signaling is particularly relevant for understanding the impact of new drugs that target this receptor. Mechanistic insight from work like this could enable new approaches to mitigate the public health impact of new psychoactive drugs. Towards that end, this manuscript seeks to understand how new psychoactive substances (NPS, e.g. MDMB-FUBINACA) elicit more signaling through βarrestin than classical cannabinoids (e.g. HU-210). The authors use an interesting combination of simulations and machine learning. 

      We thank the reviewer for the comments. We have provided point by point response to the reviewer’s comment below and incorporated the suggestions in our revised manuscript. Modified parts of manuscripts are highlighted in yellow.   

      Comments:

      (1) The caption for Figure 3 doesn't explain the color scheme, so it's not obvious what the start and end states of the ligand are. 

      We thank the reviewer to point this out. We have added the color scheme in the figure caption. 

      (2) For the metadynamics simulations were multiple Gaussian heights/widths tried to see what, if any, impact that has on the unbinding pathway? That would be useful to help ensure all the relevant pathways were explored.  

      We thank the reviewer for the suggestion. We agree with the reviewer that gaussian height/width may impact unbinding pathway. However, we like to point out that we used a well-tempered version of the metadynamics. In well-tempered metadynamics, the effective gaussian height decreases as bias deposition progresses. Therefore, we believe that the gaussian height/width should have minimal impact on the unbinding pathway. To address the reviewer's suggestion, we conducted additional well-tempered metadynamics simulations varying key parameters such as bias height, bias factor, and the deposition rate, all of which can influence the sampling space. Parameter values for bias height, bias factor and deposition rate that we originally used in the paper are 0.4 kcal/mol, 15 and 1/5 ps<sup>-1</sup>, respectively. We explored different values for these parameters and projected the sampled space on top of previously sampled region (Figure S4). We observed that new simulations sample similar unbinding pathway in the extracellular direction and discover similar space in the binding pocket as well. 

      Results and Discussion (Page 10)

      “We also performed unbinding simulations using well-tempered metadynamics parameters (bias height, bias deposition rate and bias factor) to confirm the existence of alternative pathways (Figure S4). However, the simulations show that ligands follow the similar pathway for all

      metadynamics runs.”

      (3) It would be nice to acknowledge previous applications of metadynamics+MSMs and (separately) TRAM, such as the Simulation of spontaneous G protein activation... (Sun et al. eLife 2018) and Estimation of binding rates and affinities... (Ge and Voelz JCP 2022). 

      We appreciate the reviewer's feedback. We have incorporated additional citations of studies demonstrating the use of TRAM as an estimator for both kinetics and thermodynamics (e.g. Ligand binding: Ge, Y. and Voelz, V.A., JCP, 2022[1]; Peptide-protein binding kinetics: Paul, F. et al., Nat. Commun., 2017[2], Ge, Y. et al., JCIM, 2021[3]). Additionally, we have included references to studies where biased simulations were initially used to explore the conformational space, and the results were then employed to seed unbiased simulations for building a Markov state model. (Metadynamics: Sun, X. et al., elife, 2018[4]; Umbrella Sampling: Abella, J. R. et al., PNAS, 2020[5]; Replica Exchange: Paul, F. et al., Nat. Commun., 2017[2]).

      (4) What is KL divergence analysis between macrostates? I know KL divergence compares probability distributions, but it is not clear what distributions are being compared. 

      We apologize for this confusion. The KL divergence analysis was performed on the probability distributions of the inverse distances between residue pairs from any two macrostates. Each macrostate was represented by 1000 frames that were selected proportional to the TRAM stationary density. All possible pair-wise inverse distances were calculated per frame for the purpose of these calculations. Although KL divergence is inherently asymmetric, we symmetrized the measurement by calculating the average. Per-residue K-L divergence, which is shown in the main figures as color and thickness gradient, was calculated by taking the sum of all pairs corresponding to the residue. We have included a detailed discussion of K-L divergence in Methods section.  We have also modified the result section to add a brief discussion of K-L divergence methodology.

      Results and Discussion (Page 15)

      “We further performed Kullback-Leibler divergence (K-L divergence) analysis between inverse distance of residue pairs of two macrostates to highlight the protein region that undergoes high conformational change with ligand movement.”

      Methods (Page 33)

      “Kullback–Leibler divergence (K-L divergence) analysis was performed to show the structural differences in protein conformations in different macrostates[4,114] . In this study, this technique was used to calculate the difference in the pairwise inverse distance distributions between macrostates. Each macrostate was represented by 1000 frames that were selected proportional to their TRAM weighted probabilities. Although K-L divergence is an asymmetric measurement, for this study, we used a symmetric version of the K-L divergence by taking the average between two macrostates. Per residue contribution of K-L divergence was calculated by taking the sum of all the pairwise distances corresponding to that residue. This analysis was performed by inhouse Python code.”  

      (5) I suggest being more careful with the language of universality. It can be "supported" but "showing" or "proving" its universal would require looking at all possible chemicals in the class. 

      We thank the reviewer for the suggestion. In response, we have revised the manuscript to ensure that the language reflects that our findings are based on observations from a limited set of ligands, namely one NPS and one classical cannabinoid. We have replaced references to ligand groups (such as NPS or classical cannabinoid) with the specific ligand names (such as MDMB-FUBINACA or HU-210) to avoid claims of universality and prevent any potential confusion.

      Results and Discussion (Page 19)

      “In this work, we trained the network with the NPS (MDMB-FUBINACA), and classical cannabinoid (HU-210) bound unbiased trajectories (Method Section). Here, we compared the allosteric interaction weights between the binding pocket and the NPxxY motif which involves in triad interaction formation. Results show that each binding pocket residue in MDMBFUBINACA bound ensemble shows higher allosteric weights with the NPxxY motif, indicating larger dynamic interactions between the NPxxY motif and binding pocket residues(Figure S9).  The probability of triad formation was estimated to observe the effect of the difference in allosteric control. TRAM weighted probability calculation showed that MDMB-FUBINACA bound CB1 has the higher probability of triad formation (Figure 8A). Comparison of the pairwise interaction of the triad residues shows that interaction between Y397<sup>7.53</sup>-T210<sup>3.46</sup> is relatively more stable in case of MDMB-FUBINACA bound CB1, while other two inter- actions have similar behavior for both systems (Figures S10A, S10B, and S10C). Therefore, higher interaction between Y397<sup>7.53</sup> and T210<sup>3.46</sup> in MDMB-FUBINACA bound receptor causes the triad interaction to be more probable. 

      Furthermore, we also compared TM6 movement for both ligand bound ensemble which is another activation metric involved in both G-protein and β-arrestin binding. Comparison of TM6 distance from the DRY motif of TM3 shows similar distribution for HU-210 and MDMBFUBINACA (Figure 8B). These observations support that NPS binding causes higher β-arrestin signaling by allosterically controlling triad interaction formation.” 

      Reviewer #2 (Public Review): 

      Summary: 

      The investigation provides computational as well as biochemical insights into the (un)binding mechanisms of a pair of psychoactive substances into cannabinoid receptors. A combination of molecular dynamics simulation and a set of state-of-the art statistical post-processing techniques were employed to exploit GPCR-ligand dynamics. 

      Strengths: 

      The strength of the manuscript lies in the usage and comparison of TRAM as well as Markov state modelling (MSM) for investigating ligand binding kinetics and thermodynamics. Usually, MSMs have been more commonly used for this purpose. But as the authors have pointed out, implicit in the usage of MSMs lies the assumption of detailed balance, which would not hold true for many cases especially those with skewed binding affinities. In this regard, the author's usage of TRAM which harnesses both biased and unbiased simulations for extracting the same, provides a more appropriate way out. 

      Weaknesses: 

      (1) While the authors have used TRAM (by citing MSM to be inadequate in these cases), the thermodynamic comparisons of both techniques provide similar values. In this case, one would wonder what advantage TRAM would hold in this particular case. 

      We thank the reviewer for the comment. While we agree that the thermodynamic comparisons between MSM and TRAM provide similar values in this instance, we would like to emphasize the underlying reasoning behind our choice of TRAM.

      MSM can struggle to accurately estimate thermodynamic and kinetic properties in cases where local state reversibility (detailed balance) is not easily achieved with unbiased sampling. This is especially relevant in ligand unbinding processes, which often involve overcoming high free energy barriers. TRAM, by incorporating biased simulation data (such as umbrella sampling) in addition to unbiased data, can better achieve local reversibility and provide more robust estimates when unbiased sampling is insufficient.

      The similarity in thermodynamic estimates between MSM and TRAM in our study can be attributed to the relatively long unbiased sampling period (> 100 µs) employed. With sufficient sampling, MSM can approach detailed balance, leading to results comparable to those from TRAM. However, as we demonstrated in our manuscript (Figure 4D), when the amount of unbiased sampling is reduced, the uncertainties in both the thermodynamics and kinetics estimates increase significantly for MSM compared to TRAM. Thus, while MSM and TRAM perform similarly under the conditions of extensive sampling, TRAM's advantage lies in its robustness when unbiased sampling is limited or difficult to achieve. 

      (2) The initiation of unbiased simulations from previously run biased metadynamics simulations would almost surely introduce hysteresis in the analysis. The authors need to address these issues. 

      We thank the reviewer for the comment. We acknowledge that biased simulations could potentially introduce hysteresis or result in the identification of unphysical pathways. However, we believe this issue is mitigated using well-tempered metadynamics, which gradually deposit a decaying bias. This approach enables the simulation to explore orthogonal directions of collective variable (CV) space, reducing the likelihood of hysteresis effects(Invernizzi, M. and Parrinello, M., JCTC, 2019[6]).

      Furthermore, there is precedent for using metadynamics-derived pathways to initiate unbiased simulations for constructing Markov State Models (MSMs). This methodology has been successfully applied in studying G-protein activation (Sun, X. et al., elife, 2018[4]).

      Additional support to our observation can be found in two independent binding/unbinding studies of ligands from cannabinoid receptors, which have discovered similar pathway using different CVs (Saleh, et al., Angew. Chem., 2018[7]; Hua, T. et al., Cell, 2020[8]).   

      (3) The choice of ligands in the current work seems very forced and none of the results compare directly with any experimental data. An ideal case would have been to use the seminal D.E. Shaw research paper on GPCR/ligand binding as a benchmark and then show how TRAM, using much lesser biased simulation times, would fare against the experimental kinetics or even unbiased simulated kinetics of the previous report 

      We would like to address the reviewer's concerns regarding the choice of ligands, lack of direct experimental comparison, and the use of TRAM, and clarify our rationale point by point:

      Ligand Choice: The ligands selected for this study were chosen due to their relevance and well characterized binding properties. MDMB-FUBINACA is well-known NPS ligand with documented binding properties. This ligand is still the only NPS ligand with experimentally determined CB1 bound structure (Krishna Kumar, K. et al., Cell, 2019[9]). Similarly, the classical cannabinoid (HU-210) used in this study has established binding characteristics and is one of earliest known synthetic classical cannabinoid. Therefore, these ligands serve as representative compounds within their respective categories, making them suitable for our comparative analysis.

      Experimental Comparison: We have indeed compared our simulation results to experimental data, particularly focusing on binding free energies. In the result section, we have shown that the relative binding free energy estimated from our simulation aligns closely with the experimentally measured values. Additionally, Absolute binding energy estimates are also within ~3 kcal/mol of the experimentally predicted value.

      TRAM Performance: TRAM estimated free energies, and rates have been benchmarked against experimental predictions for various studies along with our study (Peptide-protein binding: Paul, F. et al., Nat. Commun., 2017[2]; Ligand unbinding: Wu, H. et al., PNAS, 2016[10]) . As the primary goal of this study is to compare ligand unbinding mechanism, we believe benchmarking against other datasets, such as the D.E. Shaw GPCR/ligand binding paper, is not essential for this work.

      (4) The method section of the manuscript seems to suggest all the simulations were started from a docked structure. This casts doubt on the reliability of the kinetics derived from these simulations that were spawned from docked structure, instead of any crystallographic pose. Ideally, the authors should have been more careful in choosing the ligands in this work based on the availability of the crystallographic structures. 

      We thank the reviewer for the comment. We would like to clarify that we indeed used an experimentally derived pose for one of the ligands (MDMB-FUBINACA) as the cryo-EM structure of MDMB-FUBINACA bound to the protein was available (PDB ID: 6N4B) (Krishna Kumar K. et al., Cell, 2019[9]). However, as the cryo-EM structure had missing loops, we modeled these regions using Rosetta. We apologize for this confusion and have modified our method section to make this point clearer. 

      Regarding HU-210, we acknowledge that a crystallographic or cryo-EM structure for this specific ligand was not available. We selected HU-210 because it is most commonly used example of classical cannabinoid in the literature with extensively studied thermodynamic properties. Importantly, our docking results for HU-210 align closely with previously experimentally determined poses for other classical cannabinoids (Figure S11) and replicate key polar interactions, such as those with S383<sup>7.39</sup>, which are characteristic of this class of compounds. 

      System Preparation (Page 22)

      “Modeling of this membrane proximal region was also performed Remodel protocol of Rosetta loop modeling. A distance constraint is added during this modeling step between C98N−term and C107N−term to create the disulfide bond between the residues. [74,76] 

      As the cryo-EM structure of MDMB-FUBINACA was known, ligand coordinate of MDMB- FUBINACA was added to the modeled PDB structure. The “Ligand Reader & Modeler” module of CHARMM-GUI was used for ligand (e.g., MDMB-Fubinaca) parameterization using CHARMM General Force Field (CGenFF).[77]”

      (5) The last part of using a machine learning-based approach to analyze allosteric interaction seems to be very much forced, as there are numerous distance-based more traditional precedent analyses that do a fair job of identifying an allosteric job. 

      We thank the reviewer for the valuable comment. Neural relational inference method, which leverages a VAE (Variational Autoencoder) architecture, attempts to reconstruct the conformation (X) at time t + τ based on the conformation at time t. In doing so, it captures the non-linear dynamic correlations between residues in the VAE latent space. We chose this method because it is not reliant on specific metrics such as distance or angle, making it potentially more robust in predicting allosteric effects between the binding pocket residues and the NPxxY motif.

      In response to the reviewer's suggestion, we have also performed a more traditional allosteric analysis by calculating the mutual information between the binding pocket residues and the NPxxY motif. Mutual information was computed based on the backbone dihedral angles, as this provides a metric that is independent of the relative distances between residues. Our results indicate that the mutual information between the binding pocket residues and the NPxxY motif is indeed higher for the NPS binding simulation (Figure S11).

      Method

      Mutual information calculation

      Mutual information was calculated on same trajectory data as NRI analysis. Python package MDEntropy was used for estimating mutual information between backbone dihedral angles of two residues. 

      Results and Discussion (Page 21)

      “To further validate our observations, we estimated allosteric weights between the binding pocket and the NPxxY motif by calculating mutual information between residue movements. Mutual information analysis reaffirms that allosteric weights between these residues are indeed higher for the MDMB-FUBINACA bound ensemble (Figure S11).”

      Mutual Information Estimation (Page 37)

      “Mutual information between dynamics of residue pairs was computed based on the backbone dihedral angles, as this provides a metric that is independent of the relative distances between residues. The calculations were done on same trajectory data as NRI analysis. Python package MDEntropy was used for estimating mutual information between backbone dihedral angles of two residues.[124]”

      (6) While getting busy with the methodological details of TRAM vs MSM, the manuscript fails to share with sufficient clarity what the distinctive features of two ligand binding mechanisms are. 

      We thank the reviewer for the insightful comment. In the manuscript, we discussed that the overall ligand (un)binding pathways are indeed similar for both ligands. Therefore, they interact with similar residues during the unbinding process. However, we have focused on two key differences in unbinding mechanism between the two ligands:

      (1) MDMB-FUBINACA exhibits two distinct unbinding mechanisms. In one, the linked portion of the ligand exits the receptor first. In the other mechanism, the ligand rotates within the pocket, allowing the tail portion to exit first. By contrast, for HU-210, we observe only a single unbinding mechanism, where the benzopyran ring leads the ligand out of the receptor. We have highlighted these differences in the Figure 6 and 7 and talked about the intermediate states appear along these different unbinding mechanisms. For further clarification of these differences, we have added arrows in the free energy landscapes to highlight these distinct pathways.

      (2) In the bound state, a significant difference is observed in the interaction profiles. HU-210, a classical cannabinoid, forms strong polar interactions with TM7, while MDMB-FUBINACA shows weaker polar interactions with this region.

      We have discussed these differences in the Results and Discussion section (Page 13-18) & conclusion section (Page 23-24).

      Recommendations for the authors:

      Reviewer #2 (Recommendations For The Authors): 

      (1) The authors should choose at least one case where the ligand's crystallographic pose is known and show how TRAM works in comparison to MSM or experimental report. 

      We thank the reviewer for the comment. We have used the experimentally determined cryo-EM pose for one of the ligands (i.e. MDMB-FUBINACA).  We have modified the manuscript to avoid confusion. (Please refer to the response of comment 4 of reviewer 2)

      (2) The authors should consider existing traditional methods that are used to detect allostery and compare their machine-learning-based approach to show its relevance. 

      We appreciate the reviewer’s comment. We have performed the traditional analysis by calculating mutual information between residue dynamics. We have shown that the traditional analysis matches with Machine learning based NRI calculation. (Please refer to the response of comment 5 of reviewer 2)

      (3) Figure 3 doesn't provide a guide on the pathway of ligand. Without a proper arrow, it is difficult to surmise what is the start and end of the pathway. The figures should be improved. 

      We appreciate the reviewer’s suggestion. In response, we have revised Figure 3 to clearly indicate the ligand’s unbinding pathway by adding directional arrows and labeling the bound pose. Additionally, we have updated the figure caption to better clarify the color scheme used in the illustration. 

      (4) The Figure 5 presentation of free energetics has a very similar shape for the two ligands. More clarity is required on how these two ligands are different. 

      We thank the reviewer for the comment. While the overall shapes of the free energy profiles for the two ligands are indeed similar, this is expected as both ligands dissociate from the same pocket and follow a comparable pathway. However, key differences in their unbinding mechanisms arise due to variations in the ligand motion within the pocket. Specifically, the intermediate metastable minima in the free energy landscapes reflect these differences. For instance, in the NPS unbinding free energy landscape, the intermediate metastable state I1 corresponds to a conformation where the NPS ligand maintains a polar interaction with TM7, while the tail of the ligand has shifted away from TM5. This intermediate state is absent in the classical cannabinoid unbinding pathway, where no equivalent conformation appears in the landscape.  

      (6) Page 30: TICA is wrongly expressed as 'Time-independent component analysis'. It is not a time-independent process. Rather it is 'Time structured independent component analysis'. 

      We thank the reviewer for pointing this out. TICA should be expressed as Time-lagged independent component analysis or Time-structure independent component analysis. We have used the first expression and modified the manuscript accordingly.  

      (7) The manuscript's MSM theory part is quite well-known which can be removed and appropriate papers can be cited. 

      We thank the reviewer for the comment. We have removed the theory discussion of MSM and cited relevant papers.

      “Markov State Model

      Markov state model (MSM) is used to estimate the thermodynamics and kinetics from the unbiased simulation.[56,91] MSM characterizes a dynamic process using the transition probability matrix and estimates its relevant thermodynamics and kinetic properties from the eigendecomposition of this matrix. This matrix is usually calculated using either maximum likelihood or Bayesian approach.[56,97] The prevalence of MSM as a post-processing technique for MD simulations was due to its reliance on only local equilibration of MD trajectories to predict the global equilibrium properties.[92,93] Hence, MSM can combine information from distinct short trajectories, which can only attain the local equilibrium.[94–96]  

      The following steps are taken for the practical implementation of the MSM from the MD data. [4,17,98–100]”

      (8) A proper VAMP score-based analysis should be provided to show confidence in MSM's clustering metric and other hyperparameters. 

      We thank the reviewer for the recommendation. VAMP-2 score based analysis had been discussed in the method section.  We estimated VAMP-2 score of MSM built with different cluster number and input TIC dimensions (Figure S15). Model with best VAMP-2 was selected for comparison with TRAM result.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1:

      While very positive towards our manuscript, this reviewer also points out three suggestions for improvement.

      Overall, there are not many weaknesses. The main one I noticed is with the lipidomic analysis shown in Figs 3C, 7C, S1 and S3. While these data are an essential part of the analysis and provide strong evidence for the conclusions of the study, it is unfortunate that the methods used did not enable the distinction between two 18:1 isomers. These two isomers of 18:1 are important in C. elegans biology, because one is a substrate for FAT-2 (18:1n-9, oleic acid) and the other is not (18:1n-7, cis vaccenic acid). Although rarer in mammals, cisvaccenic acid is the most abundant fatty acid in C. elegans and is likely the most important structural MUFA. The measurement of these two isomers is not essential for the conclusions of the study, but the manuscript should include a comment about the abundance of oleic vs vaccenic acid in C. elegans (authors can find this information, even in the fat-2 mutant, in other publications of C. elegans fatty acid composition). Otherwise, readers who are not familiar with C. elegans might assume the 18:1 that is reported is likely to be mainly oleic acid, as is common in mammals.

      Excellent point. As suggested by the reviewer, we now include a clarification of this in the text: "Consistent with previous publications [10], the levels of 18:1 fatty acids were greatly increased in the fat-2(wa17) mutant. It is important to note that the majority of these 18:1 fatty acids is likely 18:1n7 (vaccenic acid) and not 18:1n9 (OA) [10,23], which is the substrate of FAT-2; the lipid analysis methods used here are not able to distinguish between the two 18:1 species."

      The title could be less specific; it might be confusing to readers to include the allele name in the title.

      We thank the reviewer for the suggestion, and we have now modified the title:

      "Forward Genetics In C. elegans Reveals Genetic Adaptations To Polyunsaturated Fatty Acid Deficiency"

      There are two errors in the pathway depicted in Figure 1A. The16:0-16:1 desaturation can be performed by FAT-5, FAT-6, and FAT-7. The 18:0-18:1 desaturation can only be performed by FAT-6 and FAT-7.

      We thank the reviewer for pointing out this mistake. The pathway in Fig. 1A has been corrected.

      Reviewer #2:

      This reviewer was also very positive towards our manuscript but also pointed out several suggestions for additional experiments or changes to the manuscript.

      Major recommendations

      (1) To conclude that membrane rigidification is not the major cause of defects associated with fat-2 mutations, the authors need to show that fluidity is rescued by their treatments (oleic acid or NP-40). I honestly doubt that it is the case, as oleic acid is already abundant in fat-2 mutants. It is possible that the treatments, which are effective in rescuing fluidity in paqr-2 mutants, do not have the same effects in fat-2 mutants.

      The reviewer raises an important point. In an effort to address this, we have now performed a FRAP study on fat-2(wa17) mutants with/without NP40 as a fluidizing agent (with wild-type and paqr-2 mutants as controls). The new data, now included as Fig. 2J, shows that NP40 did improve the fluidity of the intestinal cell membrane in the fat-2(wa17) mutant, though not to the same degree as in the paqr-2 mutant. This is now cited in the text as follows:

      "However, cultivating the fat-2(wa17) mutant in the presence of the non-ionic detergent NP40, which improves the growth of the paqr-2(tm3410) mutant [17], did not suppress the poor growth phenotype of the fat-2(wa17) mutant even though it did improve membrane fluidity as measured using FRAP (Fig. 2I-J). Similarly, supplementing the fat-2(wa17) mutant with the MUFA oleic acid (OA, 18:1), which also suppresses paqr-2(tm3410) phenotypes [17], did not suppress the poor growth phenotype of the fat-2(wa17) mutant (Fig 2K)."

      (2) It is not validated experimentally that the mutations converge into FTN-2 repression. This can be verified by analyzing mRNA or protein expression of FTN-2 in the egl-9 and hif-1 mutants obtained in the screening.

      Our manuscript does lean on several publications that previously established the HIF-1 pathway in C. elegans. Additionally, we now added a qPCR experiment showing that the newly isolated hif-1(et69) allele indeed suppresses the expression of ftn-2. This was an especially valuable experiment since the hif-1(et69) is proposed to act as a gain-of-function allele that would constitutively suppress ftn-2 expression. This new result is included as Fig. 6C and mentioned in the text:

      "Inhibition of egl-9 promotes HIF-1 activity [41], which we here verified for the egl-9(et60) allele using western blots (Fig 6A). Additionally, we found by qPCR that ftn-2 mRNA levels are as expected reduced by the proposed gain-of-function hif-1(et69) allele (Fig 6C). We conclude that the egl-9 and hif-1 suppressor mutations likely converge on inhibiting ftn-2 and thus act similarly to the ftn-2 loss-of-function alleles."

      (3) In the hif-1(et69) and ftn-2(et68) mutants, the rescues in lipid composition seem to be minor, with eicosapentaenoic acid (EPA) levels remaining low. The ftn-2 mutant data is especially concerning, as it suggests that egl-9 mutants rescue lipid composition via distinct mechanisms not including ftn-2 suppression. I suggest that the authors test the minimal doses of linoleic acid or EPA required to rescue fat-2 mutants and perform lipidomics to test which is the degree of EPA restoration that is needed. If a low level of restoration is sufficient, the hif-1 and ftn-2 mutants might indeed rescue phenotypes via a restoration of EPA levels. Otherwise, other mechanisms have to be considered.

      In line with the above issue, the low level or EPA restoration in hif-1 and ftn-2 mutants raise the possibility that the mutations rescue fat-2 mutants downstream of lipid changes. The reduction in HIF-1 levels in fat-2 mutants also suggest that lipid changes affect HIF-1 expression. Thus, the "impossibility to genetically compensate PUFA deficiency" might be wrong. The above experiment would answer to this point too.

      The reviewer is entirely correct to consider alternative explanations. In the lipidomics in Fig 3, we see that fat-2(wa17) worms on NGM have only ~1.5-2%mol EPA in phosphatidylcholines. When treated with 2 mM LA, the levels of EPA rise to ~10%mol, still below the ~ 25% observed in N2 but perhaps this is sufficient cause for restoring fat-2(wa17) health. Similarly, the hif-1(et69) and ftn-2(et68) mutant alleles elevate EPA levels to 5- 7% in fat-2(wa17). Thus, we have a correlation where a significant increase in EPA, obtained either through LA supplementation or through suppressor mutations (e.g. egl-9 (et60), hif-1(et69) or ftn-2(et68)), is associated with improved growth and health of the fat-2(wa17) mutant. However, correlation is of course not proof. The suggested experiment to titrate EPA to its lowest fat-2(wa17) rescuing levels and then perform lipidomics analysis was not possible in a reasonable time frame during this revision. However, preliminary experiments showed that even 25 μM LA (most of which will be converted to EPA by the worms) is enough to rescue the fat-2(wa17) or null mutant (Author response image 1), suggesting that even tiny amounts (much below the >250 μM used in our article) bring great benefits.

      Author response image 1.

      Nevertheless, we now acknowledge in the discussion that alternative explanations exist:

      "Other mechanisms are also possible. For example, mutations in the HIF-1 pathway could somehow reduce EPA turnover rates in the fat-2(wa17) mutant and allow its levels to rise above an essential threshold. This hypothesis is consistent with the observation that the suppressors can rescue both the fat-2(wa17) mutant and fat-2 RNAi-treated worms but not the fat-2 null mutant. It is even possible, though deemed unlikely, that the fat-2(wa17) suppressors act by compensating for the PUFA shortage via some undefined separate process downstream of the lipid changes and that they only indirectly result in elevated EPA levels."

      Additionally, another possible mechanism of action of the fat-2(wa17) suppressors could have been that they all cause upregulation of the FAT-2 protein. We have now explored this possibility using Western blots and found that this is an unlikely mechanism. This is presented in Fig. 6D-E and S3C-D, mentioned in the text as follows:

      "We also used Western blots to evaluate the abundance of the FAT-2 protein expressed from endogenous wild-type or mutant loci but to which a HA tag was fused using CRISPR/Cas9. We found that the FAT-2::HA levels are severely reduced when the locus contains the S101F substitution present in the wa17 allele, but restored close to wild-type levels by the fat2(et65) suppressor mutation (Fig 6D-E, S3C-D Fig). The levels of FAT-2 in the HIF-1 pathway suppressors varied between experiments, with the suppressors sometimes restoring FAT-2 levels and sometimes not even when the worms were growing well (Fig 6D-E, S3C-D Fig). The fat-2(wa17) suppressors, except for the intragenic fat-2 alleles, likely do not act by increasing FAT-2 protein levels."

      (4) It should be tested how Fe2+ levels are changed in the mutants, and how effective the ferric ammonium citrate treatment is. The authors might use a ftn-1::GFP reporter for this purpose.

      We did obtain a strain carrying the ftn-1::GFP reporter but could not generate conclusive data with it. In particular, we saw no increase in fluorescence in fat-2(wa17) worms carrying suppressor mutations. However, we also found that even FAC treatment that rescue the fat2(wa17) mutant did not result in a measurable increased GFP levels suggesting that the reporter is not sensitive enough.

      Minor comments

      (1) I think that putting Figure 6A in Figure 5 would be helpful for the readers, so that they understand that the mutations converge in the same pathway.

      This is now done.

      (2) Page 3: While it is clear that paqr-2 regulates lipid composition, I believe that it remains unclear if it "promote the production and incorporation of PUFAs into phospholipids to restore membrane homeostasis".

      A reference was missing to support that statement. Ruiz et al. (2023) is now cited for this (ref. 7).

      (3) C. elegans is extremely rich in EPA (see for example DOI: 10.3390/jcm5020019), but the lipidomics data in this study rather suggest that oleic acid is predominant. I recommend to check why this discrepancy occurs.

      OA (18:1n9) makes up only ~2%, but vaccenic acid (18:1n7) is ~21% in WT worms, EPA is slightly less at ~19% (Watts et al. 2002). These match with our lipidomics results although we cannot distinguish between 18:1n9 and n7. See also answer to Reviewer #1, comment 1.

      (4) Abstract: The authors write that mammals do not synthesize PUFAs, which is almost correct, but they still produce the PUFA mead acid. Thus, the statement is not completely right.

      Didn't know that! From literature, it is our understanding that mammals synthesize mead acid during FA deficiency but not in normal conditions, so they are not regularly producing mead acid. We have now updated the introduction:

      "An exception to this exists during severe essential fatty acid deficiency when mammals can synthesize mead acid (20:3n9), though this is not a common occurrence [11]"

      (5) Page 10: Eicosanoids are C20 lipid mediators, thus those produced from docosahexaenoic acid are not eicosanoids. Correct the statement.

      We thank the reviewer for pointing this out. We now write:

      " EPA and DHA, being long chain PUFAs should have similar fluidizing effects on membrane properties (though in vitro experiments challenge this view [78]), and both can serve as precursors of eicosanoids or docosanoids, particularly inflammatory ones [79]."

      (6) Page 7: "hif-1(et69) is similarly able to suppress fat-2(wa17) when ftn-2 is knocked out" I am not sure that the data agrees with this statement, and it is unclear what we can conclude from such observation.

      Fig. 2D shows that ftn-2(et68) suppresses fat-2(wa17) even in the presence of a hif-1(ok2654) null allele, showing that no HIF-1 function is required once ftn-2 is mutated. Conversely, Fig S2E shows that combining both the hif-1(et69) and the ftn-2(ok404) null allele also suppresses fat-2(wa17) (the worms do not fully reach N2 length, but they are significantly longer and were fertile adults); this is merely the expected outcome if the pathway converges on loss of ftn-2 function, though other interpretations could be possible from this experiment alone.

      (7) S3 Fig: in panel B, is the last column ftn-2;egl-9 mutant? I would imagine that it is ftn2;fat-2.

      We thank the reviewer for pointing this out. This has been corrected.

      (8) Fig 6B, how many times has been this experiment done?

      With these exact conditions (6h and 20h hypoxia) and order of strains the blot was done once, but the blot overall was done 5 times. We now added another replicate in Fig. S3A.

      Note also that a few minor modifications have been made throughout the text, which can be seen in the Word file with tracked changes.

    1. Author response:

      We thank the reviewers for the valuable and constructive reviews. Thanks to these, we believe the article will be considerably improved. We have organized our response to address points that are relevant to both reviewers first, after which we address the unique concerns of each individual reviewer separately. We briefly paraphrase each concern and provide comments for clarification, outlining the precise changes that we will make to the text.

      Common Concerns (Reviewer 1 & Reviewer 2):

      Can you clarify how NREM and REM sleep relate to the oneirogen hypothesis?

      Within the submission draft we tried to stay agnostic as to whether mechanistically similar replay events occur during NREM or REM sleep; however, upon a more thorough literature review, we think that there is moderately greater evidence in favor of Wake-Sleep-type replay occurring during REM sleep which is related to classical psychedelic drug mechanisms of action.

      First, we should clarify that replay has been observed during both REM and NREM sleep, and dreams have been documented during both sleep stages, though the characteristics of dreams differ across stages, with NREM dreams being more closely tied to recent episodic experience and REM dreams being more bizarre/hallucinatory (see Stickgold et al., 2001 for a review). Replay during sleep has been studied most thoroughly during NREM sharp-wave ripple events, in which significant cortical-hippocampal coupling has been observed (Ji & Wilson, 2007). However, it is critical to note that the quantification methods used to identify replay events in the hippocampal literature usually focus on identifying what we term ‘episodic replay,’ which involves a near-identical recapitulation of neural trajectories that were recently experienced during waking experimental recordings (Tingley & Peyrach, 2020). In contrast, our model focuses on ‘generative replay,’ where one expects only a statistically similar reproduction of neural activity, without any particular bias towards recent or experimentally controlled experience. This latter form of replay may look closer to the ‘reactivation’ observed in cortex by many studies (e.g. Nguyen et al., 2024), where correlation structures of neural activity similar to those observed during stimulus-driven experience are recapitulated. Under experimental conditions in which an animal is experiencing highly stereotyped activity repeatedly, over extended periods of time, these two forms of replay may be difficult to dissociate.

      Interestingly, though NREM replay has been shown to couple hippocampal and cortical activity, a similar study in waking animals administered psychedelics found hippocampal replay without any obvious coupling to cortical activity (Domenico et al., 2021). This could be because the coupling was not strong enough to produce full trajectories in the cortex (psychedelic administration did not increase ‘alpha’ enough), and that a causal manipulation of apical/basal influence in the cortex may be necessary to observe the increased coupling. Alternatively, as Reviewer 1 noted, it may be that psychedelics induce a form of hippocampus-decoupled replay, as one would expect from the REM stage of a recently proposed complementary learning systems model (Singh et al., 2022). 

      Evidence in favor of a similarity between the mechanism of action of classical psychedelics and the mechanism of action of memory consolidation/learning during REM sleep is actually quite strong. In particular, studies have shown that REM sleep increases the activity of soma-targeting parvalbumin (PV) interneurons and decreases the activity of apical dendrite-targeting somatostatin (SOM) interneurons (Niethard et al., 2021), that this shift in balance is controlled by higher-order thalamic nuclei, and that this shift in balance is critical for synaptic consolidation of both monocular deprivation effects in early visual cortex (Zhou et al., 2020) and for the consolidation of auditory fear conditioning in the dorsal prefrontal cortex (Aime et al., 2022). These last studies were not discussed in the present manuscript–we will add them, in addition to a more nuanced description of the evidence connecting our model to NREM and REM replay.

      Can you explain how synaptic plasticity induced by psychedelics within your model relates to learning at a behavioral level?

      While the Wake-Sleep algorithm is a useful model for unsupervised statistical learning, it is not a model of reward or fear-based conditioning, which likely occur via different mechanisms in the brain (e.g. dopamine-dependent reinforcement learning or serotonin-dependent emotional learning). The Wake-Sleep algorithm is a ‘normative plasticity algorithm,’ that connects synaptic plasticity to the formation of structured neural representations, but it is not the case that all synaptic plasticity induced by psychedelic administration within our model should induce beneficial learning effects. According to the Wake-Sleep algorithm, plasticity at apical synapses is enhanced during the Wake phase, and plasticity at basal synapses is enhanced during the Sleep phase; under the oneirogen hypothesis, hallucinatory conditions (increased ‘alpha’) cause an increase in plasticity at both apical and basal sites. Because neural activity is in a fundamentally aberrant state when ‘alpha’ is increased, there are no theoretical guarantees that plasticity will improve performance on any objective: psychedelic-induced plasticity within our model could perhaps better be thought of as ‘noise’ that may have a positive or negative effect depending on the context.

      In particular, such ‘noise’ may be beneficial for individuals or networks whose synapses have become locked in a suboptimal local minimum. The addition of large amounts of random plasticity could allow a system to extricate itself from such local minima over subsequent learning (or with careful selection of stimuli during psychedelic experience), similar to simulated annealing optimization approaches. If our model were fully validated, this view of psychedelic-induced plasticity as ‘noise’ could have relevance for efforts to alleviate the adverse effects of PTSD, early life trauma, or sensory deprivation; it may also provide a cautionary note against repeated use of psychedelic drugs within a short time frame, as the plasticity changes induced by psychedelic administration under our model are not guaranteed to be good or useful in-and-of themselves without subsequent re-learning and compensation.

      We should also note that we have deliberately avoided connecting the oneirogen hypothesis model to fear extinction experimental results that have been observed through recordings of the hippocampus or the amygdala (Bombardi & Giovanni, 2013; Jiang et al., 2009; Kelly et al., 2024; Tiwari et al., 2024). Both regions receive extensive innervation directly from serotonergic synapses originating in the dorsal raphe nucleus, which have been shown to play an important role in emotional learning (Lesch & Waider, 2012); because classical psychedelics may play a more direct role in modulating this serotonergic innervation, it is possible that fear conditioning results (in addition to the anxiolytic effects of psychedelics) cannot be attributed to a shift in balance between apical and basal synapses induced by psychedelic administration. We will provide a more detailed review of these results in the text, as well as more clarity regarding their relation to our model.

      Reviewer 1 Concerns:

      Is it reasonable to assign a scalar parameter ‘alpha’ to the effects of classical psychedelics? And is your proposed mechanism of action unique to classical psychedelics? E.g. Could this idea also apply to kappa opioid agonists, ketamine, or the neural mechanisms of hallucination disorders?

      We will clarify that within our model ‘alpha’ is a parameter that reflects the balance between apical and basal synapses in determining the activity of neurons in the network. For the sake of simplicity we used a single ‘alpha’ parameter, but realistically, each neuron would have its own ‘alpha’ parameter, and different layers or individual neurons could be affected differentially by the administration of any particular drug; therefore, our scalar ‘alpha’ value can be thought of as a mean parameter for all neurons, disregarding heterogeneity across individual neurons.

      There are many different mechanisms that could theoretically affect this ‘alpha’ parameter, including: 5-HT2a receptor agonism, kappa opioid receptor binding, ketamine administration, or possibly the effects of genetic mutations underlying the pathophysiology of complex developmental hallucination disorders. We focused exclusively on 5-HT2a receptor agonism for this study because the mechanism is comparatively simple and extensively characterized, but similar mechanisms may well be responsible for the hallucinatory symptoms of a variety of drugs and disorders.

      Can you clarify the role of 5-HT2a receptor expression on interneurons within your model?

      While we mostly focused on the effects of 5-HT2a receptors on the apical dendrites of pyramidal neurons, these receptors are also expressed on soma-targeting parvalbumin (PV) interneurons. This expression on PV interneurons is consistent with our proposed psychedelic mechanism of action, because it could lead to a coordinated decrease in the influence of somatic and proximal dendritic inputs while increasing the influence of apical dendritic inputs. We will elaborate on this point, and will move the discussion earlier in the text.

      Discussions of indigenous use of psychedelics over millenia may amount to over-romanticization.

      We will take great care to conduct a more thorough literature review to reevaluate our statement regarding indigenous psychedelic use (including the citations you suggested), and will either provide a more careful statement or remove this discussion from our introduction entirely, as it has little bearing on the rest of the text. The Ethics Statement will also be modified accordingly.

      You isolate the 5-HT2a agonism as the mechanism of action underlying ‘alpha’ in your model, but there exist 5-HT2a agonists that do not have hallucinatory effects (e.g. lisuride). How do you explain this?

      Lisuride has much-reduced hallucinatory effects compared to other psychedelic drugs at clinical doses (though it does indeed induce hallucinations at high doses; Marona-Lewicka et al., 2002), and we should note that serotonin (5-HT) itself is pervasive in the cortex without inducing hallucinatory effects during natural function. Similarly, MDMA is a partial agonist for 5-HT2a receptors, but it has much-reduced perceptual hallucination effects relative to classical psychedelics (Green et al., 2003) in addition to many other effects not induced by classical psychedelics.

      Therefore, while we argue that 5-HT2a agonism induces an increase in influence of apical dendritic compartments and a decrease in influence of basal/somatic compartments, and that this change induces hallucinations, we also note that there are many other factors that control whether or not hallucinations are ultimately produced, so that not all 5-HT2a agonists are hallucinogenic. We will discuss two such factors in our revision: 5-HT receptor binding affinity and cellular membrane permeability.

      Importantly, many 5-HT2a receptor agonists are also 5-HT1a receptor agonists (e.g. serotonin itself and lisuride), while MDMA has also been shown to increase serotonin, norepinephrine, and dopamine release (Green et al., 2003). While 5-HT2a receptor agonism has been shown to reduce sensory stimulus responses (Michaiel et al., 2019), 5-HT1a receptor agonism inhibits spontaneous cortical activity (Azimi et al., 2020); thus one might expect the net effect of administering serotonin or a nonselective 5-HT receptor agonist to be widespread inhibition of a circuit, as has been observed in visual cortex (Azimi et al., 2020). Therefore, selective 5-HT2a agonism is critical for the induction of hallucinations according to our model, though any intervention that jointly excites pyramidal neurons’ apical dendrites and inhibits their basal/somatic compartments across a broad enough area of cortex would be predicted to have a similar effect. Lisuride has a much higher binding affinity for 5-HT1a receptors than, for instance, LSD (Marona-Lewicka et al., 2002).

      Secondly, it has recently been shown that both the head-twitch effect (a coarse behavioral readout of hallucinations in animals) and the plasticity effects of psychedelics are abolished when administering 5-HT2a agonists that are impermeable to the cellular membrane because of high polarity, and that these effects can be rescued by temporarily rendering the cellular membrane permeable (Vargas et al., 2023). This suggests that the critical hallucinatory effects of psychedelics (apical excitation according to our model) may be mediated by intracellular 5-HT2a receptors. Notably, serotonin itself is not membrane permeable in the cortex.

      Therefore, either of these two properties could play a role in whether a given 5-HT2a agonist induces hallucinatory effects. We will provide a considerably extended discussion of these nuances in our revision.

      Your model proposes that an increase in top-down influence on neural activity underlies the hallucinatory effects of psychedelics. How do you explain experimental results that show increases in bottom-up functional connectivity (either from early sensory areas or the thalamus)?

      Firstly, we should note that our proposed increase in top-down influence is a causal, biophysical property, not necessarily a statistical/correlative one. As such, we will stress that the best way to test our model is via direct intervention in cortical microcircuitry, as opposed to correlative approaches taken by most fMRI studies, which have shown mixed results with regard to this particular question. Correlative approaches can be misleading due to dense recurrent coupling in the system, and due to the coarse temporal and spatial resolution provided by noninvasive recording technologies (changes in statistical/functional connectivity do not necessarily correspond to changes in causal/mechanistic connectivity, i.e. correlation does not imply causation).

      There are two experimental results that appear to contradict our hypothesis that deserve special consideration in our revision. The first shows an increase in directional thalamic influence on the distributed cortical networks after psychedelic administration (Preller et al., 2018). To explain this, we note that this study does not distinguish between lower-order sensory thalamic nuclei (e.g. the lateral and medial geniculate nuclei receiving visual and auditory stimuli respectively) and the higher-order thalamic nuclei that participate in thalamocortical connectivity loops (Whyte et al., 2024). Subsequent more fine-grained studies have noted an increase in influence of higher order thalamic nuclei on the cortex (Pizzi et al., 2023; Gaddis et al., 2022), and in fact extensive causal intervention research has shown that classical psychedelics (and 5-HT2a agonism) decrease the influence of incoming sensory stimuli on the activity of early sensory cortical areas, indicating decoupling from the sensory thalamus (Evarts et al., 1955; Azimi et al., 2020; Michaiel et al. 2019). The increased influence of higher-order thalamic nuclei is consistent with both the cortico-striatal-thalamo-cortical (CTSC) model of psychedelic action as well as the oneirogen hypothesis, since higher-order thalamic inputs modulate the apical dendrites of pyramidal neurons in cortex (Whyte et al., 2024).

      The second experimental result notes that DMT induces traveling waves during resting state activity that propagate from early visual cortex to deeper cortical layers (Alamia et al., 2020). There are several possibilities that could explain this phenomenon: 1) it could be due to the aforementioned difficulties associated with directed functional connectivity analyses, 2) it could be due to a possible high binding affinity for DMT in the visual cortex relative to other brain areas, or 3) it could be due to increases in apical influence on activity caused by local recurrent connectivity within the visual cortex which, in the absence of sensory input, could lead to propagation of neural activity from the visual cortex to the rest of the brain. This last possibility is closest to the model proposed by (Ermentrout & Cowan, 1979), and which we believe would be best explained within our framework by a topographically connected recurrent network architecture trained on video data; a potentially fruitful direction for future research.

      Shouldn’t the hallucinations generated by your model look more ‘psychedelic,’ like those produced by the DeepDream algorithm?

      We believe that the differences in hallucination visualization quality between our algorithm and DeepDream are mostly due to differences in the scale and power of the models used across these two studies. We are confident that with more resources (and potentially theoretical innovations to improve the Wake-Sleep algorithm’s performance) the produced hallucination visualizations could become more realistic, but we believe this falls outside the scope of the present study.

      We note that more powerful generative models trained with backpropagation are able to produce surreal images of comparable quality (Rezende et al., 2014; Goodfellow et al., 2020; Vahdat & Kautz, 2020), though these have not yet been used as a model of psychedelic hallucinations. However, the DeepDream model operates on top of large pretrained image processing models, and does not provide a biologically mechanistic/testable interpretation of its hallucination effects. When training smaller models with a local synaptic plasticity rule (as opposed to backpropagation), the hallucination effects are less visually striking due to the reduced quality of our trained generative model, though they are still strongly tied to the statistics of sensory inputs, as quantified by our correlation similarity metric (Fig. 5b). We will provide a more detailed explanation of this phenomenon when we discuss our model limitations in our revised manuscript.

      Your model assumes domination by entirely bottom-up activity during the ‘wake’ phase, and domination entirely by top-down activity during ‘sleep,’ despite experimental evidence indicating that a mixture of top-down and bottom-up inputs influence neural activity during both stages in the brain. How do you explain this?

      Our use of the Wake-Sleep algorithm, in which top-down inputs (Sleep) or bottom-up inputs (Wake) dominate network activity is an over-simplification made within our model for computational and theoretical reasons. Models that receive a mixture of top-down and bottom-up inputs during ‘Wake’ activity do exist (in particular the closely related Boltzmann machine (Ackley et al., 1985)), but these models are considerably more computationally costly to train due to a need to run extensive recurrent network relaxation dynamics for each input stimulus. Further, these models do not generalize as cleanly to processing temporal inputs. For this reason, we focused on the Wake-Sleep algorithm, at the cost of some biological realism, though we note that our model should certainly be extended to support mixed apical-basal waking regimes. We will make sure to discuss this in our ‘Model Limitations’ section.

      Your model proposes that 5-HT2a agonism enhances glutamatergic transmission, but this is not true in the hippocampus, which shows decreases in glutamate after psychedelic administration.

      We should note that our model suggests only compartment specific increases in glutamatergic transmission; as such, our model does not predict any particular directionality for measures of glutamatergic transmission that includes signaling at both apical and basal compartments in aggregate, as was measured in the provided study (Mason et al., 2020).

      You claim that your model is consistent with the Entropic Brain theory, but you report increases in variance, not entropy. In fact, it has been shown that variance decreases while entropy increases under psychedelic administration. How do you explain this discrepancy?

      Unfortunately, ‘entropy’ and ‘variance’ are heavily overloaded terms in the noninvasive imaging literature, and the particularities of the method employed can exert a strong influence on the reported effects. The reduction in variance reported by (Carhart-Harris et al., 2016) is a very particular measure: they are reporting the variance of resting state synchronous activity, averaged across a functional subnetwork that spans many voxels; as such, the reduction in variance in this case is a reduction in broad, synchronous activity. We do not have any resting state synchronous activity in our network due to the simplified nature of our model (particularly an absence of recurrent temporal dynamics), so we see no reduction in variance in our model due to these effects.

      Other studies estimate ‘entropy’ or network state disorder via three different methods that we have been able to identify. 1) (Carhart-Harris et al., 2014) uses a different measure of variance: in this case, they subtract out synchronous activity within functional subnetworks, and calculate variability across units in the network. This measure reports increases in variance (Fig. 6), and is the closest measure to the one we employ in this study. 2) (Lebedev et al., 2016) uses sample entropy, which is a measure of temporal sequence predictability. It is specifically designed to disregard highly predictable signals, and so one might imagine that it is a measure that is robust to shared synchronous activity (e.g. resting state oscillations). 3) (Mediano et al., 2024) uses Lempel-Ziv complexity, which is, similar to sample entropy, a measure of sequence diversity; in this case the signal is binarized before calculation, which makes this method considerably different from ours. All three of the preceding methods report increases in sequence diversity, in agreement with our quantification method. Our strongest explanation for why the variance calculation in (Carhart-Harris et al., 2016) produces a variance reduction is therefore due to a reduction in low-rank synchronous activity in subnetworks during resting state.

      As for whether the entropy increase is meaningful: we share Reviewer 1’s concern that increases in entropy could simply be due to a higher degree of cognitive engagement during resting state recordings, due to the presence of sensory hallucinations or due to an inability to fall asleep. This could explain why entropy increases are much more minimal relative to non-hallucinating conditions during audiovisual task performance (Siegel et al., 2024; Mediano et al., 2024). However, we can say that our model is consistent with the Entropic Brain Theory without including any form of ‘cognitive processing’: we observe increases in variability during resting state in our model, but we observe highly similar distributions of activity when averaging over a wide variety of sensory stimulus presentations (Fig. 5b-c). This is because variability in our model is not due to unstructured noise: it corresponds to an exploration of network states that would ordinarily be visited by some stimulus. Therefore, when averaging across a wide variety of stimuli, the distribution of network states under hallucinating or non-hallucinating conditions should be highly similar.

      One final point of clarification: here we are distinguishing Entropic Brain Theory from the REBUS model–the oneirogen hypothesis is consistent with the increase in entropy observed experimentally, but in our model this entropy increase is not due to increased influence of bottom-up inputs (it is due instead to an increase in top-down influence). Therefore, one could view the oneirogen hypothesis as consistent with EBT, but inconsistent with REBUS.

      You relate your plasticity rule to behavioral-timescale plasticity (BTSP) in the hippocampus, but plasticity has been shown to be reduced in the hippocampus after psychedelic administration. Could you elaborate on this connection?

      When we were establishing a connection between our ‘Wake-Sleep’ plasticity rule and BTSP learning, the intended connection was exclusively to the mathematical form of the plasticity rule, in which activity in the apical dendrites of pyramidal neurons functions as an instructive signal for plasticity in basal synapses (and vice versa): we will clarify this in the text. Similarly, we point out that such a plasticity rule tends to result in correlated tuning between apical and basal dendritic compartments, which has been observed in hippocampus and cortex: this is intended as a sanity check of our mapping of the Wake-Sleep algorithm to cortical microcircuitry, and has limited further bearing on the effects of psychedelics specifically.

      Reduction in plasticity in the hippocampus after psychedelic administration could be due to a complementary learning systems-type model, in which the hippocampus becomes partly decoupled from the cortex during REM sleep (Singh et al., 2022); were this to be the case, it would not be incompatible with our model, which is mostly focused on the cortex. Notably, potentiating 5HT-2a receptors in the ventral hippocampus does not induce the head-twitch response, though it does produce anxiolytic effects (Tiwari et al., 2024), indicating that the hallucinatory and anxiolytic effects of classical psychedelics may be partly decoupled. 

      Reviewer 2 Concerns:

      Could you provide visualizations of the ‘ripple’ phenomenon that you’re referring to?

      We will do this! For now, you can get a decent understanding of what the ‘ripple effect’ looks like from the ‘eyes closed’ hallucination condition for networks trained on CIFAR10 (Fig. 2d). The ripple effect that we are referring to is very similar, except it is superimposed on a naturalistic image under ordinary viewing conditions; to give a higher quality visualization of the ripple phenomenon itself, we will subtract out the static contribution of the image itself, leaving only the ripple phenomenon.

      Could you provide a more nuanced description of alternative roles for top-down feedback, beyond being used exclusively for learning as depicted in your model?

      For the sake of simplicity, we only treat top-down inputs in our model as a source of an instructive teaching signal, the originator of generative replay events during the Sleep phase, and as the mechanism of hallucination generation. However, as discussed in a response to a previous question, in the cortex pyramidal neurons receive and respond to a mixture of top-down and bottom-up processing.

      There are a variety of theories for what role top-down inputs could play in determining network activity. To name several, top-down input could function as: 1) a denoising/pattern completion signal (Kadkhodaie & Simoncelli, 2021), 2) a feedback control signal (Podlaski & Machens, 2020), 3) an attention signal (Lindsay, 2020), 4) ordinary inputs for dynamic recurrent processing that play no specialized role distinct from bottom-up or lateral inputs except to provide inputs from higher-order association areas or other sensory modalities (Kar et al., 2019; Tugsbayar et al., 2025). Though our model does not include these features, they are perfectly consistent with our approach.

      In particular, denoising/pattern completion signals in the predictive coding framework (closely related to the Wake-Sleep algorithm) also play a role as an instructive learning signal (Salvatori et al., 2021); and top-down control signals can play a similar role in some models (Gilra & Gerstner, 2017; Meulemans et al., 2021). Thus, options 1 and 2 are heavily overlapping with our approach, and are a natural consequence of many biologically plausible learning algorithms that minimize a variational free energy loss (Rao & Ballard, 1997; Ackley et al., 1985). Similarly, top-down attentional signals can exist alongside top-down learning signals, and some models have argued that such signals can be heavily overlapping or mutually interchangeable (Roelfsema & van Ooyen, 2005). Lastly, generic recurrent connectivity (from any source) can be incorporated into the Wake-Sleep algorithm (Dayan & Hinton, 1996), though we avoided doing this in the present study due to an absence of empirical architecture exploration in the literature and the computational complexity associated with training on time series data.

      To conclude, there are a variety of alternative functions proposed for top-down inputs onto pyramidal neurons in the cortex, and we view these additional features as mutually compatible with our approach; for simplicity we did not include them in our model, but we believe that these features are unlikely to interfere with our testable predictions or empirical results.

    1. Author response:

      The following is the authors’ response to the original reviews

      We thank the reviewers for their positive and constructive comments on the manuscript. In the revised manuscript we addressed these comments, which we believe have improved the quality of our work.

      In summary:

      (1) We acknowledge the reviewer's suggestion to incorporate open-source segmentation and tracking functionalities, increasing its accessibility to a wider user base; however, these additions fall outside the primary scope of our current work, which is to provide an analytical framework for IVM data after segmentation and tracking. Developing open-source segmentation and tracking tools represents a substantial undertaking in its own right, which has been comprehensively explored in other studies (e.g. https://doi.org/10.4049/jimmunol.2100811; https://doi.org/10.7554/eLife.60547; https://doi.org/10.1016/j.media.2022.102358; https://doi.org/10.1038/s41592024-02295-6 - now cited in our revised manuscript). 

      In our analyses, we used data processed with Imaris, a commercial software that, despite its limitations, is widely used by the intravital microscopy community due to its user-friendly platform for 3D image visualization and analysis. Nevertheless, recognizing the need for compatibility with tracking data from various pipelines, we have modified our tool to accept other data formats, such as those generated by open-source Fiji plugins like TrackMate, MTrackJ, ManualTracking (https://github.com/imAIgene-Dream3D/BEHAV3D_Tumor_Profiler?tab=readme-ov-file#data-input). These updates are available in our GitHub repository and are described in the revised manuscript. 

      (2) We appreciate the reviewer #3 suggestion to incorporate additional features into our analytical pipeline. In response, we have already updated the GitHub repository to allow users to input and select which features (dynamic, morphological, or spatial) they wish to include in the analysis (https://github.com/imAIgene-Dream3D/BEHAV3D_Tumor_Profiler?tab=readmeov-file#feature-selection ). In the revised manuscript, we highlighted this new functionality and provided examples using alternative datasets to demonstrate the application of these features.

      (3)  We appreciate the constructive feedback of reviewers #1 and #2 regarding the statistical analysis and interpretation of the data presented in Figures 3 and 4. We understand the importance of clarity and rigor in data analysis and presentation, and we addressed the concerns raised in the revised version of the manuscript.

      (4) We appreciate reviewer #1's suggestion regarding the inclusion of demo data, as we believe it would greatly enhance the usability of our pipeline. We acknowledge that this was an oversight on our part. To address this, we have now added demos to our GitHub repository (https://github.com/imAIgene-

      Dream3D/BEHAV3D_Tumor_Profiler/tree/BEHAV3D_TP-v2.0/demo_datasets). In the revised manuscript, we referenced this addition and present new figures with examples of these demo’s processing different IVM dataset (2D/3D, different tumors and healthy tissues). Additionally, we have provided processed DMG IVM movie samples in an imaging repository.

      (5) Finally, we made some small changes to the manuscript based on the reviewers’ feedback.

      Below we provide a point-by-point response to the reviewers’ comments

      Reviewer #1 (Public review):

      Comment #1: A key limitation of the pipeline is that it does not overcome the main challenges and bottlenecks associated with processing and extracting quantitative cellular data from timelapse and longitudinal intravital images. This includes correcting breathing-induced movement artifacts, automated registration of longitudinal images taken over days/weeks, and accurate, automated segmentation and tracking of individual cells over time. Indeed, there are currently no standardised computational methods available for IVM data processing and analysis, with most laboratories relying on custom-built solutions or manual methods. This isn't made explicit in the manuscript early on (described below), and the researchers rely on expensive software packages such as IMARIS for image processing and data extraction to feed the required parameters into their pipeline. This limitation unfortunately reduces the likely impact of BEHAV3D-TP on the IVM field. 

      As highlighted above, the tool does not facilitate the extraction of quantitative kinetic cellular parameters (e.g. speed, directionality, persistence, and displacement) from intravital images. Indeed, to use the tool researchers must first extract dynamic cellular parameters from their IVM datasets, requiring access to expensive software (e.g. IMARIS as used here) and/or above-average computational expertise to develop and use custom-made open-source solutions. This limitation is not made explicit or discussed in the text.

      We acknowledge the reviewer's suggestion to incorporate open-source segmentation and tracking functionalities, increasing its accessibility to a wider user base; however, these additions fall outside the primary scope of our current work and represent a substantial undertaking in their own right. Several studies (e.g., Diego Ulisse Pizzagalli et al., J Immunol (2022); Aby Joseph et al., eLife (2020); Molina-Moreno et al., Medical Image Analysis (2022); Hidalgo-Cenalmor et al., Nat Methods (2024); Ershov et al., Nat Methods (2022)) have comprehensively addressed these topics, and we now reference them in the revised manuscript to provide readers with relevant background.

      The objective of our manuscript is not to develop a complete segmentation or tracking pipeline but rather to introduce an analytical framework capable of extracting enhanced insights from the data generated by existing tools. This goal arises from our observations of the field: despite significant investment in image processing, researchers often rely on simplistic approaches, such as averaging single parameters across conditions, which can obscure tumor heterogeneity and spatial behavioral dynamics within the tumor microenvironment.

      Our current tool focuses on providing this much-needed analytical capability. For our analysis we used Imaris, a widely utilized software in the intravital microscopy (IVM) community, known for its intuitive 3D visualization and analysis platform despite certain limitations. 

      In our own literature search of recent IVM studies published by leading laboratories in high-impact journals, we found that close to half used Imaris, while the remainder primarily relied on manual workflows with Fiji plugins. Thus, we consider it valuable to offer a pipeline compatible with such commonly used software, given its prevalence in the field.

      However, following the suggestion of the reviewer, and to enhance the tool’s flexibility and compatibility, we have expanded the pipeline to accept data formats generated by open-source Fiji plugins, such as TrackMate, MTrackJ, and ManualTracking. These updates are detailed in the revised manuscript and are implemented in our GitHub repository (https://github.com/imAIgene-Dream3D/BEHAV3D_Tumor_Profiler?tab=readme-ov-file#data-input ), where we also provide several demos using TrackMate and Imaris processed data. This addition demonstrates our tool's capability to integrate with segmented and tracked datasets from diverse platforms, increasing its applicability to a broader range of researchers using both commercial and open-source pipelines.

      Comment #2: The number of cells (e.g. per behavioural cluster), and the number of independent mice, represented in each result figure, is not included in the figure legends and are difficult to ascertain from the methods.

      We appreciate the reviewer's constructive feedback regarding the clarity of the number and type of replicates used in our analyses. In the revised manuscript, we have included detailed information in the figure legends and the number of independent mice represented in each figure legend to ensure transparency. Regarding the number

      of cells, we have indicated the total number of processed cells in Figure 2b legend (953 cells). Additionally, we have now included figures (Sup Fig 4c, Sup Fig 5e-g, Fig 5c,e, Sup Fig 6 c,d) for each cluster, where individual dots represent the individual cell tracks with color indicating the position and the shape indicating individual mice.

      Comment #3: The data used to test the pipeline in this manuscript is currently not available, making it difficult to assess its usability. It would be important to include this for researchers to use as a 'training dataset'.

      As stated above we acknowledge that this was an oversight on our part and thank the reviewer for pointing this out. To address this, we have now added demo data to our GitHub repository (BEHAV3D_Tumor_Profiler/demo_datasets at main · imAIgeneDream3D/BEHAV3D_Tumor_Profiler · GitHub). In the revised manuscript we have referenced this addition in the Data availability section. Since we included now processing with Fiji as well, we provide 4 demo datasets (https://github.com/imAIgeneDream3D/BEHAV3D_Tumor_Profiler/tree/main/demo_datasets), one processed with Imaris in 3D; and one with CellPose2.0 and Trackmate in 2D; one processed with µSAM and Trackmate in 3D and one manually processed with MtrackJ in 2D . Moreover, we now provide Imaris-processed DMG IVM movie samples in an open-source repository.

      Comment #4: Precisely how the BEHAV3D-TP large-scale phenotyping module can map large-scale spatial phenotyping data generated using LSR-3D imaging data and Cytomap to 3D intravital imaging movies is unclear. Further details in the text and methods would be beneficial to aid understanding.

      We appreciate the reviewer’s comment and in the revised manuscript we have now provided details in the methods section “Tumor large-scale spatial phenotyping with Cytomap” to clarify how the BEHAV3D-TP module maps LSR-3D and Cytomap data to 3D intravital imaging movies:

      “To map the assigned regions onto IVM movies, a 3D image of the cluster distribution within the tumor was generated and exported for each sample (Figure Supplement 5a). Next, regions within the IVM movies were visually matched to the corresponding regions identified by the Large-Scale Phenotyping module of Cytomap (Figure 3c). For each mouse, at least one or two representative positions per matched region type were selected, cropped, and analyzed to assess tumor cell behavior, following the previously described cell tracking methodology (Imaris Cell tracking).”

      Moreover, we updated Figure 3 c to further clarify these steps.

      Comment #5: The analysis provides only preliminary evidence in support of the authors' conclusions on DMG cell migratory behaviours and their relationship with components of the tumour microenvironment. Conclusions should therefore be tempered in the absence of additional experiments and controls. 

      We appreciate the reviewer’s comment and acknowledge that our conclusions should be tempered due to the preliminary nature of our evidence. In the revised version of the manuscript we have revised our conclusions accordingly and emphasize the necessity for additional experiments and controls to further validate our findings on DMG cell migratory behaviors and their relationship with the tumor microenvironment.

      In discussion: “While our findings suggest that microenvironmental factors may influence tumor cell migration, further studies will be necessary to establish causal relationships. Additional experimental validation, such as macrophage ablation experiments, could help clarify the specific contributions of these factors.”

      Reviewer #1 (Recommendations for the authors): 

      (1) To test the ability of the pipeline to identify relevant patterns of migratory behaviours additional 'control' experiments would be helpful e.g. comparing non-invasive vs invasive tumour cell lines, artificially controlling migratory behaviours of cells such as implanting beads soaked in factors that would attract/repel cells? 

      (2) Does the pipeline work well for a variety of cell types/contexts? e.g. can it identify and cluster more subtle migratory behaviours such as non-tumour cells during tissue development or regeneration conditions? 

      We appreciate the reviewer’s valuable suggestions. In the revised manuscript, we have included additional examples demonstrating the capability of our pipeline to investigate heterogeneous cell behavior across two additional experimental setups:

      (1) We have now evaluated our BEHAV3D TP heterogeneity module using IVM data from breast cancer cell lines with varying migratory capacities (DOI: 10.1016/j.yexcr.2019.04.009). In these datasets, our pipeline extends beyond predefined characteristics based solely on speed, enabling the identification of distinct cell populations. Notably, our analysis reveals that the breast cancer lines exhibit different proportions of different migratory behaviors such as Fast, Intermediate, Very slow and Static (Supplementary Fig 1).

      (2) We have now evaluated our BEHAV3D TP heterogeneity module using IVM data from healthy breast epithelial cells (DOI: 10.1016/j.celrep.2024.115073), where we identify distinct morhophynamic epithelial cell populations in the terminal end but of the mammary gland that have a distinct distribution among Hormone receptor (HR) + and HR- terminal end but cells.

      (3) To support biological conclusions could the authors show that ablating tumourassociated macrophages or vasculature alters the migratory patterns of nearby tumour cells? 

      We appreciate the reviewer's suggestion regarding the potential effects of ablating tumor-associated macrophages or vasculature on the migratory patterns of nearby tumor cells. While these experiments would functionally validate the observations made by our method, we would like to clarify that the primary focus of our study was on the development and application of computational tools for behavioral analysis and thus we consider that delving deeper in understanding the biology behind our observation is out of the scope of the current study. However, as mentioned previously, we have carefully tempered our conclusions to acknowledge the limitations of our current study. In the revised manuscript, we explicitly highlight that experiments involving the ablation of tumor-associated macrophages or vasculature would be crucial for further understanding the biological relevance of our findings.

      Minor corrections to text: 

      (4) Line 63 - are references formatted correctly?

      Thank you for pointing out this error. We have corrected it in the revised manuscript.

      (5) Lines 161 -162 - 'intravitally imaged' used twice in a sentence.

      Thank you for pointing out the typo. We have corrected it in the revised manuscript.

      Reviewer #2 (Public review):

      Comment#1: The strength of democratizing this kind of analysis is undercut by the reliance upon Imaris for segmentation, so it would be nice if this was changed to an open-source option for track generation.

      As noted in our previous response to Reviewer #1, we would like to point out that although Imaris is a commercial software, it is widely used in the intravital microscopy community due to its user-friendly interface. We conducted a literature review to evaluate this aspect and below we include references from leading laboratories in the IVM field that utilize Imaris. One of its key advantages, which we also utilized, is semi-automated data tracking that allows for manual corrections in 3D—a process that can be more challenging in other open-source software with less effective data visualization.

      However, we recognize that enhancing our pipeline's compatibility with open-source options is important. To this end, we have updated our tool to support 2D and 3D data formats generated by open-source Fiji plugins like TrackMate, MTrackJ, and ManualTracking, improving compatibility with various segmentation and tracking pipelines (https://github.com/imAIgene-Dream3D/BEHAV3D_Tumor_Profiler?tab=readme-ov-file#data-input ). In the revised manuscript, we describe the new functionality and demonstrate the operation of the BEHAV3D-TP heterogeneity module across various IVM datasets, processed in both 2D and 3D with different processing pipelines (Supplementary Fig 1-3). This includes CellPose 2.0 and the novel 'Segment Anything' model, followed by TrackMate tracking, applied to both tumor and healthy IVM data. Moreover we have developed a new web application that integrates morphological and tracking information from Segment Anything segmentation and Trackmate tracking, depicted in Supplementary Fig 3 a (https://morphotrack-merger.streamlit.app/ ). Additionally, we have updated the introduction to better clarify the scope of our study and include references to existing image processing solutions.

      Comment#2: The main issue is with the interpretation of the biological data in Figure 3 where ANOVA was used to analyse the proportional distribution of different clusters. Firstly the n is not listed so it is unclear if this represents an n of 3 where each mouse is an individual or whether each track is being treated as a test unit. If the latter this is seriously flawed as these tracks can't be treated as independent. Also, a more appropriate test would be something like a Chi-squared test or Fisher's exact test. Also, no error bars are included on the stacked bar graphs making interpretation impossible. Ultimately this is severely flawed and also appears to show very small differences which may be statistically different but may not represent biologically important findings. This would need further study.

      We appreciate the reviewer’s insightful comments regarding the interpretation of the biological data in Figure 3. 

      To clarify, each imaged position is considered an independent biological replicate (n = 18 from a total of 6 mice). We acknowledge that the description of the statistical methods and the experimental units was not sufficiently clear in the previous version. In our original submission, we used an ANOVA to test whether the proportion of each behavioral cluster differed across the tumor microenvironment regions. Post hoc pairwise comparisons were performed using Tukey’s test, with the results shown in Supplementary Figure 2d (currently Fig 3d). However, we agree with the reviewer that this approach may be misleading when paired with stacked bar plots that lack error bars, as it can obscure individual variability and does not explicitly represent statistical uncertainty.

      In the revised manuscript, we present the data as boxplots with individual data points, where each dot represents an imaged position, and the shape corresponds to a specific mouse. In Figure 3 d the y-axis displays the normalized percentage of each cluster across TME regions, expressed as z-scores. This normalization corrects for inter-mouse variability and facilitates a comparison of the relative distribution of clusters across TME regions, independent of the overall abundance differences between mice. We performed an ANOVA with Tukey's post hoc test for each individual behavioral cluster to assess differences across TME regions. Additionally, for transparency, in Supplementary Figure 5 d we provide the raw percentage values. The legends provide the number of positions and mice included in the analysis. 

      Comment#3:  Figure 4 has similar statistical issues in that the n is not listed and, again, it is unclear whether they are treating each cell track as independent which, again, would be inappropriate. The best practice for this type of data would be the use of super plots as outlined in Lord et al. (2020) JCI - SuperPlots: Communicating reproducibility and variability in cell biology.

      We appreciate the reviewer’s comments and suggestions regarding Figure 4. In this case as we are comparing overall the behavioral clusters features, each individual cell is treated as a unit. In the revised manuscript, we have clarified this point in the figure legend and incorporated plots in Figure 4c and 4e, indicating the mouse and imaging position each data point originates from. This enhances the visualization of reproducibility and variability in our data, demonstrating that the results are consistent across multiple mice and positions and are not driven by a single mouse or imaging position.

      Comment#4: The main issue that this raises is that the large-scale phenotyping module and the heterogeneity module appear designed to produce these statistical analyses that are used in these figures and, if they are based on the assumption that each track is independent, then this will produce inappropriate analyses as a default.

      We appreciate the reviewer’s comment, although we are unclear about the specific concern being raised. To clarify, in our large-scale phenotyping analysis, each position is assigned to a TME niche based on the CytoMAP analysis and the workflow outlined in Figure 3c. Multiple positions are imaged per mouse. For each position, we measure the proportion of tumor cells exhibiting a specific behavioral phenotype, and these proportions are subsequently used for statistical analysis (Figure 3 d). 

      In contrast, in Supplementary Fig. 5e-g, we treat each cell track as an individual unit, grouping them by their assigned large-scale region. Here, we assess whether differences between regions can be detected using a conventional single-feature analysis—a more traditional approach. However, we find that this method loses important behavioral patterns and distinctions that BEHAV3D-TP captures.

      We hope that this explanation, along with the modifications made to the figures and figure legends, provides greater clarity.  

      Reviewer #3 (Public review):

      Comment #1: The most challenging task of analyzing 3D time-lapse imaging data is to accurately segment and track the individual cells in 3D over a long time duration. BEHAV3D Tumor Profiler did not provide any new advancement in this regard, and instead relies on commercial software, Imaris, for this critical step. Imaris is known to have a very high error rate when used for analyzing 3D time-lapse data. In the Methods section, the authors themselves stated that "Tumor cell tracks were manually corrected to ensure accurate tracking". Based on our own experience of using Imaris, such manual correction is tedious and often required for every time step of the movie. Therefore, Imaris is not a satisfactory tool for analyzing 3D time-lapse data. Moreover, Imaris is expensive and many research labs probably can't afford to buy it. The fact that BEHAV3D Tumor Profiler critically depends on the faulty ImarisTrack module makes it unclear whether the BEHAV3D tool or the results are reliable.

      If the authors want to "democratize the analysis of heterogeneous cancer cell behaviors", they should perform image segmentation and tracking using open-source codes (e.g., Cellpose, Stardisk & 3DCellTracker) and not rely on the expensive and inaccurate ImarisTrack Module for the image analysis step of BEHAV3D.

      We appreciate the reviewer’s comments on the challenges of segmenting and tracking individual cells in 3D time-lapse imaging data. As mentioned previously (please refer to comment #1 to reviewer #1), our primary focus is to develop an analytical tool for comprehensive data analysis rather than developing tools for image processing. However to enhance accessibility, we have updated our tool to support data formats from open-source Fiji plugins, such as TrackMate, which will benefit users without access to commercial software (https://github.com/imAIgeneDream3D/BEHAV3D_Tumor_Profiler?tab=readme-ov-file#data-input ). In Supplementary Figures 1, 2, and 3, we present IVM data from different sources, processed using three distinct methods: MTrackJ (Supplementary Fig. 1), Cellpose + TrackMate (Supplementary Fig. 2), and µSAM + TrackMate (Supplementary Fig. 3). The latter two represent state-of-the-art deep learning approaches.

      On the other hand, while we recognize the limitations of Imaris, it remains widely used in the intravital microscopy community due to its user-friendly interface for 3D visualization and semi-automated segmentation capabilities. Since no perfect tracking method currently exists, we initially utilized Imaris for its ability to allow manual correction of faulty tracks, ensuring the reliability of our results. This approach, not only widely used (see above) but was the best available option when we began our analysis, allowing us to obtain accurate results efficiently.

      In the revised manuscript, we clarify the scope of our study and provide information on both Imaris and alternative processing options to strengthen the reliability of our findings:

      In introduction: “While significant efforts have been made to develop opensource segmentation and tracking tools for live imaging data, including IVM22–27 fewer tools exist for the unbiased analysis of tumor dynamics. One major barrier is that implementing such analytical methods often requires substantial computational expertise, limiting accessibility for many biomedical researchers conducting IVM experiments. To bridge this gap, we present BEHAV3D Tumor Profiler (BEHAV3D-TP)  by providing a robust, user-friendly tool that allows researchers to extract meaningful insights from dynamic cellular behaviors without requiring advanced programming skills.”

      In the Methods, we describe now describe not only Imaris processing pipeline, but also the µSAM segmentation pipelines and reference to CellPose IVM processing, which are combined with TrackMate for tracking. Additionally, to integrate morphological information from µSAM with tracking data from TrackMate, we developed a web tool to merge the outputs from both processing steps: https://morphotrack-merger.streamlit.app/  

      Comment #2: The authors developed a "Heterogeneity module" to extract distinctive tumor migratory phenotypes from the cell tracks quantified by Imaris. The cell tracks of the individual tumor cells are all quite short, indicating relatively low motility of the tumor cells. It's unclear whether such short migratory tracks are sufficient to warrant the PCA analysis to identify the 7 distinctive migratory phenotypes shown in Figure 2d. It's also unclear whether these 7 migratory phenotypes correspond to unique functional phenotypes.  

      For the 7 distinctive motility clusters, the authors should provide a more detailed analysis of the differences between them. It's unclear whether the difference in retreating, slow retreating, erratic, static, slow, slow invading, and invading correspond to functional difference of the tumor cells.

      While some tumor cells exhibit limited motility, indicated by short tracks, others demonstrate significant migratory capabilities (Figure 2 Invading and Retreating cells). This variability in tumor cell behavior is a central focus of our analysis, and our tool is specifically designed to identify and distinguish these differences. Our PCA analysis effectively captures this variability, as illustrated in Figure 2 d-f. It differentiates between cells exhibiting varying degrees of migratory behavior, including both highly and less migratory phenotypes, as well as their directionality relative to the tumor core and the persistence of their movements. Thus, we believe that our approach provides valuable insights into the distinct migratory phenotypes within the tumor microenvironment. 

      While our current manuscript does not provide explicit evidence linking each motility cluster to functional differences among the tumor cells, it is important to note that the state of the field supports the idea that cell dynamics can predict cell states and phenotypes. Research conducted by ourselves (Dekkers, Alieva et al., Nat Biotech, 2023) and others, such as Craiciuc et al. (Nature, 2022) and Freckmann et al. (Nat Comm, 2022) has shown that variations in cell motility patterns are indicative of underlying functional characteristics. For instance, cell morphodynamic features have been shown to reflect differences in cell types, T cell targeting states (Dekkers, Alieva et al., Nat Biotech, 2023), immune cell types (Crainiciuc et al. (Nature, 2022)), tumor metastatic potential, and drug resistance states (Freckmann et al. (Nat Comm, 2022)). In the revised manuscript, we have referenced relevant studies to underscore the biological significance of these behaviors. By doing so, we hope to clarify the potential implications of our findings and strengthen the overall narrative of our research:

      In discussion: “While our current study does not provide direct functional validation of the distinct motility clusters identified, existing literature strongly supports the notion that cell dynamics can serve as a proxy for functional states and phenotypic heterogeneity. Prior work, including studies by our group[19,66]  as well as Crainiciuc et al.[35] and Freckmann et al.[20], has demonstrated that variations in cell motility patterns can reflect underlying functional characteristics. Specifically, cell morpho-dynamic features have been shown to correlate with differences in cell type identity, T-cell engagement, metastatic potential, and drug resistance states. This growing body of evidence suggests that tumor cell behavior, as captured by BEHAV3D-TP, may serve as a predictive tool for deciphering functional tumor heterogeneity. Future studies integrating transcriptomic or proteomic profiling of motility-defined subpopulations could further elucidate the biological significance of these behavioral phenotypes.”

      Comment #3: Using only motility to classify tumor cell behaviours in the tumor microenvironment (TME) is probably not sufficient to capture the tumor cell difference. There are also other non-tumor cell types in the TME. If the authors aim to develop a computational tool that can elucidate tumor cell behaviors in the TME, they should consider other tumor cell features, e.g., morphology, proliferation state, and tumor cell interaction with other cell types, e.g., fibroblasts and distinct immune cells.

      The authors should expand the scale of tumor behavior features to classify the tumor phenotype clusters, e.g., to include tumor morphology, proliferation state, and tumor cell interaction with other TME cell types.

      We believe that using dynamic features alone is sufficient to capture differences in tumor behavior, as demonstrated by our results in Figure 2. However, we appreciate the reviewer’s suggestion to consider additional features, such as cell morphology, to finetune our analyses. To this end, we have adapted our pipeline to be compatible with any dynamic, morphologic or spatial features present in the data. In the revised manuscript we showcase this new addition with the analyses of two new dataset: 2D IVM data from healthy epithelial breast cells (Supplementary Fig 2) and 3D IVM data from adult gliomas (Supplementary Fig 3). These analyses identified cells with specific morphodynamic characteristics, which exhibited distinct kinetic behaviors or spatial distributions.

      However, we would like to point out that not all features may provide informative insights and that a wide range of features can instead introduce biologically irrelevant noise, making interpretation more challenging. For instance, in 3D microscopy, the zaxis resolution is typically lower, which can lead to artifacts like elongation in that direction. Adding morphological features that capture this may skew the analysis. Therefore, we believe that incorporating additional features should be approached with caution. We clarify these considerations in the revised manuscript to better guide users in utilizing our computational tool effectively:

      In discussion: “In addition to motility-based classification, features such as tumor cell morphology, proliferation state, and interactions with the tumor microenvironment can further refine tumor phenotyping. BEHAV3D-TP allows for the selection of diverse feature types, supporting datasets that include both dynamic, morphological and spatial parameters. However, we recognize that expanding the feature set may introduce biologically irrelevant noise, particularly in 3D microscopy data where limited z-axis resolution can lead to morphological artifacts. This highlights the potential need in the future to include unbiased feature selection strategies, such as bootstrapping methods67, to ensure the identification of meaningful and biologically relevant parameters. Careful consideration of these aspects is key to maximizing the interpretability and predictive value of analyses performed with BEHAV3D-TP.”

      Comment #4: The authors have already published two papers on BEHAV3D [Alieva M et al. Nat Protoc. 2024 Jul;19(7): 2052-2084; Dekkers JF, et al. Nat Biotechnol. 2023 Jan;41(1):60-69]. Although the previous two papers used BEHAV3D to analyze T cells, the basic pipeline and computational steps are similar, in particular regarding cell segmentation and tracking. The addition of a "Heterogeneity module" based on PCA analysis does not make a significant advancement in terms of image analysis and quantification.

      We want to emphasize that we have no intention of duplicating our previous publications. In this manuscript, we have consistently cited our foundational papers, where BEHAV3D was first developed for T cell migratory analysis in in vitro settings. In the introduction, we clearly state that our earlier work inspired us to adopt a similar approach for analyzing cell behavior in intravital microscopy (IVM) data, addressing the specific needs and complexities of analyzing tumor cell behaviors in the tumor microenvironment.

      Importantly, our new work provides several key advancements: 1) a pipeline specifically adapted for intravital microscopy (IVM) data; 2) integration of spatial characteristics from both large-scale and small-scale phenotyping; and 3) a zero-code approach designed to empower researchers without coding skills to effectively utilize the tool. We believe that these enhancements represent meaningful progress in the analysis of cell behaviors within the tumor microenvironment which will be valuable for the IVM community. We ensure that these points are clearly articulated in the revised manuscript:

      In introduction: “In line with this concept of characterizing cellular dynamic properties for cell classification, we have previously developed an analytical platform termed BEHAV3D 19,21 allowing to perform behavioral phenotyping of engineered T cells targeting cancer. While BEHAV3D was initially developed to analyze T cell migratory behavior under controlled in vitro conditions, we sought to expand its application to investigate tumor cell behaviors in IVM data, where the complexity of the TME presents distinct analytical challenges. This manuscript builds on our foundational work but represents a significant advancement by adapting the pipeline specifically for IVM datasets.”

      Reviewer #3 (Recommendations for the authors): 

      (1) If the authors want to "democratize the analysis of heterogeneous cancer cell behaviors", they should perform image segmentation and tracking using open-source codes (e.g., Cellpose, Stardisk & 3DCellTracker) and not rely on the expensive and inaccurate ImarisTrack Module for the image analysis step of BEHAV3D. 

      We thank the reviewer for this recommendation and as stated above we recognize that enhancing our pipeline's compatibility with open-source options is important. To this end, we have updated our tool to support data formats generated by open-source Fiji plugins like TrackMate, MTrackJ, and ManualTracking, improving compatibility with various segmentation and tracking pipelines (https://github.com/imAIgeneDream3D/BEHAV3D_Tumor_Profiler?tab=readme-ov-file#data-input ). In the revised manuscript, we detail this new functionality and demonstrate the operation of the BEHAV3D-TP heterogeneity module using an example dataset of glioma tumors.

      Additionally, we have updated the introduction to better clarify the scope of our study (See comment #1 from Review #3) and include references to existing image processing solutions.

      (2) For the 7 distinctive motility clusters, the authors should provide a more detailed analysis of the differences between them. It's unclear whether the difference in retreating, slow retreating, erratic, static, slow, slow invading, and invading correspond to functional difference of the tumor cells. 

      As noted in the comment above, the revised manuscript now incorporates references to relevant literature that support our understanding that behavioral differences among cells are driven by their underlying functional differences (See comment #2 from Reviewer #3). Additionally, we would like to point to Figure 2d and Supplementary Fig 4 c that provide evidence of the functional distinctions between the identified clusters.

      (3) The authors should expand the scale of tumor behavior features to classify the tumor phenotype clusters, e.g., to include tumor morphology, proliferation state, and tumor cell interaction with other TME cell types.

      We thank the reviewer for this valuable suggestion. In the revised manuscript, we have added the flexibility to incorporate a wide range of features, including morphological ones, and enabled users to select the specific features they wish to include in their analysis. To illustrate this functionality, we have included 2 example dataset analyzed using this approach (See comment #3 from Reviewer #3). Additionally, as indicated above we emphasize the importance of careful selection and interpretation of features, as improper choices may lead to biologically irrelevant results. This clarification is intended to ensure that users apply the tool thoughtfully and derive meaningful insights.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review):

      We thank reviewer 1 for the helpful comments. As indicated in the responses below, we have taken all comments and suggestions into consideration in this revised version of the manuscript.

      Weaknesses:

      While this study convincingly describes the phenotype seen upon Drp1 loss, my major concern is that the mechanism underlying these defects in zygotes remains unclear. The authors refer to mitochondrial fragmentation as the mechanism ensuring organelle positioning and partitioning into functional daughters during the first embryonic cleavage. However, could Drp1 have a role beyond mitochondrial fission in zygotes? I raise these concerns because, as opposed to other Drp1 KO models (including those in oocytes) which lead to hyperfused/tubular mitochondria, Drp1 loss in zygotes appears to generate enlarged yet not tubular mitochondria. Lastly, while the authors discard the role of mitochondrial transport in the clustering observed, more refined experiments should be performed to reach that conclusion.

      It would be difficult to answer from this study whether Drp1 plays a role beyond mitochondrial fission in zygotes. However, the reasons why Drp1 KO zygotes differ from the somatic Drp1 KO model can be discussed as follows.

      First, the reviewer mentioned that the loss of Drp1 in oocytes leads to hyperfused/tubular mitochondria, but in fact, unlike in somatic cells, the EM images in Drp1 KO oocytes show enlarged mitochondria rather than tubular structures (Udagawa et al., Curr Biol. 2014, PMID: 25264261, Fig. 2C and Fig. S1B-D), as in the case of zygotes in this study. Mitochondria in oocytes/zygotes have the shape of a small sphere with an irregular cristae located peripherally. These structural features may be the cause of insensitivity or resistance to inner membrane fusion the resultant failure to form tubular mitochondria as seen in somatic cell models. Nonetheless, quantitative analysis of EM images in the revised version confirmed that the mitochondria of Drp1-depleted embryos were not only enlarged but also significantly elongated (Figure 2J-2M). Therefore, in Drp1-depleted embryos, significant structural and functional (e.g., asymmetry between daughters) changes in mitochondria were observed, and these are expected to lead to defects in the embryonic development.

      As for mitochondrial transport, we do not fully understand the intent of this question, but we do not entirely rule out mitochondrial transport. At least clustered mitochondria did not disperse again, but how mitochondria behave through the cytoskeleton within clusters will require further study, as the reviewer pointed out.

      Reviewer #1 (Recommendations For The Authors):

      (1) The authors show no effect of Myo19 Trim-Away, yet it remains unclear whether myo19 is involved in the positioning of mitochondria around the spindle. Judging by their co-localization during that stage, it might be. Therefore, in the absence of myo19, mitochondria might remain evenly distributed throughout mitosis, thus passively resulting in equal partitioning to daughter cells, with no severe developmental defects. Could the authors show a video of the whole process and discuss it?

      We have newly performed live imaging of mitochondria and chromosomes in Myo19 Trim-Away zygotes (n=13). As shown in Figure 1-figure supplement 2 and Figure 1-Video 2, there were no obvious changes in mitochondrial (and chromosomal) dynamics throughout the first cleavage and no significant mitochondrial asymmetry was observed, Therefore, we conclude that depletion of Myo19 does not cause mitochondrial asymmetry during embryonic cleavage. These results are described in the revised manuscript (Line 218-221).

      (2) Mitochondrial aggregation upon Drp1 depletion should be characterized in more detail: for example, % of mitochondria free, % in small clusters (> X diameter), and % in big clusters (>Y diameter).

      In the revised version, mitochondrial aggregation has been quantified by comparing the cluster size and number in control, Drp1 Trim-Away and Drp1 Trim-Away embryos expressing exogenous Drp1 (mCh-Drp1) (Figure 2G, 2H). In control embryos, mitochondria were interspersed in a large number of small clusters, while in Drp1-depleted embryos, mitochondria became highly aggregated into a small number of large clusters that was reversed by expression of mCh-Drp1. These results are described in the revised manuscript (Line 242-245).

      (3) The discrepancies with parthenogenetic embryos derived from Drp1 (-/-) parthenotes should be commented on. Quantification of the dimensions of the clusters would help establish the degree of similarity/difference. Could the authors comment on their hypothesis as to why the clusters are remarkably larger in Drp1 depleted zygotes?

      In the revised version, we have quantified the mitochondrial aggregation in Drp1 KO parthenotes (Figure 2-figure supplement 1; the data for Drp1 KO parthenotes has been reorganized into the supplemental figure, due to lack of space in figure 2 caused by the addition of quantitative data for Drp1 Trim-Away embryos). The size of mitochondrial clusters in Drp1 KO parthenotes was significantly increased compared to controls, but as the reviewer noted, mitochondrial aggregation appears to be moderate compared to that in Drp1-depleted embryos. The phenotypic discrepancies in two Drp1-deficient embryo models is discussed below.

      First, it is clear that phenotypic severity of Drp1 KO oocytes is dependent on the age of the female. Indeed, oocytes collected from 8-week-old female arrested meiosis after NEB, mainly due to marked mitochondrial aggregation (Udagawa et al., Curr Biol. 2014, PMID: 25264261), whereas oocytes from juvenile female completed meiosis (Adhikari et al., Sci Adv. 2022, PMID: 35704569), and thus Drp1 KO pathenotes were obtained from juvenile female in the present study. Comparison of mitochondrial morphology in Drp1 KO oocytes in both papers also suggests that mitochondrial aggregation in adult mice is more intense (Udagawa et al., Curr Biol. Fig. 2A) than in juvenile mice (Adhikari et al., Sci Adv. 2022: Fig. 1G, 1H), and appears to be similar to Drp1-depleted embryos in this study (Figure 2E). There may be differences in the level of Drp1 depletion in these Drp1-deficient oocytes/zygotes. Similar results occurring between juvenile and adult KO female have been reported in a previous paper (Yueh et al., Development 2021, PMID: 34935904), as adult-derived Smac3<sup>Δ/Δ<?sup> zygotes arrested at the 2-cell stage, whereas juvenile-derived Smac3<sup>Δ/Δ<?sup> zygotes have developmental competence comparable to the wild type. Remarkably, the SMC3 protein levels in juvenile Smac3<sup>Δ/Δ<?sup> oocytes was also comparable to Smc3<sup>fl/fl</sup>. The authors surmised that the decline maternal SMC3 between juvenile and sexual maturity is probably due to the continuous induction of the promoter-Cre driver, suggesting that similar induction may also occur in Drp1 KO oocytes. In addition, we also observed not only age differences but also batch differences in Drp1 KO oocytes (and resulting embryos) such that little mitochondrial aggregation was observed in oocytes collected from some juvenile KO colonies. Therefore, for KO models showing age (sexual maturation)-dependent gradual phenotypic changes, Trim-way may be an approach that provides more reproducible results as it induces acute degradation of maternal proteins.

      (4) Mitochondrial clusters in Drp1 trim-away zygotes resemble those seen when defects in mitochondrial positioning are obtained by TRAK2 induction (PMID: 38917013), pointing again to a role of actin in the clustering process. Could the authors explore the role of actin further?

      TRAK2 and microtubule-dependent mechanisms may also be involved in mitochondrial dynamics during the first cleavage division, possibly in association with migration of two pronuclei. Although the mitochondrial aggregation induced by TRAK2 overexpression is similar to that in Drp1-depleted embryos, it is unlikely that changes at the EM level occurred as seen in Drp1-depleted embryos (enlarged mitochondria, etc.). In addition, in TRAK2-overexpressing embryos, rather than uneven partitioning of mitochondria, the daughter blatomeres themselves were uneven in size after cleavage, making it difficult to precisely assess the similarity between the two models.

      Regarding the role of F-actin, we show that the subcellular distribution of cytoplasmic actin overlaps with that of mitochondria throughout the first cleavage and seems to accumulate in aggregated mitochondria, particularly during the mitotic phase, as higher correlation was observed (Figure 1E). Although it was not observed that actin and the myo19 motor regulate mitochondrial partitioning, as reported in somatic cell-based studies, it is possible that actin accumulated in mitochondria may be indirectly involved in mitochondrial dynamics via mitochondrial fission. For example, inverted formin 2 (INF2) enhance actin polymerization and is required for efficient mitochondrial fission as an upstream function of Drp1 (Korobova et al., Science 2013, PMID: 23349293). In the revised manuscript, we have added the description on this point. (Line 452-456)

      (5) Electron microscopy images showed indeed aberrant morphology of the mitochondria, yet not a hyperfused morphology. Aspect ratio (long/short axis) quantification should be included, besides the current measurement, since mitochondria in Drp1 trim-away look bigger yet as round as in the control.

      In the revised version, detailed quantitative data on EM images has been added (Figure 2J-2M). In Drp1 depleted embryos, significant increases were observed in both the major and minor axes of mitochondria. As the reviewer noted, we also assumed that mitochondria in depleted embryos were enlarged rather than elongated, but the quantification of aspect ratio shows that significant elongation occurred. These results has been described in the revised manuscript (Line 252-256).

      (6) Why are mitochondria in golgi-mcherry-expressing cells showing a different morphology of the clusters?

      As noted by the reviewer, compared to other mitochondrial images, Drp1-depleted embryos expressing Golgi-mCherry appear to have less mitochondrial aggregation. The exact reason is not known, but may be due to inter-lot variation of Trim21 mRNA used in this experiment. Nevertheless, substantial mitochondrial aggregation was observed compared to the control, which does not seem to affect the conclusion.

      (7) Authors comment on ROS being enriched (highly accumulated) in mitochondria. However, while quantification is missing, it might seem that ROS are equally distributed in control or Drp1 Trim-Away embryos. Could the authors quantify ROS signal inside and outside of the mitochondria, perhaps using a mask drawn by mitotracker? Furthermore, it would make these data more convincing to artificially induce/deplete ROS to validate the sensitivity of the technique to variations. Also, why is ROS pattern referred to as ectopic?

      Thank you for your useful suggestions. In the revised version, masked binary images were created from mitochondrial images to quantify ROS levels inside and outside mitochondria (Line 734-741). The result shows the accumulation of ROS to mitochondria in Drp1-depleted embryos (Figure 4-figure supplement 1E). The term ectopic was used to mean excessive accumulation of ROS in the mitochondria compared to normal embryos, but has been deleted as it is not very accurate.

      Minor comments:

      (A) Video 1: images at t=-00:20 and t=00:00 of the mtGFP are actually the same images as H2B-mCherry.

      Probably a faulty filter/shutter control failed to capture GFP fluorescence at these times. It appears that the autocontrast function detected a small amount of mCherry fluorescence leakage. It would be possible to replace it with another video, but as the relevant frame were unrelated to the analysis, the previous video was used as is. The same problem also occurs in the newly added Myo19-depleted zygote movie (Figure 1-Video 2, 03:15).

      (B) Could you calculate the degree of colocalization between mt-GFP and ER-mCherry in ctrl and Drp1 trim-away? While it is apparent that ER is somehow more associated with mitochondrial clusters, it would be informative to quantify it.

      Since the ER is partially confined to the mitochondrial aggregation site, it was difficult to calculate correlation coefficients from fluorescence images of mt-GFP and ER-mCherry to quantitatively assess colocalization. Instead, line scan analysis of whole mitochondrial clumps showed that the peak of the ER-mCherry signal overlaps with that of mt-GFP, but this is not the case for Golgi-mCherry or peroxisome-mCherry (Figure 2-figure supplement 2A-2C).

      (C) Regarding the developmental arrest: The quantification of the different stages at each developmental time could be more informative. For example, at E4.5 how many embryos are at each stage (2-cell, 4-cell, ... blastocyst)? Also, could the authors comment on the reduction in developmental competence in Figure 4C, regarding the blastocyst stage?

      Many arrested embryos do not maintain their morphologies and undergo a unique degenerative process over time, known as cell fragmentation. Therefore, it is difficult to accurately determine the number of each developmental stage at, for example, E4.5 days. In this study, the 2-cell stage was observed at E1.5, the 4-8 cell at E2.5-E3.0, morula at E3.5 and the blastocyst at E4.5.

      Although the rate of embryos reaching the blastocyst stage was reduced compared to that of normal embryos, the overexpression of mCh-Drp1 may explain the failure of complete restoration of developmental competence, since embryos injected solely with mCh-Drp1 mRNA also showed reduced developmental competence. For rescue experiments, the comparison with internal controls is more important and therefore we described below. This is a specific effect of Drp1 deletion because none of the internal control conditions increased arrest at the 2-cell stage and arrest was completely reversed by microinjecting Trim-away insensitive exogenous mCh-Drp1 mRNA (Line 337-340).

      (D) In lines 103 to 105, proliferation should be changed to division or development.

      In the revised version, proliferation has been changed to division (Line 103).

      (E) Could the authors reference the statement in lines 168-169?

      The following 3 references have been added (Hardy et al., 1993, PMID: 8410824; Meriano et al., 2004, PMID: 15588469; Seikkula et al., 2018, PMID: 29525505).

      (F) Line 448: "Cells lacking Drp1 have highly elongated mitochondria that cannot be divided into transportable units,..." This is clearly not the case for zygotes, so why are then these mitochondria still clustering and not transported elsewhere?

      Although it is difficult to answer this reviewer's question precisely, EM images of Drp1-depleted embryos suggest that individual mitochondria appear not only to be enlarged but also to have increased outer membrane attachment due to excessive aggregation. Thus, these large mitochondrial clumps may therefore be preventing transport.

      Reviewer #2 (Public review):

      We thank reviewer 2 for the helpful comments. As indicated in the responses below, we have taken all comments and suggestions into consideration in this revised version of the manuscript.

      Weaknesses:

      The authors first describe the redistribution of mitochondria during normal development, followed by alterations induced by Drp1 depletion. It would be useful to indicate the time post-hCG for imaging of fertilised zygotes (first paragraph of the results/Figure 1) to compare with subsequent Drp1 depletion experiments.

      In the revised version, the time after hCG has been indicated (Line 176-182). In subsequent Drp1 depletion experiments, the revised version notes that “no significant delay in cell cycle progression was observed following Drp1 depletion (data not shown) compared to control embryos (Figure 1A)” (Line 291-193). There was a slight discrepancy in the time post-hCG between live imaging and immunofluorescence analysis (Figure 1-figure supplement 1A), which may be due to manipulation of zygotes outside incubator during the microinjection of mRNA.

      It is noted that Drp1 protein levels were undetectable 5h post-injection, suggesting earlier times were not examined, yet in Figure 3A it would seem that aggregation has occurred within 2 hours (relative to Figure 1).

      As the reviewer pointed out, the depletion of Drp1 is likely to have occurred at an earlier stage. In this study, due to the injection of various mRNAs to visualize organelles such as mitochondria and chromosomes, observations were started after about 5 h of incubation for their fluorescent proteins to be sufficiently expressed. Therefore, for the Western blot analysis, samples were prepared according to the time of the start of the observation.

      Mitochondria appear to be slightly more aggregated in Drp1 fl/fl embryos than in control, though comparison with untreated controls does not appear to have been undertaken. There also appears to be some variability in mitochondrial aggregation patterns following Drp1 depletion (Figure 2-suppl 1 B) which are not discussed.

      In the revised version, mitochondrial aggregation has been quantified by comparing the cluster size and number in control, Drp1 Trim-Away and Drp1 Trim-Away embryos expressing exogenous Drp1 (mCh-Drp1) (Figure 2G, 2H). We have also quantified the mitochondrial aggregation in Drp1<sup>fl/fl</sup> and Drp1<sup>Δ/Δ</sup> parhenotes (Figure 2-figure supplement 1; note that the data for Drp1 KO parthenotes has been reorganized into the supplemental figure, due to lack of space in figure 2 caused by the addition of quantitative data for Drp1 Trim-Away embryos). Mitochondria appear to be slightly more aggregated in Drp1<sup>fl/fl</sup> embryos than in control, but no significant differences in cluster size or number were observed (data not shown). On the other hand, mitochondrial clusters in Drp1 Trim-Away embryos were remarkably larger than Drp1<sup>Δ/Δ</sup> parhenotes, Please refer to the response to reviewer 1's comment (3) for discussion of this discrepancy.

      As noted by the reviewer, compared to other mitochondrial images, Drp1-depleted embryos expressing Golgi-mCherry appear to have less mitochondrial aggregation. The exact reason is not known, but may be due to inter-lot variation of Trim21 mRNA used in this experiment. Nevertheless, substantial mitochondrial aggregation was observed compared to the control, which does not seem to affect the conclusion.

      The authors use western blotting to validate the depletion of Drp1, however do not quantify band intensity. It is also unclear whether pooled embryo samples were used for western blot analysis.

      In the revised version, the band intensities in Western blot analysis were quantified and validated the previous results (Figure 1H for Myo19 depletion, Figure 2B for Drp1 expression during preimplantation development, Figure 2D for Drp1 depletion). The number of embryos analyzed was described in Figure legends (Pooled samples ranging from 20 to 100 were used).

      Likewise, intracellular ROS levels are examined however quantification is not provided. It is therefore unclear whether 'highly accumulated levels' are of significance or related to Drp1 depletion.

      In the revised version, masked binary images were created from mitochondrial images to quantify ROS levels inside and outside mitochondria (Line 734-741). The result shows the accumulation of ROS to mitochondria in Drp1-depleted embryos (Figure 4-figure supplement 1E).

      In previous work, Drp1 was found to have a role as a spindle assembly checkpoint (SAC) protein. It is therefore unclear from the experiments performed whether aggregation of mitochondria separating the pronuclei physically (or other aspects of mitochondrial function) prevents appropriate chromosome segregation or whether Drp1 is acting directly on the SAC.

      In the revised manuscript, we have discussed this reference (Zhou et al., Nature Communications, PMID: 36513638) (Line 482-483).

      Reviewer #2 (Recommendations For The Authors):

      The authors report that disruption of F-actin organization led to asymmetry in mitochondrial inheritance, however depletion of Myo19 does not impact inheritance. The authors note in the discussion that loss of another mitochondrial motor protein, Miro, has been shown to affect mitochondrial inheritance. They suggest this may be due to reduced levels of Myo19, despite data from the present study suggesting a lack of involvement of Myo19. Given that Miro1 also interacts with microtubules, and crosstalk between actin filaments and microtubules has been reported, have the authors considered whether other motor proteins, such as KIF5, may be involved in mitochondrial movement in the zygote and therefore inheritance? Myo19 also plays a role in mitochondrial architecture. Were any differences noted at the EM level?

      During oocyte meiosis and early embryonic cleavage, kinesin-5 has been reported to be important for the formation of bipolar spindles (Fitzharris, Curr Biol., 2009, PMID: 19465601) and may have some involvement in mitochondrial dynamics. Given that the migration of two pronuclei towards the zygotic centre is dynein-dependent manner (Scheffler Nat Commun. 2021PMID: 33547291), dynein may also be involved in the process of mitochondrial accumulation around the pronuclei. Nevertheless, whether microtubule-dependent mechanisms regulate mitochondrial partitioning remains controversial. Mitochondria basically diverge from microtubules at the onset of mitosis, and indeed Miro1-deleted zygotes did not show the asymmetric mitochondrial partitioning (Lee et al., Front Cell Dev Biol. 2022, PMID: 36325364). More recently, it was reported that overexpression of TRAK2 causes significant mitochondrial aggregation in embryos (Lee et al., Proc Natl Acad Sci U S A. 2024, PMID: 36325364), but since overexpression might disrupt a regulatory balance by other motors/adaptor complexes, further investigation using TRAK2-deficient embryos is expected.

      As noted by the reviewer, myo19 seems to be important for the maintenance of mitochondrial cristae architecture and, consequently, for the regulation of mitochondrial function (Shi et al., Nat Commun. 2022, PMID: 35562374). We have not observed the EM images in myo19-depleted embryos, but we examined their membrane potential and ROS by TMRM and H2DCF staining, respectively, and confirmed that they were comparable to control embryos (data not shown). The loss of myo19 in zygotes/embryos did not cause any functional changes in mitochondria, suggesting that mitochondrial architecture may not be substantially affected either.

      Transcriptomic analysis would be useful to identify alterations in cell cycle checkpoint regulators, as well as immunofluorescence to identify changes in spindle assembly checkpoint protein recruitment.

      The present results showed that the majority of Drp1-depleted embryos arrest at the G2 stage, possibly due to cell cycle checkpoint mechanisms. Transcriptome analysis would certainly be beneficial, but eventually more detailed analysis of proteins and their phosphorylation modifications, etc. is needed for accurate assessment. These studies will be the subject of future work.

      Minor comments:

      There are many instances where the English could be improved, particularly the overuse of the word 'the'.

      We have checked the manuscript again carefully and hopefully it has been improved some.

      Line 144: replace 'took' with 'take'.

      We have corrected this in the revised version (Line 140).

      Line 157: it is unclear what is meant by 'hinders the functional importance of Drp1 in mature oocytes and embryos'.

      This description has been corrected to “complicates the functional analysis of Drp1 in mature oocytes and embryos” (Line 152-153)

      Line 198: replace with 'displayed a mitochondrial distribution pattern closely associated with'

      We have corrected this in the revised version (Line 195-196).

      Line 200: provide a time to clarify when the cytoplasmic meshwork was 'subsequently reorganized'

      In the revised version, “at the metaphase” has been added (Line 198).

      Line 204: replace 'to' with 'for'

      We have corrected this in the revised version (Line 203).

      Lines 285-87: consider rearranging the text to improve the flow.

      To improve the flow of text before and after, the following sentence has been added; We postulated that this asymmetry was due to non-uniformity in the distribution of mitochondria around the spindle (Line 295-297)

      Line 418: replace 'central' with 'centre'

      We have corrected this in the revised version (Line 430).

      Line 427: replace 'pertaining' with 'partitioning'

      We have corrected this in the revised version (Line 438).

      Line 574: clarify to what '1-5% of that of the oocytes' refers

      We have corrected it to “1-5% of the total volume of the zygote.” (Line 587-588).

      Line 619: indicate the dilution used

      We apologize for the previous incorrect description. We used a part of the extract as the template, not a dilution, and have corrected it to be accurate (Line 631-632).

      Line 634: replace 'on' with 'in' and detail in which medium embryos were mounted.

      We have corrected this in the revised version (Line 647).

      Please check all spelling in the figures.

      Figure 1J - inheritance is spelt incorrectly.

      Figure-Suppl 1, D: Interphase (PN) and (2-cell) is spelt incorrectly. G: inheritance is spelt incorrectly.

      Figure 5F - bottom section prior to cytokinesis, spindle is spelt 'spincle'

      Ensure consistency in abbreviation use (e.g. use of NEB and NEBD).

      Thank you for your careful correction of typographical errors. In the revised version, all points raised by the reviewers have been corrected.

      Reviewer #3 (Public review):

      We thank reviewer 2 for the helpful comments. As indicated in the responses below, we have taken all comments and suggestions into consideration in this revised version of the manuscript.

      Seemingly, there are few apparent shortcomings. Following are the specific comments to activate the further open discussion.

      Line 246: Comments on cristae morphology of mitochondria in Drp1-depleted embryos would better be added.

      In the revised manuscript, we have added the following comment; swollen or partially elongated mitochondria with lamella cristae structures in the inner membrane were observed in Drp1 depleted embryos. In addition, the quantification of aspect ratio (long/short axis) shows that significant mitochondrial elongation was occurred (Figure 2M). These results has been described in the revised manuscript (Line 251-256).

      - Regarding Figure 2H: If possible, a representative picture of Ateam would better be included in the figure. As the authors discussed in line 458, Ateam may be able to detect whether any alterations of local energy demand occurred in the Drp1-depleted embryos.

      Thank you for your very useful comments. Although it would be interesting to investigate whether alterations in ATP levels occurred in localized areas (e.g., around the spindle), the present study used conventional fluorescence microscope instead of confocal laser microscopy to observe ATeam fluorescence in order to quantify the fluorescence intensity in the whole embryo (or whole blastomere) and thus we currently cannot provide the images that reviewer expected. As shown in Figure-figure supplement 1C, the ATP levels tend to be higher at the cell periphery in control and at the mitochondrial aggregation areas in Drp1-depleted embryos, but it would need high resolution images using confocal microscopy to show it clearly.

      - Line 282: In Figure 3-Video 1, mitochondria were seemingly more aggregated around female pronucleus. Is it OK to understand that there is no gender preference of pronuclei being encircled by more aggregated mitochondria?

      Review of multiple videos shows that aggregated mitochondria were localized toward the cell center, but did not exhibit the behavior of preferentially concentrating near the female pronucleus.

      - Line 317: A little more explanation of the "variability" would be fine. Does that basically mean that the Ca<sup>2+</sup> response in both Drp1-depleted blastomeres were lower than control and blastomere with more highly aggregated mitochondria show severer phenotype compared to the other blastomere with fewer mito?

      We think that the reviewer's comments are mostly correct. It is clear that there is a bias in Ca<sup>2+</sup> store levels between blastomeres of Drp1 depleted embryos, However, since mitochondria were not stained simultaneously in this experiment, we cannot draw conclusions in detail, such that daughter blastomere that inherit more mitochondria have higher Ca<sup>2+</sup> stores, or that blastomere with more aggregated mitochondria have lower Ca<sup>2+</sup> stores.

      - Regarding Figure 5B (& Figure 1-figure supplement 1B): Do authors think that there would be less abnormalities in the embryos if Drp1 is trim-awayed after 2-cell or 4-cell, in which mitochondria are less involved in the spindle?

      The marked centration of mitochondrial clusters in Drp1-depleted embryos appears to be associated with migration of the pronuclei toward the cell center, which is unique to the first embryonic cleavage. Since the assembly of the male and female pronuclei at the cell center is also unique to the first cleavage, binucleation due to mitochondrial misplacement was observed only in the first cleavage. Therefore, if Drp1 is depleted at the 2-cell or 4-cell stage, chromosome segregation errors may be less frequent. However, since unequal partitioning of mitochondria is thought to occur, some abnormalities in embryonic development is likely to be observed.

      Reviewer #3 (Recommendations For The Authors):

      Specific comments

      - Line 262: "Since mitochondrial dynamics are spatially coordinated at the ER-mitochondria MCSs," adequate ref. would better be added.

      We have added an adequate reference to the revised manuscript (Friedman et al., 2011, PMID: 21885730).

      - Line 333-336: "...as assessed by the presence of the nuclear envelope." Do authors show the data? In Figure 4-figure supplement 1A, the difference of the phosphoH3-ser10 signal between control and Trim-Away group might be weak. For clarity, it would be helpful if authors indicate the different points to note in the figure.

      Although the data is not shown, nuclear staining of arrested 2-cell stage embryos exhibited clear nuclear membranes, similar to the DAPI image in Figure 4-figure supplement 1A. We have indicated that the data is not shown in the revised version (Line 345). Based on a report that phosphorylated histone H3 (Ser10) localizes in pericentromeric heterochromatin that hat can be visualized by DAPI staining in late G2 interphase cell (Hendzel et al., 1997, Chromosoma, PMID: 9362543), this study qualitatively estimated the G2 phase from the phosphorylated histone H3 signal and the DAPI counterstained images. We have noted this point in the revised figure legend (Line 1012-1014).

      Typos or points for reword/rephrase

      - Line 149: "molecular identification" may better be " molecular characteristics".

      We have corrected this in the revised version (Line 145).

      - Line 157: "hinders the functional importance" would be "implies the functional importance" or "complicates the functional analysis".

      We have corrected this in the revised version (Line 152-153).

      - Line 208: "Since the role of F-actin in many cellular events, such as cytokinesis, preclude them as targets for experimentally manipulating mitochondrial distribution, " may better be "Given many cellular roles, disruption of F-actin per se was unsuitable as a strategy for manipulating mitochondrial distribution", for example.

      We have corrected this in the revised version (Line 207-208).

      - Line 260: "with MCSs with the plasma.." may better be "with MCSs such as with the plasma..".

      We have corrected this in the revised version (Line 267-268).

      - Line 312: "distribution and segregation" may better be "distribution and the resulting segregation of the inter-organelle contacts".

      We have corrected this in the revised version (Line 324-325).

      - Line 427: "pertaining" might be "partitioning".

      We have corrected this in the revised version (Line 438).

      Line 463: "loss of Drp1 induced mitochondrial aggregation disturbs" may better be "mitochondrial aggregation induced by the loss of Drp1 disturbs".

      We have corrected this in the revised version (Line 478-479).

      - Line 752: "endoplasmic reticulum (pink) " would be " endoplasmic reticulum (aqua) ".

      We have corrected this in the revised version (Line 780).

      - Figure 5E: "(Noma 2-cell embryos)" would be "(Nomal 2-cell embryos)".

      - Figure 5F: "Mitochondrial centration prevents dual spincle assembly" would be "Mitochondrial centration prevents dual spindle assembly".

      Thank you for your careful correction of typographical errors. We have corrected all the words/expressions the reviewer pointed out in the revised version.

    1. Author response:

      The following is the authors’ response to the original reviews

      The main criticisms levied by both reviewers can be traced down to our use of a long-term video archive to assess for the effects of aging on individual chimpanzees over extended time periods. Specifically, the reviewers raised several points surrounding whether we could exclude ecological variation over years as the explanation of changes with aging, rather than aging itself. Whilst we acknowledge there are limitations to our approach, we provide a comprehensive response to these points highlighting:

      (1) Where ecological variables have been accounted for using controls (including the behaviors of other individuals, or an aging individuals’ behavior at younger ages).

      (2) Where ecological data may be missing, thus a potential limitation to our study, and further data would be beneficial.

      (3) Whether, in light of these limitations, interannual ecological variation offers a likely explanation for the behavioral changes we have identified. We provide an argument that whilst ecological data would be desirable for our study, interannual changes in ecology are unlikely to explain the trends in our data. Additionally, we explain why age-related changes, such as senescence, are more likely to underpin the patterns described in our manuscript.

      Across 1-3, we have made substantial changes to the reporting of our manuscript to ensure that our results are communicated transparently, and conclusions are made with appropriate care. We have also moved all discussion of coula-nut cracking to the supplementary materials, given the points raised by reviewers about the lack of data describing coula-nut cracking in earlier field seasons.

      We hope that these modifications will enhance both the editors’ and reviewers’ assessment of our manuscript, where we have aimed to make careful conclusions that are supported by our available data. Similarly, we have aimed to communicate the importance of our results across fields of research including primatology, evolutionary anthropology, and comparative gerontology, and hope that our research will be of use to further studies within these subfields.

      Reviewer 1 (Recommendations for the authors):

      (1) If possible, include results or a summary of the behaviour of younger adults using stone tools during the same period. It would be helpful to know if they had the same or different pattern to exclude other factors that may influence the tool use (harder nuts in a particular season, diseases, motivation for other foods, etc). 

      We include data for other individuals when analyzing attendance. However, we did not collect comparable long-term efficiency data on younger adult individuals for this study. This is, in part, due to the time constraints imposed by long-term behavior coding. Additionally, only one adult was both present at Bossou throughout the 1999-2016 period, and younger than the threshold for our old-age category across these years (thus, the baseline used to compare with older adults would be just one younger adult, thus would not have been useful for characterizing normal variation of many younger adults over time). However, given the longitudinal data we present, we can use data from the earlier field seasons for each elderly focal individual as a personalized baseline control. Previous studies at Bossou find that across the majority of adulthood, efficiency varies between individuals, but is stable within individuals over time (e.g., Berdugo et al. 2024, cited). We detected similar stability in individuals’ efficiency over the first three field seasons sampled in our analysis, where there was very little intra-individual variation in tool-using efficiency. However, in later years, two individuals (Velu & Yo) began to exhibit relatively large reductions in efficiency.

      These results are unlikely to be explained by ecological variation. If there was a change in ecology underpinning our results, we would expect: [1] changes in ecology to also introduce variation in earlier field seasons, and [2] to influence all individuals in our study similarly. As such, if the changes observed in later field seasons were due to ecological changes, they should have caused a reduced efficiency across individuals, and to a similar degree – we did not observe this result, with large reductions in efficiency were confined to two individuals.   Moreover, for Yo (the individual who exhibited the largest reduction in efficiency) we found some additional evidence that changes in oil-palm-nut cracking efficiency extended beyond the period we sampled, i.e. they were evident even in 2018, reflecting a long-term, directional reduction in efficiency as compared to earlier years of her life. This consistent reduction in tool-using efficiency over multiple years adds further weight to the hypothesis that changes at the level of the individual were causing reduced tool-using efficiency, rather than our results being underpinned by interseasonal variation in ecology.

      Whilst we agree that our study is limited in the extent to which we can analytically assess ecological explanations for changes in nut-cracking efficiency, we believe that hypothetical ecological changes across field seasons do not predict our results. We now raise both sides of this debate in our discussion, where we outline our limitations (see lines 535-593).

      (2) The data from 2011 was scarce, with only one individual having 10 encounters. It would be better to be cautious with this season's results. 

      We appreciate this limitation raised by the reviewer. Velu and Yo were only encountered a few times in 2011; however, both were encountered more frequently in 2016. For 2011, we did not collect oil-palm nut cracking data for either Yo or Velu. Thus, their change in efficiency was detected by models using data from all other years, regardless of the few encounters in 2011. This sparsity of data may still have influenced our metrics for the proportion of time chimpanzees spent engaging in different behaviors when present at the outdoor laboratory in 2011, particularly for Velu, who was one of the two individuals who exhibited a change in behavior in this year (along with Fana, N = 10 for 2011). We have therefore added a line in our results and discussion highlighting the sparsity of data for Velu when estimating these proportions for 2011 (see lines 255-256 & 410).

      Minor corrections 

      (1) The last paragraph of the introduction presents many results, which should be in the results section. 

      We would like to keep this section of the introduction. Our paper investigates the effect of aging on many different aspects of nut cracking, which could become confusing for readers unless laid out clearly. We believe that having a short summary early on in the paper assists readers with following the methods and arguments presented within our paper.

      (2) The first section (Sampled data) of the results contains much information that belongs in the methods section. 

      We appreciate that there is some overlap between our methods and results section. However as the results section comes before the methods in our manuscript, we wanted to ensure that there is suitable information in our results that allow our results to be interpreted clearly by readers, and that the methods used to generate these results are transparently communicated. For these reasons, we will leave this information in the results, as we believe it increases our paper’s readability. 

      Reviewer 2 (Public review):

      One of the main limitations of this study is the small sample size. There are only 5 of the old-aged individuals, which is not enough to draw any inferences about aging for chimpanzees more generally. Howard-Spink and colleagues also study data from only five of the 17 years of recorded data at Bossou. The selection of this subset of data requires clarification: why were these intervals chosen, why this number of data points, and how do we know that it provides a representative picture of the age-related changes of the full 17 years? 

      We note that our sample size is limited to 5 individuals. This is an inevitable constraint of analyzing aging longitudinally in long-lived species, as only few individuals will live to old age. We argue that 17 years is a long enough period of study, as in the initially sampled field season (1999) focal individuals are reaching a mature age of adulthood (39-44 years) and begin to age progressively up to ages that are typically considered to be on the extreme side for chimpanzees’ lifespans in the wild (56-61 years). We raise in our methods that whilst it is difficult to determine precisely when chimpanzees become ‘old aged’, previous studies use the age of around 40 years, as from this age survivorship begins to decrease more rapidly (see Wood et al., Science 2023). Indeed, one focal individual (Tua) disappeared during the period of our study (presumed dead), and one other individual died in 2017 (Velu), the year after our final sampled field season. As of 2025, two other focal females have since died, and only one focal individual was still alive at Bossou (Jire, the individual exhibiting the least evidence for senescence over our study period). These observations suggest that we successfully captured data from chimpanzees during the oldest ages of their lives for most individuals in the community. Moreover, the period of 1999-2016 contains the majority of data available within the Bossou Archive, with years before and after this window containing comparably less data. This information is included within our results and methods (see sections 2.1 and 4.1).

      For our earliest field season (1999), it is unlikely that senescence had already had an effect on stone-tool use, as we measured efficiency to be high across all efficiency metrics for all individuals. For example, in 1999, the median number of hammer strikes performed by focal chimpanzees ranged from 2-4 strikes, and this was comparable to the efficiency reported across all adults observed in previous studies at Bossou (Biro et al. 2003, Anim. Cog.). This finding suggests that senescence effects had not yet taken place, allowing us to evaluate whether aging affects efficiency over subsequent field seasons. This point is now included in the manuscript on lines 449-452. 

      We sampled at 4-to-5-year intervals to balance the time-intensive nature of fine-scale behavior coding against the need to sample data across the extended 17-year time window available in our study. We limited the final year to 2016 as, in following years, data were collected using different sampling protocols (though, see limited data from 2018 in the supplementary materials). We aimed to keep the intervals between years as consistent as possible (approx. 4 years); however, for some years data were not collected at Bossou, due to disease outbreaks in the region. In these instances, we selected the closest field season where suitable data were available for study (always +/- 1 year). We have provided further clarification surrounding our sampling regime in the methods (see amendments in section 4.1)

      With measuring and interpreting the 'efficiency' of behaviors, there are in-built assumptions about the goals of the agents and how we can define efficiency. First, it may be that efficiency is not an intentional goal for nut-cracking at all, but rather, e.g., productivity as far as the number of uncrushed kernels (cf. Putt 2015). Second, what is 'efficient' for the human observer might not be efficient for the chimpanzee who is performing the behavior. More instances of tool-switching may be considered inefficient, but it might also be a valid strategy for extracting more from the nuts, etc. Understanding the goals of chimpanzees may be a difficult proposition, but these are uncertainties that must be kept in mind when interpreting and discussing 'decline' or any change in technological behaviors over time.

      We agree that knowing precisely how chimpanzees perceive their own efficiency during tool use is unlikely to be available through observation alone. However, under optimal foraging theory, it is reasonable to assume that animals aim to economize foraging behaviors such that they maximize their rate of energy intake. Moreover, a wealth of studies demonstrate that adult chimpanzees acquire and refine tool-using skill efficiency throughout their lives. For example, during nut cracking, adults often select tools with specific properties that aid efficient nut cracking (Braun et al. 2025, J. Hum. Evol.; Carvalho et al. 2008, J. Hum. Evol.; Sirianni et al. 2015, Anim. Behav.); perform nut cracking using more streamlined combinations of actions than less experienced individuals (Howard-Spink et al. 2024, Peer J; Inoue-Nakamura & Matsuzawa 1997, J. Comp. Psychol.), and as a result end up cracking nuts using fewer hammer strikes, indicating a higher level of skill (Biro et al. 2003, Anim. Cogn.; Boesch et al. 2019, Sci. Rep.). Ultimately, these factors suggest that across adulthood, experienced chimpanzees perform nut cracking with a level of efficiency which exceeds novice individuals, including across the whole behavioral sequence for tool use, even if they are not aware or intending to do so. Previous studies at Bossou have also highlighted that there are stable inter-individual differences in efficiency of individuals over time (Berdugo et al. 2024, Nat. Hum. Behav.). This pattern of findings allows us to ask whether this acquired level of skill is stable across the oldest years of an individual’s life, or whether some individuals experience decreased efficiency with age. In addition, our selection of efficiency metrics is in keeping with a wealth of studies which examine the efficiency of stone-tool using in apes, thus, we argue that this is not problematic for our study.

      As we stated in our initial responses to reviewers, it is unlikely that tool switching is a valid strategy for tool use, as it is so rarely performed by proficient adult nut crackers (including earlier in life for our focal individuals). Nevertheless, we did not find a significant change in tool switching for oil-palm nut cracking, and this behavioral change was only observed when Yo was cracking coula nuts. As we have now moved discussion of coula nut cracking to the supplementary materials (and tempered discussion of coula nut cracking to emphasize the need for more data) this behavioral variable does not influence our reported results. 

      In our discussion, we also highlight how seemingly less efficient actions may reflect a valid strategy for nut cracking. E.g. a greater number of tool strikes may reflect a strategy of compensation for progressive tool wear. This would still reflect a reduced efficiency (e.g. in terms of the rate at which kernels can be consumed), but may perhaps borne for the necessity to accommodate for changes in an individuals’ physical affordances with aging. Thus, we do take the Reviewer’s point into account, but by using an alternative, more likely, example given the available data. We have now emphasized this point in lines 521-527.

      We have also clarified these matters by adding more information into our methods (see lines 798-802 and 828-829), highlighting that we take a perspective on efficiency that reflects the speed of nut processing and kernel consumption, and the number of different behavioral elements required to do so. Our phrasing now explicitly avoids using language that assumes that individuals’ have some perception of their own efficiency during tool use.

      For the study of the physiological impact of senescence of tool use (i.e., on strength and coordination), the study would benefit from the inclusion of variables like grip type and (approximate) stone size (Neufuss et al., 2016). The size and shape of stones for nut-cracking have been shown to influence the efficacy and 'efficiency' of tool use (i.e., the same metrics of 'efficiency' implemented by Howard-Spink et al. in the current study), meaning raw material properties are a potential confound that the authors have not evaluated. 

      We did not collect this data as part of our study. Whilst grip type could be a useful variable to measure for future studies, it is not necessary to demonstrate senescence per se. However, we agree that this could be a fruitful avenue to understand changes in behavior at greater granularity, and have added this as a recommendation for further study. We also now provide a discussion on stone dimensions and materials as part of our limitations (see lines 581-589 for both points).

      Similarly, inter- and intraspecific variation in the properties of nuts being processed is another confound (Falótico et al., 2022; Proffitt et al., 2022;). If oil palm nuts were varying year-to-year, for example, this would theoretically have an effect on the behavioral forms and strategies employed by the chimpanzees, and thus, any metric of efficiency being collected and analyzed. Further, it is perplexing that the authors analyze only one year where the coula nuts were provided at the test site, but these were provided during multiple field seasons. It would be more useful to compare data from a similar number of field seasons with both species if we are to study age-related changes in nut processing over time (one season of coula nut-cracking certainly does not achieve this). 

      We have moved all discussion of coula nuts to the supplementary materials so as to avoid any confusion with oil-palm nuts (see comments from Reviewer 2, and our response). Nut hardness may influence the difficulty with which nuts are cracked, with one of the most likely factors influencing nut hardness being its age: young nuts are relatively harder to crack, whereas older nuts, which are often worm-eaten or can be empty, crack more easily, yet are not worth cracking (Sakura & Matsuzawa, 1991; Ethology). We largely controlled for this in our study, as the nuts provided at outdoor laboratories were inspected to ensure that the majority of them were of suitable maturity for cracking, and we now clarify this control in our methods (see lines 678-680) and when discussing our study limitations (see lines 551-558). In these sections, we also highlight a previous study at Bossou that shows chimpanzees select nuts which can be readily cracked, based on their age (Sakura & Matsuzawa, 1991; Ethology).

      We acknowledge that we are limited in the extent to which we can control for interannual variation in ecology with our available data. However, we highlight why interannual variability is unlikely to fully explain our results (see lines 551-580 and response to comments from Reviewer 1). We also highlight in our limitations section that future studies should (where possible) aim to collect more ecological data to account for possible confounds more rigorously.

      Both individual personality (especially neophilia versus neophobia; e.g., Forss & Willems, 2022) and motivation factors (Tennie & Call, 2023) are further confounds that can contribute to a more valid interpretation of the patterns found. To draw any conclusions about age-related changes in diet and food preferences, we would need to have data on the overall food intake/preferences of the individuals and the food availability in the home range. The authors refer briefly to this limitation, but the implications for the interpretation of the data are not sufficiently underlined (e.g., for the relevance of age-related decline in stone tool-use ability for individual survival). 

      In our discussion, we highlight that multiple aging factors may influence apes’  dietary preferences and motivations to attend experimental (and perhaps also naturally-occurring) nut cracking sites (see lines 397-443 and 542-550). We do not believe that neophobia is a likely driver underlying our results, given that the outdoor laboratory has been used to collect data for many decades, including over a decade prior to the first field season in which data were sampled for our study (now highlighted in lines 692-694). In addition, previous studies at Bossou have determined that the outdoor laboratory is visited with comparable frequency to naturallyoccurring nut cracking sites, which makes any form of novelty bias unlikely (this information is now included in our methods, see lines 397-400, and also 687-689). 

      We agree that further information is required about foraging behaviours across the home range to understand changes in attendance at the outdoor laboratory, and have now provided more clarity on this within the limitations section of our discussion 542-550. In our discussion of individual survivability, we state clearly that we cannot make a conclusion about how changes in tool use influence survival with the available data, and assert that this would require data across the home range (see lines 627-638). We agree that future research is needed to assess whether changes in tool use would influence survivability, and also suggest that it may not be survival-relevant; instead changes in tool use with aging may simply be a litmus test for detecting more generalized senescence.

      Generally speaking, there is a lack of consideration for temporal variation in ecological factors. As a control for these, Howard-Spink and colleagues have examined behavioral data for younger individuals from Bossou in the same years, to ostensibly show that patterns in older adults are different from patterns in younger adults, which is fair given the available data. Nonetheless, they seem to focus mostly on the start and end points and not patterns that occur in between. For example, there is a curious drop in attendance rate for all individuals in the 2008 season, the implications of which are not discussed by the authors. 

      As the reviewer points out, when examining the attendance rates of older individuals over sampled field seasons, we used the attendance rates of younger individuals as a control. However, we do not run this analysis using start and end points only. Attendance rates were included in our model across the full range of sample field seasons. However, as the key result here is an interaction term between age cohort (old) and the field season (scaled about the mean), we supplement this significant statistical result with a digestible comparison of attendance rates between the first and last field season, to give a general sense of effect size. We have clarified that all data were used in our model (see line 229, and also the legend for Table 2), and in this section we also provide all key model outputs and signpost where the full model output can be found in the supplementary materials.

      As far as attendance, Howard-Spink and colleagues also discuss how this might be explained by changes in social standing in later life (i.e., chimpanzees move to the fringes of the social network and become less likely to visit gathering sites). This is not senescence in the sense of physiological and cognitive decline with older age. Instead, the reduced attendance due to changes in social standing seems rather to exacerbate signs of aging rather than be an indicator of it itself. The authors also mention a flu-like epidemic that caused the death of 5 individuals; the subsequent population decline and related changes in demography also warrant more discussion and characterization in the manuscript. 

      We have adapted this part of the discussion to make it clear that social aging is not necessarily equivalent to physiological and cognitive aging. We have also clarified in this section the changes in demography at Bossou during our study, which may have further impacted social behaviors (see lines 423-443). 

      Understandably, some of these issues cannot be evaluated or corrected with the presented dataset. Nonetheless, these undermine how certain and/or deterministic their conclusions can really be considered. Howard-Spink et al. have not strongly 'demonstrated' the validity of relationships between the variables of the study. If anything, their cursory observations provide us with methods to apply and hypotheses to test in future studies. It is likely that with higher-resolution datasets, the individual variability in age-related decline in tool-use abilities will be replicated. For now, this can be considered a starting point, which will hopefully inspire future attempts to research these questions. 

      We thank the reviewer for their comments. We have adapted our manuscript to highlight that we agree that it serves a starting point for answering these valuable questions; however, we do feel that we can contribute meaningful evidence that it is likely aging effects underlying the findings in our data (see responses above). We agree with the reviewer that further study is needed to understand these questions in more detail, and have tried to ensure that our conclusions are suitably tempered, and the recommendations for research are heavily encouraged to build on our findings.  

      Falótico, T., Valença, T., Verderane, M. & Fogaça, M. D. Stone tools differences across three capuchin monkey populations: food's physical properties, ecology, and culture. Sci. Rep. 12, 14365 (2022). 

      This has now been cited.

      Forss, S. & Willems, E. The curious case of great ape curiosity and how it is shaped by sociality. Ethology 128, 552-563 (2022). 

      We do not cite this – see above.

      Neufuss, J., Humle, T., Cremaschi, A. & Kivell, T. L. Nut-cracking behaviour in wild-born, rehabilitated bonobos (Pan paniscus): a comprehensive study of hand-preference, hand grips and efficiency. Am. J. Primatol. 79, e22589 (2016). 

      This has now been cited.

      Proffitt, T., Reeves, J. S., Pacome, S. S. & Luncz, L. V. Identifying functional and regional differences in chimpanzee stone tool technology. R. Soc. Open Sci. 9, 220826 (2022). 

      This has now been cited.

      Putt, S. S. The origins of stone tool reduction and the transition to knapping: An experimental approach. J. Archaeol. Sci.: Rep. 2, 51-60 (2015). 

      We do not cite this, as we instead cite studies which highlight chimpanzees’ ability to become more efficient in tool use with repeated practice (see above). 

      Tennie, C. & Call, J. Unmotivated subjects cannot provide interpretable data and tasks with sensitive learning periods require appropriately aged subjects: A Commentary on Koops et al. (2022) "Field experiments find no evidence that chimpanzee nut cracking can be independently innovated". ABC 10, 89-94 (2023). 

      We do not cite this – see above

      Reviewer #2 (Recommendations for the authors):

      Minor Comments: 

      (1) Line 494: Citation #53 is listed twice. 

      This has been amended.

      (2) Line 501: The term 'culturally-dependent' as used here is, at best, controversial, and at worst, misapplied. I would recommend replacing it with simply the term 'cultural'. 

      This has been changed to ‘cultural’.

      Major Comments: 

      For the Introduction, in the paragraph starting on Line 91, and the Discussion, starting on Line 369, I would recommend some simple re-structuring of the argumentation. As many in the Public Review, the changes in social standing according to age are not necessarily a case of senescence in the very sense of physiological or cognitive changes of the individual. This seems to have had an effect on attendance rates, which then could have been a driver of behavioral changes and even cognitive decline as ostensibly measured by the other variables. The social impact of aging should be mentioned in the Introduction (it is not currently) and the social and physiological/cognitive effects of aging should be separated in the Discussion. You can then discuss more clearly how the former via other behavioral changes can accelerate the latter (or not). 

      We take the point raised about social aging. Integrating information about social aging into the introduction was challenging without disrupting the flow of the paper; however, we have included these valuable points in the discussion (see lines 423-443). We now structure this section to clearly distinguish social aging, and discuss how, in tandem with changes in demography at Bossou, it may have influenced rates of attendance to the outdoor laboratory over the years. We do not go into detail about how social aging may interact with physiological or cognitive effects of aging, as we cannot support this with the available data, however we highlight at the end of this paragraph how all of these possible factors require further investigation.

      For the present study, it will either be impossible or impractical to gather data on the yearly ecological conditions, contextualized dietary preferences, individual personalities, etc., so I would not ask that you do so. It is important, however, to temper some of the claims being made in the manuscript about what you have 'determined' about the nature of senescence in chimpanzees and to be more transparent about the limitations and potential confounds when interpreting the data. To avoid repetition, the key points can be found in the Public Review under 'Weaknesses'. 

      We appreciate the reviewer’s understanding of the limitations of our study. Some of these factors – such as individual personalities and dietary preferences – are addressed somewhat by our use of long-term data at the level of the individual, particularly in the analyses of efficiency, where we model individuals’ behaviors compared to those in earlier years offers an individuallybespoke control. However, there are other ecological variables of possible importance that we cannot evaluate. We now address several of these points raised by reviewers in the discussion, to ensure transparency of reporting (see limitations section of our discussion, and results to the comments provided by Reviewer 1, and our responses to points raised in the Public Review). We have also tempered some of the phrasing surrounding our conclusions, where we say that this is the first evidence that aging can impact chimpanzee tool use, we also highlight the need for an assortment of further studies. 

      Finally, the integration of the coula nut-cracking data is not well-executed as it stands. I would recommend that they collect and analyze equivalent behavioral data from the other years where coula nuts were provided. By examining only one season of coula nut-cracking, we cannot contextualize the data to past seasons; there is no sense in comparing one season of coula nut-cracking (i.e., in a sense of efficiency) to roughly contemporary seasons of palm-nut cracking due to, as you describe, differences in physical properties of the nuts. If you are not able to collect the additional data and carry out the requisite analysis, then I would recommend that the coula nut-related sections be removed from the manuscript, so that it does not detract from the logical flow of arguments and distract from the other data, which is more logically-attuned to your research questions. 

      We have removed this from the main manuscript. We have decided to include the information surrounding coula nut cracking in the supplementary materials, as this information is still relevant to the findings of our study, and may interest some readers. However, we have phrased this information to make it clear that further data is needed to compare coula nut cracking across years.

      These criticisms do not subtract from the (potential) value or importance of the work for the field. This is, of course, an important contribution to an understudied topic. As such, I would gladly advocate for the manuscript, assuming the authors would reflect on the listed caveats and make changes in response to the 'Major Comments'. 

      We thank the reviewer for their comments.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer 1 (Public reviews):

      (1) Commander-Independent Role of COMMD3: While the authors provided evidence to support the Commander-independent role of COMMD3-such as the absence of other Commander subunits in the CRISPR screen and not decreased COMMD3 levels in other subunit-KO cells- direct evidence is lacking. The mutation that specifically disrupts the COMMD3-ARF1 interaction could serve as a valuable tool to directly address this question.

      The Reviewer raised an excellent point. We fully agree with the Reviewer that multiple lines of evidence are needed to support the novel Commander-independent function of COMMD3.

      Comparative genetic analyses in Figures 4 and 5 indicate that COMMD3 regulates endosomal retrieval independently of the Commander complex. In Figure 8 of the revised manuscript, we show that point mutations introduced into the COMMD3:ARF1 interface impair this Commander-independent function. Moreover, Figure 6 demonstrates that ARF1 upregulation fully rescues the KO phenotype of COMMD3. In addition, Figure S2 further supports that COMMD3 levels, but not those of other Commander subunits, correspond to its Commander-independent function in endosomal trafficking. We have also revised the Discussion section to elaborate on the implications of these findings. We appreciate the Reviewer’s advice.

      (2) Role of ARF1 in Cargo Selection: The Commander-independent function of COMMD3 appears cargo-dependent and relies on ARF1's role in cargo selection. The authors should investigate whether KO/KD of ARF1 reduces cell surface levels of ITGA6 and TfR.

      The Reviewer correctly pointed out that KO/KD of ARF1 may provide further insights into the Commander-independent function of COMMD3. However, since ARF1 is involved in cargo sorting at both the endosome and the trans-Golgi network, its KO would disrupt multiple trafficking routes, making the data difficult to interpret. Instead, we focused on point mutations in the NTD that specifically disrupt ARF1 binding without affecting the function of the Commander complex (Fig. 8). As these mutations impair the Commander-independent function of COMMD3, our data strongly support a direct role for ARF1 in this recycling pathway. We note that the discovery of a novel trafficking pathway inevitably opens many research directions. One such direction is to systematically identify cargoes that rely on COMMD3 but not the Commander complex for endosomal retrieval.

      (3) Impact on TfR Stability: Figure 7D suggests that TfR protein levels are reduced in COMMD3-KO cells, potentially due to degradation caused by disrupted recycling. This raises the question of whether the observed reduction in cell surface TfR is due to impaired endosomal recycling or decreased total protein levels. The authors should quantify the ratio of cell surface protein to total protein for TfR, GLUT-SPR, and ITGA6 in COMMD3-KO cells.

      Based on the Reviewer's suggestion, we quantified both the total levels and the surface-tototal ratio of TfR, as shown in Figure S1 of the revised manuscript. These new data further support the conclusion that defects in TfR retrieval lead to its lysosomal degradation. The GLUT-SPR data presented in the main figures represent the surface-to-total ratio of the GLUT-SPR reporter. We thank the Reviewer for the important suggestion.

      Reviewer #1 (Recommendations for the authors):

      (1) Commander-Independent Role of COMMD3: The mutation that specifically disrupts the COMMD3-ARF1 interaction could serve as a valuable tool to directly address this question. The authors should evaluate whether the full-length mutant of COMMD3 can rescue decreased levels of CCDC93 and VPS35L, as well as cell surface ITGA6, TfR, and GLUT4 inCOMMD3-KO cells.

      This is an excellent point. In our mechanistic experiments, we focused on the NTD of COMMD3 because this domain mediates its Commander-independent function and is not involved in forming the Commander holo-complex. This approach allowed us to draw unambiguous conclusions. Nevertheless, we anticipate that full-length COMMD3 carrying these point mutations would also be defective in regulating Commander-independent cargo.

      (2) Role of ARF1 in Cargo Selection: The authors should investigate whether KO/KD of ARF1 reduces cell surface levels of ITGA6 and TfR. Was ARF1 identified in the initial CRISPR screen? If so, this should be explicitly noted. Alternatively, does ARF1 overexpression rescue ITGA6 levels in COMMD3-KO cells? Furthermore, does ARF1 overexpression rescue TfR levels in COMMD3 and CCDC93 double-KO cells?

      Reinto the Commander-independent function of COMMD3. However, since ARF1 is involved in cargo sorting at both the endosome and the trans-Golgi network, its KO would disrupt multiple trafficking routes, making the data difficult to interpret. Instead, we focused on point mutations that specifically disrupt ARF1 binding without affecting the function of the Commander complex (Fig. 8). Since these mutations impair the Commander-independent function of COMMD3, our data strongly support a direct role for ARF1 in this novel recycling pathway. Based on our genetic data, we anticipate that all COMMD3-dependent cargoes will be similarly rescued in ARF1-overexpressing cells. In line with the Reviewer's comment, a key research direction we are currently pursuing is systematically determining how surface protein levels are affected by COMMD3 KO and ARF1 overexpression using surface proteomics.

      (3) Inconsistency in COMMD3 Rescue Levels (Figure 5A): Figure 5A shows comparable or higher levels of COMMD3 in rescued cells than in CCDC93-KO and VPS35L-KO cells. However, COMMD3 rescue did not increase cell surface TfR as much as in CCDC93-KO and VPS35L-KO cells. This inconsistency should be discussed or validated.

      To address the Reviewer’s inquiry, we quantified COMMD3 expression levels in these cell lines using multiple independent experiments. The new data are presented in Figure S2 of the revised manuscript. These expanded datasets allowed us to more accurately determine the relationship between COMMD3 expression and our genetic data. Since the Commander complex remains intact in the COMMD3 rescue cells, a significant portion of COMMD3 proteins are expected to be incorporated into the Commander complex, which does not regulate TfR recycling. In contrast, because the Commander complex is disrupted in Ccdc93 and Vps35l KO cells, all COMMD3 proteins are available to regulate TfR recycling in a Commander-independent manner. These findings are fully consistent with the similar surface TfR levels observed in Ccdc93/Vps35l KO cells and COMMD3 overexpressing cells. We thank the Reviewer for this excellent suggestion.

      (4) Significance of NTD in COMMD3 Function: The conclusion that "the NTD of COMMD3 mediates its Commander-independent function and interacts with ARF1" (Page 12) is not fully supported without a side-by-side comparison of NTD, CTD, and FL COMMD3 in the same experiment (e.g., Figures 6B and 6G). Additional data is needed to strengthen this claim.

      We conducted the experiment suggested by the Reviewer and included the data in Figure S3. Our results indicate that the COMMD3 CTD cannot mediate the Commander-independent function of COMMD3 in endosomal retrieval. We appreciate the Reviewer’s suggestion.

      (5) ARF1 Stabilization Experiments: To substantiate the claim that COMMD3 binds and stabilizes the GTP-form of ARF1, the authors should include a comparative experiment showing GTP-form, GDPform, and wild-type ARF1 (e.g., Figures 6G and 7C).

      We fully agree with the Reviewer that it would be important to compare how the ARF1:COMMD3 interaction is influenced by the nucleotide-binding state. However, trapping ARF1 in its GDP-bound state remains unfeasible, and nucleotide-free small GTPases are inherently unstable. In addition, WT ARF1 likely exists as a mixture of GTP- and GDP-bound forms, further complicating the analysis. To address the Reviewer’s comment, we used AlphaFold3 predictions. Interestingly, we found that the ipTM score of GTP-ARF1:COMMD3 is significantly higher than that of GDP-ARF1:COMMD3 or apo-ARF1:COMMD3, supporting our conclusion that COMMD3 recognizes and stabilizes the active form of ARF1.

      (6) Validation of NTD Mutation (Figure 8): Co-immunoprecipitation or cellular co-localization experiments should be performed to confirm that the NTD mutation disrupts the interaction between COMMD3 and ARF1, as depicted in Figure 8.

      This is an important question, and the best approach to address it would be to measure the binding affinity of the WT and mutant proteins using ITC or SPR. However, this is currently unfeasible, as we have not yet obtained pure recombinant COMMD3 and GTP-ARF1 proteins. Co-IP, by nature, is a crude assay that often fails to detect changes in binding affinity. A previous study on other proteins showed that mutations in protein-binding interfaces strongly reduced binding affinity as measured by SPR, but these changes would have been missed by co-IP assays (PMID: 25500532). In agreement with this limitation, our co-IP experiments did not yield conclusive results. Instead, we focused on structure-guided genetic experiments, which unequivocally demonstrated the effects of targeted mutations on the Commander-independent function of COMMD3. 

      Reviewer #2 (Public review):

      (1) All existing data suggest that COMMD3 is a subunit of the Commander complex. Is there any evidence that COMMD3 can exist as a monomer?

      The Reviewer raised an intriguing point. Indeed, COMMD proteins, including COMMD3, can exist outside the Commander holo-complex and form homo- or hetero-oligomers, as monomeric COMMD proteins are likely unstable. These observations align well with the Commander-independent function identified in this study. We have revised the Discussion section of the manuscript to further elaborate on this point and thank the Reviewer for the suggestion.

      (2) In Figure 9, the author emphasizes COMMD3-dependent cargo and Commander-dependent cargo. Can the authors speculate what distinguishes these two types of cargo? Do they contain sequence-specific motifs?

      This is another important question. Our data clearly demonstrate that COMMD3 has a Commander-independent function in addition to its canonical role within the Commander holocomplex. Since cargo proteins typically possess multiple sorting signals that operate at different stages of the exocytic and endocytic pathways, identifying COMMD3-dependent sorting signals remains a challenge. ARF4 has been shown to specifically recognize the VXPX motif (PMID: 15728366), suggesting that ARF1 may similarly bind cytosolic sorting signals, with COMMD3 stabilizing this interaction. A key future direction is to systematically identify COMMD3-dependent cargo proteins and elucidate the mechanisms underlying their endosomal sorting. We have revised the Discussion section of the manuscript to explicitly address this point and thank the Reviewer for this important suggestion.

      (3) What could be the possible mechanism underlying the observation that the knockout of COMMD3 results in larger early endosomes? How is the disruption of cargo retrieval related to the increase in endosome size?

      The endosomal retrieval process is critical for recycling membrane proteins and lipids back to the plasma membrane or the trans-Golgi network. When this process is disrupted, cargo that should be recycled accumulates within endosomes, leading to their enlargement. For example, defects in retromer function can cause endosomal swelling due to cargo accumulation (PMID: 33380435). We added this citation to the revised manuscript and thank the Reviewer for the advice. 

      Reviewer 3 (Recommendations for the authors):

      (1) Figure 4: How do the authors define Commander-dependent vs. Commander-independent cargos?

      In Figure 4, the surface expression of ITGA6 is reduced to approximately 0.75 across all knockouts. However, there is a similar level of reduction for GLUT4-SPR in the commd5 knockout and for LAMP1 in the commd5 and commd1 knockouts. Are GLUT4-SPR and LAMP1 Commander-dependent or Commander-independent cargos? Additionally, how does COMMD3 specifically identify/distinguish these cargos?

      This is an excellent point. Our data suggest that TfR is a COMMD3-dependent but Commander-independent cargo, whereas ITGA6 is a Commander-dependent cargo that does not involve COMMD3-specific functions. The other two cargoes we examined—GLUT-SPR and LAMP1—primarily rely on COMMD3, with the Commander complex playing a minor role. Together, these observations clearly demonstrate that COMMD3 has a Commander-independent function in addition to its canonical role within the Commander holo-complex. Since cargo proteins typically possess multiple sorting signals that operate at different stages of the exocytic and endocytic pathways, identifying COMMD3-dependent sorting signals remains a challenge. ARF4 has been shown to specifically recognize the VXPX motif (PMID: 15728366), suggesting that ARF1 may similarly bind cytosolic sorting signals, with COMMD3 stabilizing this interaction. A key future direction is to systematically identify COMMD3-dependent cargo proteins and elucidate the mechanisms underlying their endosomal sorting. We have revised the Discussion section of the manuscript to explicitly address this point. We thank the Reviewer for this important suggestion.

      (2) There is an increase in the surface expression of GLUT4-SPR in the commd1 knockout. Is this increase significant? The figure suggests a significant increase, but the text states it remains unchanged. Clarification is needed.

      We found that surface levels of GLUT-SPR were slightly increased in Commd1 KO cells, in stark contrast to the strong reduction observed in Commd3 KO cells (Fig. 4B). This finding is consistent with our conclusion that COMMD3 has a distinct role from other Commander subunits. We have revised the Results section to more clearly describe these data and thank the Reviewer for the advice.

      (3) Figure 5A: To support the claim that COMMD3 is upregulated in the vps35l KO/Ccdc93 KO, the authors should quantify COMMD3 expression. Also, why is there a Vps35l band present in the Vps35l knockout cells?

      Based on the Reviewer’s suggestion, we quantified the total levels of COMMD3 and included these new data in Figure S2. In this study, gene deletion was achieved through the simultaneous introduction of two independent gRNAs. Based on our previous experience, this strategy typically results in the complete loss of gene expression. We posit that the residual band observed in Vps35l KO cells originates from background signals, such as nonspecific staining by the antibody.

      (4) Figure 7: It is intriguing that COMMD3 stabilizes Arf1-GTP and can compensate for COMMD3 in knockout cells. However, is this stabilization specific to TfR cargo only? The authors should test additional Commander-dependent and Commander-independent cargos to clarify this point.

      Based on our genetic data, we anticipate that all COMMD3-dependent cargoes will be similarly rescued in ARF1-overexpressing cells. In line with the Reviewer's comment, an important direction we are pursuing is the use of surface proteomics to systematically determine how surface protein levels are affected by COMMD3 KO and ARF1 overexpression.

      (5) Is Arf1 interaction specific to COMMD3? The authors should investigate the effects of Arf1 knockout on COMMD3 expression and test its role in regulating Commander-dependent and Commander-independent cargos.

      The Reviewer raised an excellent point. Since ARF1 is involved in cargo sorting at both the endosome and the trans-Golgi network, its KO would interfere with multiple trafficking routes and the data would be difficult to interpret. Thus, in this work, we focused on the function and mechanism of the COMMD3:ARF1 complex on the endosome. Based on the suggestion of the Reviewer, we used AlphaFold3 to predict ARF1 binding to COMMD proteins. Interestingly, the complex with the highest predicted ipTM score is COMMD3:ARF1, while other COMMD proteins have much lower predicted binding scores. These results are consistent with the results of our unbiased CRISPR screens and targeted gene KO, and further support the conclusion that the COMMD3:ARF1 binding is specific and physiologically important in endosomal trafficking.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review):

      Weaknesses:

      (1) The selection of inactivated conformations based on AlphaFold modeling seems a bit biased. The authors base their selection of the “most likely” inactivated conformation on the expected flipping of V625 and the constriction at G626 carbonyls. This follows a bit of the “Streetlight effect”. It would be better to have selection criteria that are independent of what they expect to find for the inactivated state conformations. Using cues that favour sampling/modeling of the inactivated conformation, such as the deactivated conformation of the VSD used in the modeling of the closed state, would be more convincing. There may be other conformations that are more accurately representing the inactivated state. I see no objective criteria that justify the non-consideration of conformations from cluster 3 of the inactivated state modeling. I am not sure whether pLDDT is a good selection criterion. It reports on structural confidence, but that may not relate to functional relevance.

      We sincerely thank the reviewer for their perceptive critique highlighting potential bias in selecting the inactivated conformation. We recognize that over-relying on preconceived traits could limit exploration of diverse inactivated states, and we appreciate the opportunity to address this concern.

      Although we selected the model with the flipped V625 in the selectivity filter (SF) from the first round of inactivated-state sampling as the template for the second round, the resulting models still exhibited substantial diversity in their SF conformations. This selection primarily served to steer predictions away from the open-state configuration observed in the PDB 5VA2 SF, and we have clarified this rationale in the Methodology section. To assess conformational variability, we examined backbone dihedral angles (phi φ and psi ψ) at key residues in the selectivity filter (S624 – G628) and drugbinding region on the pore-lining S6 segment (Y652, F656), of all 100 models sampled in the subsequent inactivatedstate-sampling attempt. By overlaying the φ and ψ dihedral angles from different models, including the open state (PDB 5VA2-based), the closed state, and representative models from AlphaFold inactivated-state-sampling Cluster 2 and Cluster 3, we found that these conformations consistently fall within or near high-probability regions of the dihedral angle distributions. This indicates that these structural states are well represented within the ensemble of conformations sampled by AlphaFold within the scope of this study, particularly at functionally critical positions.

      Following the analysis above and consistent with the reviewer’s suggestion, we evaluated the top representative model from inactivated-state-sampling Cluster 3 (named “AF ic3”), which we had initially excluded. This model demonstrated SF residue G626 carbonyl oxygen flipped away from the conduction pathway, hinting at potential impact on ion conduction, yet its pore region structurally resembled the open state (Figure S9a, b). To test this objectively, we ran molecular dynamics (MD) simulations (2 runs, 1 μs long each, with applied 750 mV voltage) with varied initial ion/water configurations in the SF, finding it consistently open and conducting throughout (Figure S9c, d), consistent with our previous observations in Figure S11 that ion conduction can still occur when the upper SF is dilated. Drug docking (Figure S12) further revealed that the model exhibited binding affinities similar to those for the PDB 5VA2-based openstate structure. These findings combined led us to classify it as a possible alternative open-state conformation.

      Models from Cluster 4 were not tested due to extensive steric clashes, where residues in the SF overlapped with neighboring residues from adjacent subunits. The remaining models displayed SF conformations that combined features from earlier clusters. However, due to subunit-to-subunit variability, where individual subunits adopted differing conformations, they were classified as outliers. This combination of features may be valuable to investigate further in a follow-up study.

      We acknowledge that our approach is just one of many ways to sample different states, and alternative strategies, such as generating more models, varying multiple sequence alignment (MSA) subsampling, or testing different templates, might reveal improved models. Given that hERG channel inactivation likely spans a spectrum of conformations, our resource limitations may have restricted us to exploring and validating only part of this diversity. Nevertheless, the putative inactivated (AlphaFold Cluster 2) model’s non-conductivity and improved affinity for drugs targeting the inactivated state observed in our study suggests that this approach may be capturing relevant features of the inactivated-state conformation. We look forward to investigating deeper other possibilities in a future study and are grateful for the reviewer’s feedback.

      (2) The comparison of predicted and experimentally measured binding affinities lacks an appropriate control. Using binding data from open-state conformations only is not the best control. A much better control is the use of alternative structures predicted by AlphaFold for each state (e.g. from the outlier clusters or not considered clusters) in the docking and energy calculations. Using these docking results in the calculations would reveal whether the initially selected conformations (e.g. from cluster 2 for the inactivated state) are truly doing a better job in predicting binding affinities. Such a control would strengthen the overall findings significantly.

      We appreciate the reviewer’s insightful suggestion. To address this, we extended our analysis by incorporating an alternative AlphaFold2-predicted model from inactivated-state-sampling cluster 3 as a structural control. This model was established in a previously discussed analysis to be open and conducting as a follow up to comment #1, so we will call it Open (AF ic3) to differentiate it from Open (PDB 5VA2). We evaluated this new model in single-state and multi-state contexts alongside our original open-state model based on the experimental PDB 5VA2 structure. Additionally, we expanded the drug docking procedure to explore a broader region around the putative drug binding site by increasing the sampling space, and we adopted an improved approach for selecting representative docking poses to better capture relevant binding modes.

      Shown in Figure 7 are comparisons of experimental drug potencies with the binding affinities from the molecular docking calculations under the following conditions:

      (a) Single-state docking using the experimentally derived open-state structure (PDB 5VA2)

      (b) Multi-state docking incorporating open (PDB 5VA2), inactivated, and closed-state conformations weighted by experimentally observed state distributions

      (c) Single-state docking using an alternative AlphaFold-predicted open-state (inactivated-state-sampling cluster 3, AF ic3)

      (d) Multi-state docking combining the AlphaFold-predicted open-state (inactivated-state-sampling cluster 3, AF ic3)

      Using only the open-state model (PDB 5VA2) yielded a moderate correlation with experimental data (R<sup>2</sup> = 0.43, r = 0.66, Figure 7a). Incorporating multi-state binding (weighted by their experimental distributions) improved the correlation substantially (R<sup>2</sup> = 0.63, r = 0.79, Figure 7b), boosting predictive power by 47% and underscoring the value of multi-state modeling. Importantly, this improvement was achieved without considering potential drug-induced allosteric effects on the hERG channel conformation and gating, which will be addressed in future work.

      Next, we substituted the PDB 5VA2-based open-state model with the AF ic3 open-state model. Docking to this alternative model alone produced similar performance (R<sup>2</sup> = 0.44, r = 0.66, Figure 7c), and incorporating it into the multi-state ensemble further improved the correlation with experiments (R<sup>2</sup> = 0.64, r = 0.80, Figure 7d), representing a 45% gain in R<sup>2</sup> and matching the performance of multi-state docking results based on the PDB 5VA2-derived model.

      These findings suggest that the predictive power of computational drug docking is enhanced not merely by the accuracy of individual models, but by the structural diversity and complementarity provided by an ensemble of protein conformations. Rather than relying solely on a single experimentally determined protein structure, the ensemble benefits from incorporating AlphaFold-predicted models that capture alternative conformations identified through our state-specific sampling approach. These diverse protein models reflect different structural features, which together offer a more comprehensive representation of the ion channel’s binding landscape and enhance the predictive performance of computational drug docking. Overall, these results reinforce that multi-state modeling offers a more realistic and predictive framework for understanding drug – ion channel interactions than traditional single-state approaches, emphasizing the value of both individual model evaluation and their collective integration. We are grateful for the reviewer’s suggestion.

      (3) Figures where multiple datapoints are compared across states generally lack assessment of the statistical significance of observed trends (e.g. Figure 3d).

      We appreciate the reviewer’s comment on the statistical significance assessment in Figure 3d. To clarify, the comparisons shown in the subpanels are based on three selected representative models for each state, rather than a broader population sample (similarly for Figure 3b). In the closed-state predicted models, the strong convergence of the voltagesensing domain (VSD), with an all-atom RMSD of 0.36 Å between cluster 1 and 2 closed-state sampling models and 0.95 Å to the outlier cluster, indicates minimal structural variation. Those RMSD values shown in the manuscript text demonstrates good convergence and by themselves represent statistical significance assessment of those models. This trend extends to open-state and inactivated-state AlphaFold models with similarly limited differences in the VSD regions among them. This convergence suggests that population-based statistical analysis may not reveal meaningful deviations, as the low variability among models limits the insights beyond those obtained from comparing representative structures.

      Nonetheless, we acknowledge this limitation. In future studies, we plan to explore alternative modeling approaches to introduce greater variability, enabling a more robust statistical evaluation of state-specific trends in the predictions.

      (4) Figure 3 and Figures S1-S4 compare structural differences between states. However, these differences are inferred from the initial models. The collection of conformations generated via the MD runs allow for much more robust comparisons of structural differences.

      We have explored these conformational state dynamics through MD simulations for the Open (5VA2-based), Inactivated (AlphaFold Cluster 2), and Closed-state models, as presented in Figures S7, S8, S10, S11. These figures provide detailed insights: Figure S7-S8 analyzes SF and pore conformation dynamics, including averaged pore radii with and without voltage and superimposed conformational ensembles; Figure S10 tracks cross-subunit distances between protein backbone carbonyl oxygens, revealing sequential SF dilation steps near residues F627 an G628; and Figure S11 illustrates this SF dilation process over time, highlighting residue F627 carbonyl flipping and SF expansion. We appreciate the opportunity to clarify our approach.

      Reviewer #2 (Recommendations for the authors):

      Major concerns:

      (1) Protein fragments are used to model the closed and inactivated states of hERG, but the choices of fragments are not well justified. For instance, in Figure 1a, helices from 8EP1 (deactivated voltage-sensing domain) and a helix+loop from 5VA2 (selectivity filter) are used. Why just the selectivity filter and not the cytosolic domain, for instance? Why not some parts of the helices attached to the selectivity filter, or the whole membrane inserted domain of 8EP1? Same for the inactivated conformation in Figure 1c: why the cytosolic domain only?

      We thank the reviewer for their thoughtful questions regarding our choice of protein fragments for modeling the closed and inactivated states of hERG in Figures 1a and 1c, and we appreciate the opportunity to justify these selections more clearly. Our approach to template selection was guided by our experience that providing AlphaFold2 with larger templates often leads it to overly constrain predictions to the input structure, reducing its flexibility to explore alternative conformations. In contrast, smaller, targeted fragments increase the likelihood that AlphaFold2 will incorporate the desired structural features while predicting the rest of the protein. We have provided a more detailed discussion of this in the methodology section.

      For the closed state (Figure 1a), we chose the deactivated voltage-sensing domain (VSD) from the rat EAG channel (PDB 8EP1) to inspire AlphaFold2 to predict a similarly deactivated VSD conformation characteristic of hERG channel closure, as this domain’s downward shift is a hallmark of potassium channel closure. We paired this with the selectivity filter (SF) and adjacent residues from the open-state hERG structure (PDB 5VA2) to maintain its conductive conformation, as it is generally understood that K<sup>+</sup> channel closure primarily involves the intracellular gate rather than significant SF distortion. Including additional helices (e.g., S5–S6) or the entire membrane domain from PDB 8EP1 risked biasing the model toward the EAG channel’s pore structure, which differs from hERG’s, while omitting the cytosolic domain ensured focus on the VSD-driven closure without over-constraining cytoplasmic domain interactions.

      For the inactivated state (Figure 1c), we initially used only the cytosolic domain from PDB 5VA2 to anchor the prediction while allowing AlphaFold2 to freely sample transmembrane domain conformations, particularly the SF, where the inactivation occurs via its distortion. Excluding the SF or attached helices at this stage avoided locking the model into the open-state SF, and the cytosolic domain alone provided a minimal scaffold to maintain hERG’s intracellular architecture without dictating pore dynamics. Following the initial prediction, we initiated more extensive sampling by using one of the predicted SFs that differs from the open-state SF (PDB 5VA2) as a structural seed, aiming to guide predictions away from the open-state configuration. The VSD and cytosolic domain were also included in this state to discourage pore closure during prediction. Using larger fragments, like the full membrane-spanning domains or additional cytosolic regions from the open-state structure might reduce AlphaFold2’s ability to deviate from the open-state conformation, undermining our goal of capturing more diverse, state-specific features.

      It is worth noting that multiple strategies could potentially achieve the predicted models in our study, and here we only present examples of the paths we took and validated. It is likely that many of the steps may be unnecessary and could be skipped, and future work building on our approach can further explore and streamline this process. A consistent theme underlies our choices: for the closed state, we know the VSD should adopt a deactivated (“down”) conformation, so we provide AlphaFold2 with a specific fragment to guide this outcome; for the inactivated state, we recognize that the SF must change to a non-conductive conformation, so we grant AlphaFold2 flexibility to explore diverse conformations by minimizing initial constraints on the transmembrane region.

      With greater sampling and computational resources, it is possible we could identify additional plausible, non-conductive conformations that might better represent an inactivated state, as hERG inactivation may encompass a spectrum of states. In this study, due to resource limitations, we focused on generating and validating a subset of conformations. Still, we acknowledge that broader exploration could further refine these models, which could be pursued in future studies. We updated the Methods and Discussion sections to reflect this perspective, and we are grateful for the reviewer’s input, which encourages us to clarify our rationale and highlight the adaptability of our approach.

      To demonstrate the broader feasibility of this approach, we applied it to another ion channel system, voltage-gated sodium channel Na<sub>V</sub> 1.5, as illustrated in Figure S14. In this example, a deactivated VSD II from the cryo-EM structure of a homologous ion channel Na<sub>V</sub>1.7 (PDB 6N4R) (DOI: 10.1016/j.cell.2018.12.018), which was trapped in a deactivated state by a bound toxin, was used as a structural template. This guided AlphaFold to generate a Na<sub>V</sub>1.5 model in which all four voltage sensor domains (VSD I–IV) exhibit S4 helices in varying degrees of deactivation. Compared to the cryo-EM openstate Na<sub>V</sub>1.5 structure (PDB 6LQA) (DOI: 10.1002/anie.202102196), the predicted model displays a visibly narrower pore, representing a plausible closed state. This example underscores the versatility of our strategy in modeling alternative conformational states across diverse ion channels.

      (2) While the authors rely on AF2 (ColabFold) for the closed and inactivated states, they use Rosetta to model loops of the open state. Why not just supply 5VA2 as a template to ColabFold and rebuild the loops that way? Without clear explanations, these sorts of choices give the impression that the authors were looking for specific answers that they knew from their extensive knowledge of the hERG system. While the modeling done in this paper is very nice, its generalizability is not obvious.

      We appreciate the reviewer’s question about our use of Rosetta to model loops in the open-state hERG channel (PDB

      5VA2) rather than rebuilding it entirely with ColabFold. In the study, we conducted a control experiment supplying parts of PDB 5VA2 to ColabFold to rebuild the loops, generating 100 models (Figure 2a: predicted open state). The top-ranked model (by pLDDT) differed from our Rosetta-modelled structure by only 0.5 Å RMSD, primarily due to the flexible extracellular loops as expected, with the pore and selectivity filter (our areas of focus) remaining nearly identical. We chose the Rosetta-refined cryo-EM structure as this structure and approach have been widely used as an open-state reference in our other hERG channel studies, such as by Miranda et al. (DOI: 10.1073/pnas.1909196117) and Yang et al. (DOI: 10.1161/CIRCRESAHA.119.316404), to ensure that our results are more directly comparable to prior work in the field. Nonetheless, as both models (with loops modeled by Rosetta or AlphaFold) were virtually identical, we would expect no significant differences if either were used to represent the open state in our study. We have incorporated this clarification into the main text.

      (3) pLDDT scores were used as a measure of reliable and accurate predictions, but plDDT is not always reliable for selecting new/alternative conformations (see https://doi.org/10.1038/s41467-024-515072 and https://www.nature.com/articles/s41467-024-51801-z).

      We acknowledge that while pLDDT is a valuable indicator of structural confidence in AlphaFold2 predictions, its limitations warrant consideration. In our revision, we mitigated this by not relying solely on pLDDT, but we also performed protein backbone dihedral angle analysis of the protein regions of focus in all predicted models to ensure comprehensive coverage of conformational variations. From our AlphaFold modeling results, we tested a model from cluster 3 of the inactivated-state sampling process, which exhibited lower pLDDT scores, and included these results in our revised analysis. We included a note in the revised manuscript’s Discussion section: “As noted in recent studies, pLDDT scores are not reliable indicators for selecting alternative conformations (DOI: 10.1038/s41467-024-51507-2 and DOI: 10.1038/s41467-024-51801-z). To address this, we performed a protein backbone dihedral angle analysis in the regions of interest to ensure that our evaluation captured a representative range of sampled conformations.”

      (4) Extensive work has been done using AF2 to model alternative protein conformations (https://www.biorxiv.org/content/10.1101/2024.05.28.596195v1.abstract, along with some references the authors cite, such as work by McHaourab); another group recently modeled the ion channel GLIC (https://www.biorxiv.org/content/10.1101/2024.09.05.611464v1.abstract). Therefore, this work, though generally solid and thorough, seems more like a variation on a theme than a groundbreaking new methodology, especially because of the generalizability issues mentioned above.

      We sincerely thank the reviewer for acknowledging the solidity of our study and for drawing our attention to the impressive recent efforts using AlphaFold2 to explore alternative protein conformations. These studies are valuable contributions that highlight the versatility of AlphaFold2, and we are grateful for their context in evaluating our work.

      Building on these efforts, our approach not only enhances the prediction of conformational diversity but also introduces a twist by incorporating structural templates to guide AlphaFold2 toward specific functional protein states. More significantly, our study advances beyond mere structural modeling by integrating these conformations with their rigorous validation by incorporating multiple simulation results tested against experimental data to reveal that AlphaFold-predicted conformations can align with distinct physiological ion channel states. A key finding is that drug binding predictions using AlphaFold-derived hERG channel states substantially improve correlation with experimental data, which is a longstanding challenge in computational screening of multi-state proteins like the hERG channel, for which previous structural models have been mostly limited to the open state based on the cryo-EM structures. Our approach not only captures this critical state dependence but also reveals potential molecular determinants underlying enhanced drug binding during hERG channel inactivation, a phenomenon observed experimentally but poorly understood. These insights advance drug safety assessment by improving predictive screening for hERG-related cardiotoxicity, a major cause of drug attrition and withdrawal.

      We view our methodology as a natural evolution of the advancements cited by the reviewer, offering an approach that predicts diverse hERG channel conformational states and links them to meaningful functional and pharmacological outcomes. To address the reviewer’s concern about generalizability, we have expanded the methodology section to make it easier to follow and include additional details. As an example, we show how our approach can be applied to model another ion channel system, Na<sub>V</sub>1.5, in Figure S14.

      Furthermore, to enhance the applicability of our methodology, we have uploaded the scripts for analyzing AlphaFoldpredicted models to GitHub (https://github.com/k-ngo/AlphaFold_Analysis), ensuring they are adaptable for a wide range of scenarios with extensive documentation. This enables users, even those not focused on ion channels, to effectively apply our tools to analyze AlphaFold predictions for their own projects and produce publication-ready figures.

      While it is likely that multiple modeling approaches could lead AlphaFold to model alternative protein conformations, the key challenge lies in validating the physiological relevance of those predicted states. This study is intended to support other researchers in applying our template-guided approach to different protein systems, and more importantly, in rigorously in silico testing and validation of the biological significance of the conformation-specific structural models they generate.

      Minor concerns:

      (1) The authors mention in the Introduction section that capturing conformational states, especially for membrane proteins that may be significant as drug targets, is crucial. It would be helpful to relate their work to the NMR studies domains of the hERG channel, particularly the N-terminal “eag” domain, which is crucial for channel function and can provide insights into conformational changes associated with different channel states (https://doi.org/10.1016/j.bbrc.2010.10.132 ).

      We appreciate the reviewer’s insightful comment regarding the PAS domain and the potential influence of other regions, such as the N-linker and distal C-region, on drug binding and state transitions.

      The PAS domain did appear in the starting templates used for initial structural modeling (as shown in Figure 1a, b, c), but it was not included in the final models used for subsequent analyses. The omission was primarily due to hardwareimposed constraints, as including these additional regions would exceed the memory capacity of our current graphics processing unit (GPU) card, leading to failures during the prediction step.

      The PAS domain, even if not serving as a conventional direct drug-binding site, can influence the gating kinetics of hERG channels. By altering the probability and duration with which channels occupy specific states, it can indirectly affect how well drugs bind. For example, if the presence of the PAS domain shifts hERG channel gating so that more channels enter (and remain in) the inactivated state as was shown previously (e.g., DOI: 10.1085/jgp.201210870), drugs with a higher affinity for that state would appear to bind more potently, as observed in previous electrophysiological experiments (e.g., DOI: 10.1111/j.1476-5381.2011.01378.x). It is also plausible that the PAS domain could exert allosteric effects that alter the conformational landscape of the hERG channel during gating transitions, potentially impacting drug accessibility or binding stability. This is an intriguing hypothesis and an important avenue for future research.

      With access to more powerful computational resources, it would be valuable to explore the full-length hERG channel, including the PAS domain and associated regions, to assess their potential contributions to drug binding and gating dynamics. We incorporated a discussion of these points into the main text, acknowledging the limitations of our current models and highlighting the need for future studies to explore these regions in greater detail. The addition reads: “…Our models excluded the N-terminal PAS domain due to GPU memory limitations, despite its inclusion in initial templates. This omission may overlook its potential roles in gating kinetics and allosteric effects on drug binding (e.g., PMID: 21449979, PMID: 23319729, PMID: 29706893, PMID: 30826123, DOI:10.4103/jpp.JPP_158_17). Future research will explore the full-length hERG channel with enhanced computational resources to assess these regions’ contributions to conformational state transitions and pharmacology.”

      (2) In the second-to-last paragraph of the Introduction, the authors describe how AlphaFold2 works. They write, “AlphaFold2 primarily requires the amino acid sequence of a protein as its input, but the method utilizes other key elements: in addition to the amino acid sequence, AlphaFold2 can also utilize multiple sequence alignments (MSAs) of similar sequences from different species, templates of related protein structures when available, and/or homologous proteins (Jumper et al., 2021a). Evolutionarily conserved regions over multiple isoforms and species indicated that the sequence is crucial for structural integrity”. The last sentence is confusing; if the authors mean that all information required to fold the protein into its 3D structure is present in its primary sequence, that has been the paradigm. It is unclear from this paragraph what the authors wanted to convey.

      We apologize for any confusion caused by this phrasing. Our intent was not to restate the well-established paradigm that a protein’s primary sequence contains the information needed for its 3D structure, but rather to emphasize how

      AlphaFold2 leverages evolutionary conservation, via multiple sequence alignments (MSAs), to infer structural constraints beyond what a single sequence alone might reveal. Specifically, we aimed to highlight that conserved regions across species and isoforms provide additional context that AlphaFold2 uses to enhance the accuracy of its predictions, complementing the use of templates and homologous structures as described in Jumper et al. (2021). To clarify this, we revised the sentence in the manuscript to read: “AlphaFold2 primarily requires a protein's amino acid sequence as input, but it also leverages other critical data sources. In addition to the sequence, it incorporates multiple sequence alignments (MSAs) of related proteins from different species, available structural templates, and information on homologous proteins. While the primary sequence encodes the 3D structure, AlphaFold2 harnesses evolutionary conservation from MSAs to reveal structural insights that extend beyond what a single sequence can provide.” We thank the reviewer for pointing out this ambiguity.

      (3) In the Results section, the authors state that the predictions generated by their method are evaluated by standard accuracy metrics, please elaborate - what standard metrics were used to judge the predictions and why (some references would be a nice addition). Further, on Page 6, the sentence “There are fewer differences between the open- and closed-state models (Figure S2b, d)” is confusing, fewer differences than what? or there are a few differences between the two states/models? Please clarify.

      The original sentence referring to “standard accuracy metrics” is somewhat misplaced, as our intent was not to apply any conventional “benchmarking” to judge the predictions, but rather to evaluate functional and structural relevance in a physiologically meaningful context. Specifically, we assessed drug binding affinities from molecular docking simulations (in Rosetta Energy Units, R.E.U.) against experimental drug potency data (e.g., IC<sub>50</sub> values converted to free energies in kcal/mol, Figure 7), analyzed differences in interaction networks across states in relation to known mutations affecting hERG inactivation (Figure 4, Table 2), validated ion conduction properties through MD simulations with the applied voltage against expected state-dependent hERG channel behavior (Figure 5), and compared predicted structural models to available experimental cryo-EM structures (Figure 3). We clarified in the text that our assessment emphasized the physiological plausibility of the generated conformations, drawing on evidence from existing computational and experimental studies at each step of the analysis above.

      As for the sentence on page 6, “There are fewer differences between the open- and closed-state models,” we apologize for the ambiguity; we meant that the hydrogen bond networks in the selectivity filter region exhibit fewer differences between the open and closed states compared to the more pronounced variations seen between the open and inactivated states. We revised this sentence to read: “The open- and closed-state models show fewer differences in their selectivity filter hydrogen bond networks compared to those between the open and inactivated states,” to enhance readability.

      (4) In the Discussion, the authors reiterate that this methodology can be extended to sample multiple protein conformations, and their system of choice was hERG potassium channel. I think this methodology can be applied to a system when there is enough knowledge of static structures, and some information on dynamics (through simulations) and mutagenesis analysis available. A well-studied system can benefit from such a protocol to gauge other conformational states.

      We agree that this approach is well-suited to systems with sufficient static structures, dynamic insights from simulations, and mutagenesis data, as seen with the hERG channel. We appreciate the reviewer’s implicit concern about generalizability to less-characterized systems and addressed this in the Discussion as a limitation, noting that the method’s effectiveness may depend on prior knowledge. Future studies can explore whether the advent of AlphaFold3 and other deep learning approaches can enhance its applicability to systems with more limited data. We have added this comment to the Discussion: “…A limitation of our methodology is its reliance on well-characterized systems with ample static structures, molecular dynamics simulation data, and mutagenesis insights, as demonstrated with the hERG channel, which may limit its applicability to less-studied proteins.”

      (5) The Methods section must be broken down into steps to make it easier to follow for the reader (if they want to implement these steps for themselves on their system of choice).

      a. Is possible to share example scripts and code used to piece templates together for AF2. Also, since the AF3 code is now available, the authors may comment on how their protocol can be applicable there or have plans to implement their protocol using AF3 (which is designed to work better for binding small molecules). Please see https://github.com/google-deepmind/alphafold3 for the recently released code for AF3.

      We appreciate the reviewer’s suggestion to improve the Methods section and their comments on scripts and AlphaFold3 (AF3). We revised the Methods to separate it into clear steps (e.g., template preparation, AF2 setup, clustering, and refinement) for better readability and reproducibility, and uploaded the sample scripts along with the instructions to GitHub (https://github.com/k-ngo/AlphaFold_Analysis).

      Regarding AF3’s recent code release, we plan to explore the applicability of our methodology to AF3 in a follow-up study, leveraging its advanced features to refine conformational predictions and state-specific drug docking, and added a brief comment to the Discussion to reflect this future direction: “…Following the recent release of AlphaFold3’s source code, we plan to explore the applicability of our template-guided methodology in a follow-up study, leveraging AF3’s advanced diffusion-based architecture to enhance protein conformational state predictions and state-specific drug docking, particularly given its improved capabilities for modeling small molecule – protein interactions…”

      b. The authors modified the hERG protein by removing a segment, the N-terminal PAS domain (residues M1 - R397) because of graphics card memory limitation. Would the removal of the PAS domain affect the structure and function of the channel protein? HERG and other members of the “eag K<sup>+</sup> channel” family contain a PAS domain on their cytoplasmic N terminus. Removal of this domain alters a physiologically important gating transition in HERG, and the addition of the isolated domain to the cytoplasm of cells expressing truncated HERG reconstitutes wild-type gating. (see https://doi.org/10.1371/journal.pone.0059265). Please elaborate on this.

      We thank the reviewer for raising an important point about the removal of the N-terminal PAS domain and for highlighting its physiological role in hERG channel gating transitions. In our study, unlike experimental settings where PAS removal alters gating, we believe this omission has minimal impact on our key analyses.

      The drug docking procedure focuses on optimizing drug binding poses with minor protein structural refinement around the putative drug binding site, which in our case is the hERG channel pore region, where hERG-blocking drugs predominantly bind. The cytoplasmic PAS domain, located distally from this site, remains outside the protein structure refinement zone during drug docking simulations. However, one aspect we have not yet considered is the potential effect of drug modulation of the hERG channel gating and vice versa particularly given the PAS domain’s role in gating. This interplay could be significant but requires investigation beyond our current drug docking framework. We plan to explore this in future studies using alternative simulation methodologies, such as extended MD simulations or enhanced sampling techniques, to comprehensively capture these dynamic protein - ligand interactions.

      Similarly, in our 1 μs long MD simulations assessing ion conductivity (Figure 4), the timescale is too short for PASmediated gating changes to propagate through the protein and meaningfully influence ion conduction and channel activation dynamics, which occurs on a millisecond time scale (see e.g., DOI: 10.3389/fphys.2018.00207). To fully address this limitation, we plan to explore the inclusion of the PAS domain in a follow-up study with enhanced computational resources, allowing us to investigate its structural and functional contributions more comprehensively.

      (6) The first paragraph of the Methods reads as though AF2 has layers that recycle structures. We doubt that the authors meant it that way. Please update the language to clarify that recycling is an iterative process in which the pairwise representation, MSA, and predicted structures are passed (“recycled”) through the model multiple times to improve predictions.

      We agree that the phrasing might suggest physical layers recycling structures, which was not our intent. Instead, we meant to describe AlphaFold2’s iterative refinement process, where intermediate outputs, such as the pairwise residue representations, multiple sequence alignments (MSAs), and predicted structures, are iteratively passed (or “recycled”) through the model to enhance prediction accuracy. To clarify this, we revised the relevant sentence to read: “A critical feature of AlphaFold2 is its iterative refinement, where pairwise residue representations, MSAs, and initial structural predictions are recycled through the model multiple times, improving accuracy with each iteration.”

      Reviewer #3 (Recommendations for the authors):

      The authors should integrate the very recently published CryoEM experimental data of hERG inhibition by several drugs (Miyashita et al., Structure, 2024; DOI: 10.1016/j.str.2024.08.021).

      We thank the reviewer for the suggestion. Here, we compare drug binding in our open-states (PDB 5VA2-derived and an additional AlphaFold-predicted model from Cluster 3 of inactivated-state-sampling attempt named “AF ic3”) and inactivated-state models, using the cationic forms of astemizole and E-4031, with the corresponding experimental structures (Figure S13). Drug binding in the closed state is excluded as the pore architecture deviates too much from those in the cryo-EM structures. Experimental data (DOI: 10.1124/mol.108.049056) indicate that both astemizole and E4031 bind more potently to the inactivated state of the hERG channel.

      Astemizole (Figure S13a):

      - In the PDB 5VA2-derived open-state model, astemizole binds centrally within the pore cavity, adopting a bent conformation that allows both aromatic ends of the molecule to engage in π–π stacking with the side chains of Y652 from two opposing subunits. Hydrophobic contacts are observed with S649 and F656 residues.

      - In the AF ic3 open-state model, the ligand is stabilized through multiple π–π stacking interactions with Y652 residues from three subunits, forming a tight aromatic cage around its triazine and benzimidazole rings. Hydrophobic interactions are observed with hERG residues T623, S624, Y652, F656, and S660.

      - In the inactivated-state model, astemizole adopts a compact, horizontally oriented pose deeper in the channel pore, forming the most extensive interaction network among all the states. The ligand is tightly stabilized by multiple π–π stacking interactions with Y652 residues across three subunits, and forms hydrogen bonds with residues S624 and Y652. Additional hydrophobic contacts are observed with residues F557, L622, S649, and Y652.

      - Consistent with our findings, electrophysiology study by Saxena et al. identified hERG residues F557 and Y652 as crucial for astemizole binding, as determined through mutagenesis (DOI: 10.1038/srep24182).

      - In the cryo-EM structure (PDB 8ZYO) (DOI: 10.1016/j.str.2024.08.021), astemizole is stabilized by π–π stacking with Y652 residues. However, no hydrogen bonds are detected which may reflect limitations in cryo-EM resolution rather than true absence of contacts. Additional hydrophobic interacts are observed with L622 and G648 residues.

      E-4031 (Figure S13b):

      - In the PDB 5VA2-derived open-state model, E-4031 binds within the central cavity primarily through polar interactions. It forms a π–π stacking interaction with residue Y652, anchoring one end of the molecule. Polar interactions are observed with residues A653 and S660. Additional hydrophobic contacts are observed with residues A652 and Y652.

      - In the AF ic3 open-state model, E-4031 adopts a slightly deeper pose within the central cavity stabilized by dual π–π stacking interactions between its aromatic rings and hERG residue Y652. Additional hydrogen bonds are observed with residues S624 and Y652, and hydrophobic contacts are observed with residues T623 and S624.

      - In the inactivated-state model, E-4031 adopts its deepest and most stabilized binding pose, consistent with its experimentally observed preference for this state. The ligand is stabilized by multiple π–π stacking interactions between its aromatic rings and hERG residues Y652 from opposing subunits. The sulfonamide nitrogen engages in hydrogen bonding with residue S649, while the piperidine nitrogen hydrogen bonds with residue Y652. Hydrophobic contacts with residues S624, Y652, and F656 further reinforce the binding, enclosing the ligand in a densely packed aromatic and polar environment.

      - Previous mutagenesis study showed that mutations involving hERG residues F557, T623, S624, Y652, and F656 affect E-4031 binding (DOI: 10.3390/ph16091204).

      - In the cryo-EM structure (PDB 8ZYP) (DOI: 10.1016/j.str.2024.08.021), E-4031 engages in a single π–π stacking interaction with hERG residue Y652, anchoring one end of the molecule. The remainder of the ligand is stabilized predominantly through hydrophobic contacts involving residues S621, L622, T623, S624, M645, G648, S649, and additional Y652 side chains, forming a largely nonpolar environment around the binding pocket.

      In both cryo-EM structures, astemizole and E-4031 adopt binding poses that closely resembles the inactivated-state model in our docking study, consistent with experimental evidence that these drugs preferentially bind to the inactivated state (DOI: 10.1124/mol.108.049056). This raises the possibility that the cryo-EM structures may capture an inactivatedlike channel state. However, closer examination of the SF reveals that the cryo-EM conformations more closely resemble the open-state PDB 5VA2 structure (DOI: 10.1016/j.cell.2017.03.048), which has been shown to be conductive here and in previous studies (DOI: 10.1073/pnas.1909196117, 10.1161/CIRCRESAHA.119.316404).

      The conformational differences between the cryo-EM and open-state docking results may reflect limitations of the docking protocol itself, as GALigandDock assumes a rigid protein backbone and cannot account for ligand-induced large conformational changes. In our open-state models, the hydrophobic pocket beneath the selectivity filter is too small to accommodate bulky ligands (Figure 3a, b), whereas the cryo-EM structures show a slight outward shift in the S6 helix that expands this space (Figure S13).These allosteric rearrangements, though small, falls outside the scope of the current docking protocol, which lacks flexibility to capture these local, ligand-induced adjustments (DOI: 10.3389/fphar.2024.1411428).

      In contrast, docking to the AlphaFold-predicted inactivated-state model reveals a reorganization beneath the selectivity filter that creates a larger cavity, allowing deeper ligand insertion. Notably, neither our inactivated-state docking nor the available cryo-EM structures show strong interactions with F656 residues. However, in the AlphaFold-predicted inactivated model, the more extensive protrusion of F656 into the central cavity may further occlude the drug’s egress pathway, potentially trapping the ligand more effectively. This could explain why mutation of F656 significantly reduces the binding affinity of E-4031 (DOI: 10.3390/ph16091204). These findings suggest that inactivation may trigger a series of modular structural rearrangements that influence drug access and binding affinity, with different aspects potentially captured in various computational and experimental studies, rather than resulting from a single, uniform conformational change.

      Discussion of the original Wang and Mackinnon finding, DOI: 10.1016/j.cell.2017.03.048 regarding C-inactivation, pore mutation S631A and F627 rearrangement is likely warranted. Since hERG inactivation is present at 0 mV in WT channels (the likely voltage for the CryoEM study) please discuss how this might affect interpretations of starting with this structure as a template for models presented here, perhaps as part of Figure S1.

      We sincerely thank the reviewer for bringing up the insightful findings from Wang and MacKinnon regarding hERG C-type inactivation as well as the voltage context of their cryo-EM structure (PDB 5VA2). We recognize that WT hERG exhibits inactivation at 0 mV, likely the condition of the cryo-EM study, raising the possibility that PDB 5VA2, while classified as an open state, might subtly reflect features of inactivation. Notably, PDB 5VA2 has been widely adopted in numerous studies and consistently found to represent a conducting state, such as in Yang et al. (DOI: 10.1161/CIRCRESAHA.119.316404) and Miranda et al. (DOI: 10.1073/pnas.1909196117). Our MD simulations further support this, showing K<sup>+</sup> conduction in the 5VA2-based open-state model (Figure 4a, c), consistent with its selectivity filter conformation (Figure S1a). Although we used PDB 5VA2 as a starting template for predicting inactivated and closed states, our AlphaFold2 predictions did not rigidly adhere to this structure, as evidenced by distinct differences in hydrogen bond networks, drug binding affinities, pore radii, and ion conductivity between our state-specific hERG channel models (Figures S2, 5, 3b, 4). Nevertheless, this does not preclude the possibility that PDB 5VA2’s certain potential inactivated-like traits at 0 mV could subtly influence our predictions elsewhere in the model, which warrants further exploration in future studies. In our revised analysis, we also tested an alternative AlphaFold-predicted conformation, referred to as Open (AlphaFold cluster 3), which, while sharing some similarities with PDB 5VA2, exhibits subtle differences in the selectivity filter and pore conformations. This structure was also found to be conducting ions and showed a drug binding profile similar to that of the PDB 5VA2-based open-state model. We greatly appreciate this feedback which helped us refine and strengthen our analysis.

      Page 8, the significance of 750 and 500 mV in terms of physiological role?

      We appreciate this opportunity to clarify the methodological rationale. Although these voltages significantly exceed typical physiological membrane potentials, their use in MD simulations is a well-established practice to accelerate ion conduction events. This approach helps overcome the inherent timescale limitations of conventional MD simulations, as demonstrated in previous studies of hERG and other ion channels. For instance, Miranda et al. (DOI: 10.1073/pnas.1909196117), Lau et al. (DOI: 10.1038/s41467-024-51208-w), Yang et al. (DOI: 10.1161/CIRCRESAHA.119.316404) applied similarly high voltages (500~750 mV) to study hERG K<sup>+</sup> conduction, which is notably small under physiological conditions at ~2 pS (DOI: 10.1161/01.CIR.94.10.2572), necessitating amplification to observe meaningful permeation within nanosecond-to-microsecond timescales. Likewise, studies of other K<sup>+</sup> ion channels, such as Woltz et al. (DOI: 10.1073/pnas.2318900121) on small-conductance calcium-activated K<sup>+</sup> channel SK2 and Wood et al. (DOI: 10.1021/acs.jpcb.6b12639) on Shaker K<sup>+</sup> channel, have used elevated voltages (250~750 mV) to probe ion conduction mechanisms via MD simulations. In addition, the typical timescale of these simulations (1 μs) is too short to capture major structural effects such as those leading to inactivation or deactivation which occur over milliseconds in physiological conditions.

      The abstract could be edited a bit to more clearly state the novel findings in this study.

      We thank the reviewer for their suggestion. We have revised the abstract to read: “To design safe, selective, and effective new therapies, there must be a deep understanding of the structure and function of the drug target. One of the most difficult problems to solve has been resolution of discrete conformational states of transmembrane ion channel proteins. An example is K<sub>V</sub>11.1 (hERG), comprising the primary cardiac repolarizing current, I<sub>kr</sub>. hERG is a notorious drug antitarget against which all promising drugs are screened to determine potential for arrhythmia. Drug interactions with the hERG inactivated state are linked to elevated arrhythmia risk, and drugs may become trapped during channel closure. While prior studies have applied AlphaFold to predict alternative protein conformations, we show that the inclusion of carefully chosen structural templates can guide these predictions toward distinct functional states. This targeted modeling approach is validated through comparisons with experimental data, including proposed state-dependent structural features, drug interactions from molecular docking, and ion conduction properties from molecular dynamics simulations. Remarkably, AlphaFold not only predicts inactivation mechanisms of the hERG channel that prevent ion conduction but also uncovers novel molecular features explaining enhanced drug binding observed during inactivation, offering a deeper understanding of hERG channel function and pharmacology. Furthermore, leveraging AlphaFold-derived states enhances computational screening by significantly improving agreement with experimental drug affinities, an important advance for hERG as a key drug safety target where traditional single-state models miss critical state-dependent effects. By mapping protein residue interaction networks across closed, open, and inactivated states, we identified critical residues driving state transitions validated by prior mutagenesis studies. This innovative methodology sets a new benchmark for integrating deep learning-based protein structure prediction with experimental validation. It also offers a broadly applicable approach using AlphaFold to predict discrete protein conformations, reconcile disparate data, and uncover novel structure-function relationships, ultimately advancing drug safety screening and enabling the design of safer therapeutics.”

      Many of the Supplemental figures would fit in better in the main text, if possible, in my opinion. For instance, the network analysis (Fig. S2) appears to be novel and is mentioned in the abstract so may fit better in the main text. The discussion section could be focused a bit more, perhaps with headers to highlight the key points.

      Yes, we agree with the reviewer and made the suggested changes. We moved Figure S2 as a new main-text figure.

      Additionally, we revised the Discussion section to improve focus and clarity.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The study significantly advances our understanding of how exosomes regulate filopodia formation. Filopodia play crucial roles in cell movement, polarization, directional sensing, and neuronal synapse formation. McAtee et al. demonstrated that exosomes, particularly those enriched with the protein THSD7A, play a pivotal role in promoting filopodia formation through Cdc42 in cancer cells and neurons. This discovery unveils a new extracellular mechanism through which cells can control their cytoskeletal dynamics and interaction with their surroundings. The study employs a combination of rescue experiments, live-cell imaging, cell culture, and proteomic analyses to thoroughly investigate the role of exosomes and THSD7A in filopodia formation in cancer cells and neurons. These findings offer valuable insights into fundamental biological processes of cell movement and communication and have potential implications for understanding cancer metastasis and neuronal development.

      Weaknesses:

      The conclusions of this study are in most cases supported by data, but some aspects of data analysis need to be better clarified and elaborated. Some conclusions need to be better stated and according to the data observed.

      We appreciate the reviewer's recognition of the impact of our study. We will address the concerns about data analysis and the statement of our conclusions in our full response to reviewers.

      Reviewer #2 (Public review):

      Summary:

      The authors show that small EVs trigger the formation of filopodia in both cancer cells and neurons. They go on to show that two cargo proteins, endoglin, and THSD7A, are important for this process. This possibly occurs by activating the Rho-family GTPase CDC42.

      Strengths:

      The EV work is quite strong and convincing. The proteomics work is well executed and carefully analyzed. I was particularly impressed with the chick metastasis assay that added strong evidence of in vivo relevance.

      Weaknesses:

      The weakest part of the paper is the Cdc42 work at the end of the paper. It is incomplete and not terribly convincing. This part of the paper needs to be improved significantly

      We appreciate the reviewer's recognition of the impact of our study. Indeed, more work needs to be done to clarify the role of Cdc42 in the induction of filopodia by exosome-associated THSD7A. We anticipate that this will be a separate manuscript, delving in-depth into how exosome-associated THSD7A interacts with recipient cells to activate Cdc42 and carrying out a variety of assays for Cdc42 activation.

      Reviewer #3 (Public review):

      Summary:

      The authors identify a novel relationship between exosome secretion and filopodia formation in cancer cells and neurons. They observe that multivesicular endosomes (MVE)-plasma membrane (PM) fusion is associated with filopodia formation in HT1080 cells and that MVEs are present in filopodia in primary neurons. Using overexpression and knockdown (KD) of Rab27/HRS in HT1080 cells, melanoma cells, and/or primary rat neurons, they found that decreasing exosome secretion reduces filopodia formation, while Rab27 overexpression leads to the opposite result. Furthermore, the decreased filopodia formation is rescued in the Rab27a/HRS KD melanoma cells by the addition of small extracellular vesicles (EVs) but not large EVs purified from control cells. The authors identify endoglin as a protein unique to small EVs secreted by cancer cells when compared to large EVs. KD of endoglin reduces filopodia formation and this is rescued by the addition of small EVs from control cells and not by small EVs from endoglin KD cells. Based on the role of filopodia in cancer metastasis, the authors then investigate the role of endoglin in cancer cell metastasis using a chick embryo model. They find that injection of endoglin KD HT1080 cells into chick embryos gives rise to less metastasis compared to control cells - a phenotype that is rescued by the co-injection of small EVs from control cells. Using quantitative mass spectrometry analysis, they find that thrombospondin type 1 domain containing 7a protein (THSD7A) is downregulated in small EVs from endoglin KD melanoma cells compared to those from control cells. They also report that THSD7A is more abundant in endoglin KD cell lysate compared to control HT1080 cells and less abundant in small EVs from endoglin KD cells compared to control cells, indicating a trafficking defect. Indeed, using immunofluorescence microscopy, the authors observe THSD7A-mScarlet accumulation in CD63-positive structures in endoglin KD HT1080 cells, compared to control cells. Finally, the authors determine that exosome-secreted THSD7A induces filopodia formation in a Cdc42-dependent mechanism.

      Strengths:

      (1) While exosomes are known to play a role in cell migration and autocrine signaling, the relationship between exosome secretion and the formation of filopodia is novel.

      (2) The authors identify an exosomal cargo protein, THSD7A, which is essential for regulating this function.

      (3) The data presented provide strong evidence of a role for endoglin in the trafficking of THSD7A in exosomes.

      (4) The authors associate this process with functional significance in cancer cell metastasis and neurological synapse formation, both of which involve the formation of filopodia.

      (5) The data are presented clearly, and their interpretation appropriately explains the context and significance of the findings.

      Weaknesses:

      (1) A better characterization of the nature of the small EV population is missing:

      It is unclear why the authors chose to proceed to quantitative mass spectrometry with the bands in the Coomassie from size-separated EV samples, as there are other bands present in the small EV lane but not the large EV lane. This is important to clarify because it underlies how they were able to identify THSD7A as a unique regulator of exosome-mediated filopodia formation. Is there a reason why the total sample fractions were not compared? This would provide valuable information on the nature of the small and large EV populations.

      We would like to clarify that there are two sets of proteomics data in the manuscript. The first was comparing bands from a colloidal Coomassie-stained gel from two samples: small EVs and large EVs from B16F1 cells. In this proteomics experiment, we identified endoglin as present in small EVs, but not large EVs. For this experiment, we only sent four bands from the small EV lane, chosen based on their obvious banding pattern difference on the Coomassie gel.

      In the second proteomics experiment, we used quantitative iTRAQ proteomics to compare small EVs purified from B16F1 control (shScr) and endoglin KD (shEng1 and shEng2) cell lines. In this experiment, we sent total protein extracted from small EV samples for analysis. So, these samples included the entire EV content, not just selected bands from a gel. In this experiment, we identified THSD7A as reduced in the shEng small EVs.

      (2) Data analysis and quantification should be performed with increased rigor:

      a) Figure 1C - The optical and temporal resolution are insufficient to conclusively characterize the association between exosome secretion and filopodia. Specifically, the 10-second interval used in the image acquisitions is too close to the reported 20-second median time between exosome secretion and filopodia formation. Two-5 sec intervals should be used to validate this. It would also be important to correlate the percentage of filopodia events that co-occur with exosome secretion. Is this a phenomenon that occurs with most or only a small number of filopodia? Additionally, resolution with typical confocal microscopy is subpar for these analyses. TIRF microscopy would offer increased resolution to parse out secretion events. As the TIRF objective is listed in the Methods section, figure legends should mention which images were acquired using TIRF microscopy.

      We acknowledge that the frame rate naturally limits our estimates of the timing of filopodia formation after exosome secretion. We set out to show a relationship between exosome secretion and filopodia formation, based on their proximity in timing. While our data set shows a median time interval of 20 seconds, the true median could be between 10-30 seconds, based on our frame rate. Regardless of the exact timing, our data show that exosome secretion is rapidly followed by filopodia formation events.

      To address the question of the percentage of filopodia events that are preceded by exosome secretion, the reviewer is correct in stating that we might need TIRF microscopy and a faster frame rate to observe all the MVB fusion events and get an accurate calculation of this number. The timing of the acquisition was based on the typical timing of filopodia formation, which is slow relative to MVB fusion. Thus, with the current dataset, we could miss secretion events taking place between the 10 second time intervals. Therefore, to address this question, we would need to acquire a new dataset with a much more rapid frame acquisition (multiple frames per second rather than one frame every ten seconds). Regardless, for the secretion events that we visualized with the current dataset, we always observed subsequent filopodia formation.

      No TIRF imaging was used in this manuscript. A TIRF objective was used for selected neuron imaging (see methods); however, it was used for spinning disk confocal microscopy, not for TIRF imaging. This is stated in the methods.

      b) Figure 2 - It would be important to perform further analysis to concretely determine the relationship between exosome secretion and filopodia stability. Are secretion events correlated with the stability of filopodia? Is there a positive feedback loop that causes further filopodia stability and length with increased secretion? Furthermore, is there an association between the proximity of secretion with stability? Quantification of filopodia more objectively (# of filopodia/cell) would be helpful.

      Our data show that manipulation of general exosome secretion, via Hrs knockdown, affects both de novo filopodia formation and filopodia stability (Fig 2g,h). Interestingly, knockdown of endoglin only affects de novo filopodia formation, while filopodia stability is unaffected (Fig 4g,h). These results suggest that filopodia stability is dependent upon exosome cargoes besides endoglin/THSD7A. Such cargoes might include other extracellular matrix molecules, such as fibronectin. We previously showed that exosomes promote nascent cell adhesion and rapid cell migration, through exosome-bound fibronectin (Sung et al., Nature Communications, 6:7164, 2015). We also previously found that inhibition of exosome secretion affects the persistence of invadopodia, which are filopodia-dependent structures (Hoshino et al., Cell Reports, 5:1159-1168, 2013). We agree that this is an interesting research direction, and perhaps future work could focus on exosomal factors that are responsible for filopodia persistence. This would possibly involve more proteomics analysis to identify candidate exosomal cargoes involved in this process.

      With regard to the way we plotted the filopodia data, we plotted the cancer cell data as filopodia per cell area so that it matched the neuron data, which was plotted as filopodia per 100 µm of dendrite distance. Since the neurons cannot be imaged as a whole cell, the quantification is based on the length of the dendrite in the image. We found that graphing the cancer cell data as filopodia per cell gave similar results as filopodia per cell area. To demonstrate that this quantification gives similar results, we have now plotted the filopodia per cell area data from Fig 2 as filopodia per cell and placed these new plots in Supp Fig 2.

      c) Figure 6 - Why use different gel conditions to detect THSD7A in small EVs from B16F1 cells vs HT1080 and neurons? Why are there two bands for THSD7A in panels C and E? It is difficult to appreciate the KD efficiency in E. The absence of a signal for THSD7A in the HT1080 shEng small EVs that show a signal for endoglin is surprising. The authors should provide rigorous quantification of the westerns from several independent experimental repeats.

      Detection of THSD7A via Western blot was, unfortunately, not straightforward and simple. Due to the large size (~260 kDa) of THSD7A, its low level of expression in cancer cells, as well as the inconsistency of commercially available THSD7A antibodies, we had to troubleshoot multiple conditions. We found that it was much easier to detect THSD7A in the human fibrosarcoma cell line HT1080 than in the mouse B16F1 cells, both in the cell lysates and in the small EVs. We were unable to detect THSD7A using the same (reducing) conditions for the mouse melanoma B16F1 samples but were successful using native gel conditions. We also detected THSD7A in rat primary neuron samples. All these samples were from different source organisms (human, mouse, rat) and from either cell lysates or extracellular vesicles, further complicating the analyses. Expression and maturation of THSD7A in these different cell types and compartments could involve different post-translational modifications, such as glycosylation, thus requiring different methods needed to detect THSD7A on Western blots and leading to different banding patterns.

      With regard to the level of knockdown of THSD7A in the Western blot shown in Figure 6E, the normalized level is quantitated below the bands. If you compare that quantitation to the filopodia phenotypes in the same panel, they are quite concordant. Figures 7B and 7C show quantification of triplicate Western blots, highlighting the significant accumulation of THSD7A in shEng cell lysates, as well as significant small EV secretion of THSD7A in control and WT rescued conditions.

      (3) The study lacks data on the cellular distribution of endoglin and THSD7A:

      a) Figure 6 - Is THSD7A expected to be present in the nucleus as shown in panel D (label D is missing in the Figure). It is not clear if this is observed in neurons. a Western of endogenous THSD7A on cell fractions would clarify this. The authors should further characterize the cellular distribution of THSD7A in both cell types. Similarly, the cellular distribution of endoglin in the cancer cells should be provided. This would help validate the proposed model in Figure 8.

      The image in figure 6D shows an HT1080 cell stained with phalloidin-Alexa Fluor 488 to visualize F-actin with or without expression of THSD7A-mScarlet. In order to fully visualize the thin filopodia protrusions, the cellular plane of focus of the images for this panel was purposely taken at the bottom of the cell, where the cell is attached to the coverslip glass. Thus, we interpret the red signal across the cell body as THSD7A-mScarlet expression on the plasma membrane underneath the cell, not in the nucleus. The neuron images only include the dendrite portion of the neurons; therefore, there is no nucleus present in the neuronal images. For the cellular distribution of endoglin, we agree that this is an important future direction to understand how endoglin regulates THSD7A trafficking. We have added the lack of these data to the “Limitations” section at the end of the manuscript.

      b) Figure 7 - Although the western blot provides convincing evidence for the role of endoglin in THSD7A trafficking, the microscopy data lack resolution as well as key analyses. While differences between shSCR and shEng cells are clear visually, the insets appear to be zoomed digitally which decreases resolution and interferes with interpretation. It would be crucial to show the colocalization of endoglin and THSD7A within CD63-postive MVE structures. What are the structures in Figure 7E shSCR zoom1? It would be important to rule out that these are migrasomes using TSPAN4 staining. More information on how the analysis was conducted is needed (i.e. how extracellular areas were chosen and whether the images are representative of the larger population). A widefield image of shSCR and shEng cells and DAPI or HOECHST staining in the higher magnification images should be provided. Additionally, the authors should quantify the colocalization of external CD63 and mScarlet signals from many independently acquired images (as they did for the internal signals in panel F). Is there no external THSD7A signal in the shEng cells?

      The images for Figure 7E were taken with high resolution on a confocal microscope. Insets for Figure 7E were digitally zoomed so that readers could see the tiny structures. Zoom 1 in Figure 7E shows areas of extracellular deposition, whereas Zoom 2 shows THSD7A colocalization with CD63 in MVE. In the extracellular areas (Zoom 1), we observe small punctate depositions that are positive for CD63 and/or THSD7A-mScarlet. Our interpretation of this staining is that the cells are secreting heterogeneous small EVs that are then attached to the glass coverslip. The images and zooms in Fig 7E were chosen to be representative and indeed reveal that there is more extracellular deposition of THSD7A-mScarlet outside the control shScr cells compared to the shEng cells, consistent with more secretion of THSD7A in small EVs from shScr cells when compared to those of shEng cells (Fig 7A,B). However, we did not quantify this difference, as these experiments were conducted with transient transfection of THSD7A-mScarlet, and it is challenging to determine which cell the extracellular THSD7A-mScarlet came from, complicating any quantitative analysis on a per-cell basis.

      Quantification of internal THSD7A localization is much more straightforward in this experimental regime. Indeed, in Figure 7F, we quantitated internal colocalization of THSD7A-mScarlet and CD63, which we obtained by choosing only cells that were visually positive for THSD7A-mScarlet in each transient transfection and omitting all extracellular signals. Quantifying the extracellular colocalization of THSD7A and CD63 could certainly be a future direction for this project and would require establishing cells that stably express THSD7A-mScarlet.

      With regard to whether the extracellular deposits are migrasomes, we have no reason to believe that they would be migrasomes. The preponderance of our evidence points to exosomes as carrying THSD7A and inducing filopodia. Furthermore, CD63 is an exosome marker (Sung et al., Nat Comm, 2020) and does not induce migrasomes, unlike many other tetraspanins (Huang et al., Nat Cell Bio, 2019).

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The authors need to clarify the figure labeling and description and conclusions would be better to be drawn based on the findings. Some figures need to more clear e.g. Figure 1E needs to have information on what are green and red fluorescent proteins. Do all figures in 1A have the same scale bar or different? Figure 3A lacks a scale bar. In Figure 3, the GFP signal is in yellow, does it represent a merge or is it just the GFP alone? Figure 6D is missing a D. Figure 4D needs to be better explained. Additionally, both figures 8B and 8C since represent a model based on all the findings of the study would be better to stand alone as a separate figure from figure 8A.

      The figure legend for figure 1E notes that green corresponds to GFP-Rab27b and the red corresponds to mCherry filler. In addition, the labels are marked to the right of the figure. For Figure 1A, we have now indicated in the legend that all scale bars = 10 µm. In figure 3, neurons were co-transfected with GFP or GFP-Rab27b. Thus, the yellow signal in these images is the merge of the mCherry filler with either GFP (expression throughout the neuron body and dendrites) or GFP-Rab27b (punctate colocalization). We have added a scale bar to Fig 3A. Figure 6D has been corrected, with a “D” label added. Figure 4D shows representative images of cells with filopodia under the various conditions, including add-back of control or endoglin-KD EVs. We have clarified the conditions in the figure legend for 4D. For Figure 8, we have now split it into 2 figures: one with data (Fig 8) and one with the model (Fig 9).

      Reviewer #2 (Recommendations for the authors):

      For the most part, this story is strong and well-presented. The findings are interesting and will significantly advance our understanding of how EVs affect various processes such as cancer metastasis. However, the Cdc42 work is not great. They only indirectly implicate Cdc42 with a somewhat iffy inhibitor (ML141) and a constitutively active form transfected into cells. Both approaches have drawbacks such as off-target effects in the case of the inhibitor and possible cross-talk to other GTPases in the case of the active mutant. The activation of Cdc42 should be demonstrated by an activity assay. Several commercial kits are available. Inhibition of Cdc42 should be tested by knockdown in addition to the inhibitor.

      We appreciate the reviewer’s recognition of our work. To address the limitations of our study, particularly the Cdc42 mechanistic work, we have now added a “Limitations of the study” section at the end of the text. Here, we address our experimental limitations and future directions.

      Reviewer #3 (Recommendations for the authors):

      (1) Since the purified small EVs contain canonical exosomal markers and originate from MVEs, the authors should consider a more consistent use of the term "exosome" to avoid confusion.

      We acknowledge that the usage of both “exosomes” and “small extracellular vesicles” can seem confusing to many readers. Typically in the EV field, we use the term “exosome” when we can reliably determine that the EVs originate from the endocytic pathway. Thus, we use this term when we have specifically perturbed this pathway by targeting Hrs or Rab27. We use the term “small extracellular vesicles” or SEVs when referring to a purified heterogeneous population of SEVs from unknown or a variety of origins. Thus, when referring to vesicles isolated from the conditioned media, we call them SEVs because we cannot determine their origin. Clarification of this terminology has been added to the introduction of the paper.

      (2) 1st results section - expressing mCherry as a "filler" is confusing, clarify that this is meant to identify cellular background.

      This has now been clarified in the paper.

      (3) Figure 3 - Although Rab27a and Rab27b play a role in exosome secretion, Rab27b does not have redundant functions with Rab27a in every cellular context. The authors should mention the specific roles of Rab27a and Rab27b in promoting MVE fusion with the PM and in regulating the anterograde movement of MVEs to the PM, respectively (Ostrowski et al. 2010, Citation 52 in the ms). Although Rab27a is not highly expressed in neurons, it is not currently clear whether Rab27b has a redundant function with Rab27a or whether there is another unknown factor that plays this role. As neurons also do not express endoglin, the mechanisms that mediate how EVs regulate filopodia formation in these cells are most probably different than in cancer cells. This should be highlighted in the discussion.

      We have now added a couple of clarifying sentences about the roles of Rab27a and Rab27b to the results section, including the Ostrowski reference and another reference suggesting possible redundancy of Rab27a and Rab27b. With regard to endoglin not being expressed by neurons, that is one reason why we carried out the proteomics with control and endoglin-KD EVs to find a universal cargo that would directly induce filopodia formation. Indeed, THSD7A seems to be such a universal cargo, expressed in both cancer cell and neuron EVs and inducing filopodia in both cell types. This point, along with the requirement for regulation of THSD7A by other molecules in neurons, is discussed in the results and discussion sections.

      (4) As the authors note, the mechanistic link between endoglin-sorted, exosomal THSD7A and Cdc42-mediated filopodia formation remains unclear. While the findings on Cdc-42 are clear, they are not surprising. What is the role of mDia/ENA/VASP or BAR proteins in this? The authors should also consider an assay to determine whether exosomal THSD7A binds to the PM to cause the signaling or if the cargo is first internalized before performing its function. Since this process is both autocrine and paracrine, the authors could co-culture THSD7A-mScarlet cells with vector control cells and observe how THSD7A-mScarlet is localized in the non-expressing cells.

      As other reviewers also noted, the Cdc42 mechanistic data at the end of the paper has clear limitations that are now addressed within the manuscript in a “Limitations of the Study” section. Here we discuss our experimental troubleshooting and approach to assaying Cdc42 involvement in this process. We acknowledge there are many rigorous experiments that could be pursued in the future to strengthen our mechanism and proposed model.

      We also agree that elucidating how THSD7A specifically interacts with target cells would be very informative and insightful. This would be most effectively assayed using a cell line that is stably expressing THSD7A-mScarlet and could be a future direction of this project. However, it is out of the scope of this current publication.

    1. Author Response:

      We appreciate the reviewers’ thoughtful assessments and constructive feedback on our manuscript. The central goal of our study was to propose a simple and biologically inspired model-based reinforcement learning (MBRL) framework that draws on mechanisms observed in episodic memory systems. Unlike model-free approaches that require processing at each state transition, our model uses sequential activity (= transition model) to predict environmental changes in the long term by leveraging episode-like representations.

      While many prior studies have focused on optimizing task performance in MBRL, our primary aim is to explore how flexible, context-dependent behavior—reminiscent of that observed in biological systems—can be instantiated using simple, neurally plausible mechanisms. In particular, we emphasize the use of an Amari-Hopfield network for the context selection module. This network, governed by Hebbian learning, forms attractors that can correct for sensory noise and facilitate associative recall, allowing dynamic separation of prediction errors due to sensory noise versus those due to contextual mismatches. However, we acknowledge that our explanation of these mechanisms, especially in relation to sensory noise, was not sufficiently developed in the current manuscript. We plan to revise the text to clarify this limitation and to expand on the implications of these mechanisms in the context of psychiatric disorder-like behaviors, as illustrated in Figure 5. Several reviewers raised concerns about the clarity of our model. Our implementation is intentionally algorithmic rather than formal, designed to provide an accessible proof-of-concept model. We will revise the manuscript to better describe the core logic of the model—namely, the bidirectional interaction between the Hopfield network (X) and the hippocampal sequence module (H), where X sends the information on estimated current context to H, and H returns a future prediction based on the episode to X. This interaction forms a loop enabling the current context estimation and its reselection.

      The key advantage of this architecture is its ability to flexibly adjust the temporal span of episodes used for inference and control, providing a potential solution to the challenge of credit assignment over variable time scales in MBRL. Because our model forms and stores the variable length of episodes depending on the context, it can handle both short-horizon and long-horizon tasks simultaneously. Moreover, because each episode is organized by context, reselecting contexts enables rapid switching between these variable timescales. This flexibility addresses a challenge in MBRL—the assignment of credit across variable time scales—without requiring explicit optimization. To better illustrate this important feature, we plan to include additional experiments in the revised manuscript that demonstrate how context-dependent modulation of episode length enhances behavioral flexibility and task performance.

      Finally, we will address the comments on the presentation and the biological grounding of our model. To improve clarity and biological relevance, we will revise the Methods section to explicitly describe how the model is grounded in mechanisms observed in real neural systems. Also, we will clarify which parts of our figures represent computational results versus schematic illustrations and more clearly explain how each model component relates to known neural mechanisms. These revisions aim to improve both clarity and accessibility for a broad audience, while reinforcing the biological relevance of our approach.

      We thank the reviewers again for their insightful comments, which will help us substantially improve the manuscript. We look forward to submitting a revised version that more clearly conveys the contributions and implications of our work.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      In this study, Hama et al. explored the molecular regulatory mechanisms underlying the formation of the ULK1 complex. By employing the AlphaFold structural prediction tool, they showed notable differences in the complex formation mechanisms between ULK1 in mammalian cells and Atg1 in yeast cells. Their findings revealed that in mammalian cells, ULK1, ATG13, and FIP200 form a complex with a stoichiometry of 1:1:2. These predicted interaction regions were validated through both in vivo and in vitro assays, enhancing our understanding of the molecular mechanisms governing ULK1 complex formation in mammalian cells. Importantly, they identified a direct interaction between ULK1 and FIP200, which is crucial for autophagy. However, some aspects of this manuscript require further clarification, validation, and correction by the authors.

      Thank you for your thorough evaluation of our manuscript. We have carefully revised the manuscript to address your concerns by performing extra experiments and providing additional clarifications, validations, and corrections as written below.

      Reviewer #2 (Public review):

      Summary:

      This is important work that helps to uncover how the process of autophagy is initiated - via structural analyses of the initiating ULK1 complex. High-resolution structural details and a mechanistic insight of this complex have been lacking and understanding how it assembles and functions is a major goal of a field that impacts many aspects of cell and disease biology. While we know components of the ULK1 complex are essential for autophagy, how they physically interact is far from clear. The work presented makes use of AlphaFold2 to structurally predict interaction sites between the different subunits of the ULK1 complex (namely ULK1, ATG13, and FIP200). Importantly, the authors go on to experimentally validate that these predicted sites are critical for complex formation by using site-directed mutagenesis and then go on to show that the three-way interaction between these components is necessary to induce autophagy in cells.

      Strengths:

      The data are very clear. Each binding interface of ATG13 (ATG13 with FIP300/ATG13 with ULK1) is confirmed biochemically with ITC and IP experiments from cells. Likewise, IP experiments with ULK1 and FIP200 also validate interaction domains. A real strength of the work in in their analyses of the consequences of disrupting ATG13's interactions in cells. The authors make CRISPR KI mutations of the binding interface point mutants. This is not a trivial task and is the best approach as everything is monitored under endogenous conditions. Using these cells the authors show that ATG13's ability to interact with both ULK1 and FIP200 is essential for a full autophagy response.

      Thank you for your thoughtful review and for highlighting the importance of our approach.

      Weaknesses:

      I think a main weakness here is the failure to acknowledge and compare results with an earlier preprint that shows essentially the same thing (https://doi.org/10.1101/2023.06.01.543278). Arguably this earlier work is much stronger from a structural point of view as it relies not only on AlphaFold2 but also actual experimental structural determinations (and takes the mechanisms of autophagy activation further by providing evidence for a super complex between the ULK1 and VPS34 complexes). That is not to say that this work is not important, as in the least it independently helps to build a consensus for ULK1 complex structure. Another weakness is that the downstream "functional" consequences of disrupting the ULK1 complex are only minimally addressed. The authors perform a Halotag-LC3 autophagy assay, which essentially monitors the endpoint of the process. There are a lot of steps in between, knowledge of which could help with mechanistic understanding. Not in the least is the kinase activity of ULK1 - how is this altered by disrupting its interactions with ATG13 and/or FIP200?

      Thank you for this valuable feedback. In response, we performed a detailed structural comparison between the cryo-EM structure reported in the referenced preprint and our AlphaFold-based model. We have summarized both the similarities and differences in newly included figures (revised Figure 2A, B, 3B, S1F) and provided an in-depth discussion in the main text. Furthermore, to address the downstream consequences of ULK1 complex disruption, we have investigated the impact on ULK1 kinase activity, specifically examining how mutations affecting ATG13 or FIP200 interaction alter ULK1’s phosphorylation of a key substrate ATG14. In addition, we analyzed the effect on ATG9 vesicle recruitment. We provide the corresponding data as Figure S3C-E and detailed discussions in the revised manuscript.

      Reviewer #3 (Public review):

      In this study, the authors employed the protein complex structure prediction tool AlphaFold-Multimer to obtain a predicted structure of the protein complex composed of ULK1-ATG13-FIP200 and validated the structure using mutational analysis. This complex plays a central role in the initiation of autophagy in mammals. Previous attempts at resolving its structure have failed to obtain high-resolution structures that can reveal atomic details of the interactions within the complex. The results obtained in this study reveal extensive binary interactions between ULK1 and ATG13, between ULK1 and FIP200, and between ATG13 and FIP200, and pinpoint the critical residues at each interaction interface. Mutating these critical residues led to the loss of binary interactions. Interestingly, the authors showed that the ATG13-ULK1 interaction and the ATG13-FIP200 interaction are partially redundant for maintaining the complex.

      We are grateful for your high evaluation of our work.

      The experimental data presented by the authors are of high quality and convincing. However, given the core importance of the AlphaFold-Multimer prediction for this study, I recommend the authors improve the presentation and documentation related to the prediction, including the following:

      (1) I suggest the authors consider depositing the predicted structure to a database (e.g. ModelArchive) so that it can be accessed by the readers.

      We have deposited the AlphaFold model to ModelArchive with the accession code ma-jz53c, which is indicated in the revised manuscript.

      (2) I suggest the authors provide more details on the prediction, including explaining why they chose to use the 1:1:2 stoichiometry for ULK1-ATG13-FIP200 and whether they have tried other stoichiometries, and explaining why they chose to use the specific fragments of the three proteins and whether they have used other fragments.

      We appreciate your suggestion. As we noted in the original manuscript, previous studies have shown that the C-terminal region of ULK1 and the C-terminal intrinsically disordered region of ATG13 bind to the N-terminal region of the FIP200 homodimer (Alers, Loffler et al., 2011; Ganley, Lam du et al., 2009; Hieke, Loffler et al., 2015; Hosokawa, Hara et al., 2009; Jung, Jun et al., 2009; Papinski and Kraft, 2016; Wallot-Hieke, Verma et al., 2018). We relied on these findings when determining the specific regions to include in our complex prediction and when selecting a 1:1:2 stoichiometry for ULK1–ATG13–FIP200 which was reported previously (Shi et al., 2020). We also used AlphaFold2 to predict the structures of the full-length ULK1–ATG13 complex and the complex of the FIP200N dimer with full-length ATG13, confirming that there were no issues with our choice of regions (revised Figure S1A-C). In the revised manuscript, we have provided a more detailed explanation of our rationale based on the previous reports and additional AlphaFold predictions.

      (3) I suggest the authors present the PAE plot generated by AlphaFold-Multimer in Figure S1. The PAE plot provides valuable information on the prediction.

      We provided the PAE plot in the revised Figure S1C.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) In Figure 1D, the labels for the input and IP of ATG13-FLAG should be corrected to ATG13-FLAG FIP3A.

      We thank the reviewer for pointing out these labeling mistakes. We revised the labels based on the suggestions.

      (2) In the discussion section, the authors should address why ATG13-FLAG ULK1 2A in Fig. 2D leads to a significantly lower expression of ULK1 and provide possible explanations for this observation.

      ATG13 and ATG101, both core components of the ULK1 complex, are known to stabilize each other through their mutual interaction. Loss or reduction of one protein typically leads to the destabilization of the other. In this context, ULK1 is similarly stabilized by binding to ATG13. Therefore, ATG13-FLAG ULK2A mutant, which has reduced binding to ULK1, likely loses this stabilizing activity and ULK1 becomes destabilized, resulting in the lower expression levels of ULK1. We added these discussions in the revised manuscript.

      (3) In Figure 4B, the authors should explain why Atg13-FLAG KI significantly affects the expression of endogenous ULK1. Could Atg13-FLAG KI be interfering with its binding to ULK1? Experimental evidence should be provided to support this. Additionally, does Atg13-FLAG KI affect autophagy? Wild-type HeLa cells should be included as a control in Figure 4C and 4D to address this question.

      Thank you for your constructive suggestion. We found a technical error in the ULK1 blot of Figure 4B. Therefore, we repeated the experiment. The results show that ULK1 expression did not significantly change in the ATG13-FLAG KI. These findings are consistent with Figure S3A. We have replaced Figure 4B with this new data.

      We agree that including wild-type HeLa cells as a control is essential to determine whether ATG13-FLAG KI affects autophagy. We performed the same experiments in wild-type HeLa cells and found that ATG13-FLAG KI does not significantly impact autophagic flux. Accordingly, we have replaced Figures 4D and 4E with these new data.

      (4) In Figure 3C, the authors used an in vitro GST pulldown assay to detect a direct interaction between ULK1 and FIP200, which was also confirmed in Figure 3E. However, since FLAG-ULK1 FIP2A affects its binding with ATG13 (Fig. 3E), it is possible that ULK1 FIP2A inhibits autophagy by disrupting this interaction. The authors should therefore use an in vitro GST pulldown assay to determine whether GST-ULK1 FIP2A affects its binding with ATG13. Additionally, the authors should investigate whether the interaction between ULK1 and FIP200 in cells requires the involvement of ATG13 by using ATG13 knockout cells to confirm if the ULK1-FIP200 interaction is affected in the absence of ATG13.

      Thank you for the valuable suggestion. We examined the effect of the FIP2A mutation on the ULK1–ATG13 interaction using isothermal titration calorimetry (ITC) to obtain quantitative binding data. The results showed that the FIP2A mutation does not markedly alter the affinity between ULK1 and ATG13 (revised Figure S2B), suggesting that FIP2A mainly weakens the ULK1–FIP200 interaction. Regarding experiments in ATG13 knockout cells, ULK1 becomes destabilized in the absence of ATG13, making it technically difficult to assess how the ULK1–FIP200 interaction is affected under those conditions.

      Reviewer #2 (Recommendations for the authors):

      I feel the manuscript would benefit from a more detailed comparison with the Hurely lab paper - are the structural binding interfaces the same, or are there differences?

      We appreciate the suggestion to compare our results more closely with the work from the Hurley lab. We performed a detailed structural comparison between the cryo-EM structure reported in the referenced preprint and our AlphaFold-based model (revised Figure 2A, B, 3B, S1F) and provided an in-depth discussion in the main text.

      As mentioned, what happens downstream of disrupting the ULK1 complex? How is ULK1 activity changed, both in vitro and in cells? Does disruption of the ULK1 complex binding sites impair VPS34 activity in cells (for example by looking at PtdIns3P levels/staining)?

      Thank you for your insightful comments. We focused on elucidating how disrupting the ULK1 complex leads to impaired autophagy. To assess ULK1 activity, we measured ULK1-dependent phosphorylation of ATG14 at Ser29 (PMID: 27046250; PMID: 27938392). In FIP3A and FU5A knock-in cells, ATG14 phosphorylation was significantly reduced, indicating decreased ULK1 activity (revised Figure S3D, E). This observation is consistent with previous work showing that FIP200 recruits the PI3K complex. Notably, in ATG13 knockout cells, ATG14 phosphorylation became almost undetectable, though the underlying mechanism remains to be fully investigated. Altogether, these data point to reduced ULK1 activity as a key factor explaining the autophagy deficiency observed in FU5A knock-in cells.

      We also explored possible downstream mechanisms. One well-established function of ATG13 is to recruit ATG9 vesicles (PMID: 36791199). These vesicles serve as an upstream platform for the PI3K complex, providing the substrate for phosphoinositide generation (PMID: 38342428). To clarify how our mutations impact this step, we starved ATG13-FLAG knock-in cells and observed ATG9 localization. Unexpectedly, even in FU5A knock-in cells where ATG13 is almost completely dissociated from the ULK1 complex, ATG9A still colocalized with FIP200 (revised Figure S3C). These puncta also overlapped with p62, likely because p62 bodies recruit both FIP200 and ATG9 vesicles. Although we suspect that ATG9 recruitment is nonetheless impaired under these conditions, we were unable to definitively demonstrate this experimentally and consider it an important avenue for future study.

      Reviewer #3 (Recommendations for the authors):

      Here are some additional minor suggestions:

      (1) The UBL domains are only mentioned in the abstract but not anywhere else in the manuscript. I suggest the authors add descriptions related to the UBL domains in the Results section.

      We thank the reviewer for pointing out the lack of description of UBL domains, which we added in Results in the revised manuscript.

      (2) The authors may want to consider adding a diagram in Figure 1A to show the domain organization of the three full-length proteins and the ranges of the three fragments in the predicted structure.

      We have added a proposed diagram as Figure 1A.

      (3) I suggest the authors consider highlighting in Figure 1A the positions of the binding sites shown in Figure 1B, for example, by adding arrows in Figure 1A.

      We have added arrows in the revised Figure 1B (which was Figure 1A in the original submission).

      (4) In Figure 1D, "Atg13-FLAG" should be "Atg13-FLAG FIP3A".

      We have revised the labeling in Figure 1D.

      (5) "the binding of ATG13 and ULK1 to the FIP200 dimer one by one" may need to be re-phrased. "One by one" conveys a meaning of "sequential", which is probably not what the authors meant to say.

      We have revised the sentence as “the binding of one molecule each of ATG13 and ULK1 to the FIP200 dimer”.

      (6) In "Wide interactions were predicted between the four molecules", I suggest changing "wide" to "extensive".

      We have changed “wide” to “extensive” in the revised manuscript.

      (7) In "which revealed that the tandem two microtubule-interacting and transport (MIT) domains in Atg1 bind to the tandem two MIT interacting motifs (MIMs) of ATG13", I suggest changing the two occurrences of "tandem two" to "two tandem" or simply "tandem".

      We simply used "tandem" in the revised manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Recent work has demonstrated that the hummingbird hawkmoth, Macroglossum stellatarum, like many other flying insects, use ventrolateral optic flow cues for flight control. However, unlike other flying insects, the same stimulus presented in the dorsal visual field elicits a directional response. Bigge et al., use behavioral flight experiments to set these two pathways in conflict in order to understand whether these two pathways (ventrolateral and dorsal) work together to direct flight and if so, how. The authors characterize the visual environment (the amount of contrast and translational optic flow) of the hawkmoth and find that different regions of the visual field are matched to relevant visual cues in their natural environment and that the integration of the two pathways reflects a priortiziation for generating behavior that supports hawkmoth safety rather than than the prevalence for a particular visual cue that is more prevalent in the environment.

      Strengths:

      This study creatively utilizes previous findings that the hawkmoth partitions their visual field as a way to examine parallel processing. The behavioral assay is well-established and the authors take the extra steps to characterize the visual ecology of the hawkmoth habitat to draw exciting conclusions about the hierarchy of each pathway as it contributes to flight control.

      Weaknesses:

      The work would be further clarified and strengthened by additional explanation included in the main text, figure legends, and methods that would permit the reader to draw their own conclusions more feasibly. It would be helpful to have all figure panels referenced in the text and referenced in order, as they are currently not. In addition, it seems that sometimes the incorrect figure panel is referenced in the text, Figure S2 is mislabeled with D-E instead of A-C and Table S1 is not referenced in the main text at all. Table S1 is extremely important for understanding the figures in the main text and eliminating acronyms here would support reader comprehension, especially as there is no legend provided for Table S1. For example, a reader that does not specialize in vision may not know that OF stands for optic flow. Further detail in figure legends would also support the reader in drawing their own conclusions. For example, dashed red lines in Figures 3 and 4 A and B are not described and the letters representing statistical significance could be further explained either in the figure legend or materials to help the reader draw their own conclusions.

      We appreciate the suggestions to improve the clarity of the manuscript. We have extensively re-structured the entire manuscript. Among others, we have referenced all figure panels in the text in the order they appear. To do so, we combined the optic flow and contrast measurements of our setup with the methods description of the behavioural experiments (formerly Figs. 5 and 2, respectively). This new figure 2 now introduces the methods of the study, while the remainder of Fig. 2, which presented the experiments that investigated the vetrolateral and dorsal response in more detail, is now a separate figure (Fig. 3). This arrangement also balances the amount of information contained  in each figure better.

      Reviewer #2 (Public review):

      Summary:

      Bigge and colleagues use a sophisticated free-flight setup to study visuo-motor responses elicited in different parts of the visual field in the hummingbird hawkmoth. Hawkmoths have been previously shown to rely on translational optic flow information for flight control exclusively in the ventral and lateral parts of their visual field. Dorsally presented patterns, elicit a formerly completely unknown response - instead of using dorsal patterns to maintain straight flight paths, hawkmoths fly, more often, in a direction aligned with the main axis of the pattern presented (Bigge et al, 2021). Here, the authors go further and put ventral/lateral and dorsal visual cues into conflict. They found that the different visuomotor pathways act in parallel, and they identified a 'hierarchy': the avoidance of dorsal patterns had the strongest weight and optic flow-based speed regulation the lowest weight.

      Strengths:

      The data are very interesting, unique, and compelling. The manuscript provides a thorough analysis of free-flight behavior in a non-model organism that is extremely interesting for comparative reasons (and on its own). These data are both difficult to obtain and very valuable to the field.

      Weaknesses:

      While the present manuscript clearly goes beyond Bigge et al, 2021, the advance could have perhaps been even stronger with a more fine-grained investigation of the visual responses in the dorsal visual field. Do hawkmoths, for example, show optomotor responses to rotational optic flow in the dorsal visual field?

      We thank the reviewer for the feedback, and the suggestions for improvement of the manuscript (our implementations are detailed below). We fully agree that this study raises several intriguing questions regarding the dorsal visual response, including how the animals perceive and respond to rotational optic flow in their dorsal visual field, particularly since rotational optic flow may be processed separately from translational optic flow.

      In our free-flight setup, it was not possible to generate rotational optic flow in a controlled manner. To explore this aspect more systematically, a tethered-flight setup would be ideal, or alternatively, a free-flight setup integrated with virtual reality. This would be a compelling direction for a follow-up study.

      Reviewer #3 (Public review):

      The central goal of this paper as I understand it is to extract the "integration hierarchy" of stimulus in the dorsal and ventrolateral visual fields. The segregation of these responses is different from what is thought to occur in bees and flies and was established in the authors' prior work. Showing how the stimuli combine and are prioritized goes beyond the authors' prior conclusions that separated the response into two visual regions. The data presented do indeed support the hierarchy reported in Figure 5 and that is a nice summary of the authors' work. The moths respond to combinations of dorsal and lateral cues in a mixed way but also seem to strongly prioritize avoiding dorsal optic flow which the authors interpret as a closed and potentially dangerous ecological context for these animals. The authors use clever combinations of stimuli to put cues into conflict to reveal the response hierarchy.

      My most significant concern is that this hierarchy of stimulus responses might be limited to the specific parameters chosen in this study. Presumably, there are parameters of these stimuli that modulate the response (spatial frequency, different amounts of optic flow, contrast, color, etc). While I agree that the hierarchy in Figure 5 is consistent for the particular stimuli given, this may not extend to other parameter combinations of the same cues. For example, as the contrast of the dorsal stimuli is reduced, the inequality may shift. This does not preclude the authors' conclusions but it does mean that they may not generalize, even within this species. For example, other cue conflict studies have quantified the responses to ranges of the parameters (e.g. frequency) and shown that one cue might be prioritized or up-weighted in one frequency band but not in others. I could imagine ecological signatures of dorsal clutter and translational positioning cues could depend on the dynamic range of the optic flow, or even having spatial-temporal frequency-dependent integration independent of net optic flow.

      We absolutely agree that in principle, an observed integration hierarchy is only valid for the stimuli tested. Yet, we do believe that we provide good evidence that our key observations are robust also for related stimuli to the ones tested:

      Most importantly, we found that both pathways act in parallel (and are not mutually exclusive, or winner-takes-all, for example), when the animals can enact the locomotion induced by the dorsal and ventrolateral pathway. We tested this with the same dorsal cue (the line switching direction), but different behavioural paradigms (centring vs unilateral avoidance), and different ventrolateral stimuli (red gratings of one spatial frequency, and 100% nominal contrast black-and-white checkerboard stimuli which comprised a range of spatial frequencies) – and found the same integration strategy.

      Certainly, if the contrast of the visual cues was reduced to the point that the dorsal or ventrolateral responses became weaker, we would expect this to be visible in the combined responses, with the respective reduction in response strength for either pathway, to the same degree as they would be reduced when stimuli were shown independently in the dorsal and ventrolateral visual field.

      For testing whether the animals would show a weighting of responses when it was not possible to enact locomotion to both pathways, we felt it was important to use similar external stimuli to be able to compare the responses. So we can confidently interpret their responses in terms of integration. Indeed, how this is translated to responses in the two pathways depends a) on the spatiotemporal tuning, contrast sensitivity and exact receptive fields of the two systems, b) the geometry of the setup and stimulus coverage, and therefore the ability of the animals to enact responses to both pathways independently and c) on the integration weights.

      It would indeed be fascinating to obtain this tuning and the receptive fields, and having these, test a large array of combinations of stimuli and presentation geometries, so that one could extract integration weights for different presentation scenarios from the resulting flight responses in a future study.

      We also expanded the respective discussion section to reflect these points: l. 391-417. We also updated the former Fig. 5, now Fig. 6 to reflect this discussion.

      The second part of this concern is that there seems to be a missed opportunity to quantify the integration, especially when the optic flow magnitude is already calculated. The discussion even highlights that an advantage of the conflict paradigm is that the weights of the integration hierarchy can be compared. But these weights, which I would interpret as stimulus-responses gains, are not reported. What is the ratio of moth response to optic flow in the different regions? When the moth balances responses in the dorsal and ventrolateral region, is it a simple weighted average of the two? When it prioritizes one over the other is the response gain unchanged? This plays into the first concern because such gain responses could strongly depend on the specific stimulus parameters rather than being constant.

      Indeed, we set up stimuli that are comparable, as they are all in the visual domain, and since we can calculate their external optic flow and contrast magnitudes, to control for imbalances in stimulus presentation, which is important for the interpretation of the resulting data.

      As we discussed above, we are confident that we are observing general principles of the integration of the two parallel pathways. However, we refrained from calculating integration weights, because these might be misleading for several reasons:

      (1) In situations where the animals can enact responses to both pathways, we show that they do so at the full original magnitudes. So there are no “weights” of the hierarchy in this case.

      (2) Only when responses to both systems are not possible in parallel, do we see a hierarchy. However, combined with point (1), this hierarchy likely depends on the geometry of the moths’ environment: it will be more pronounced the less both systems can be enacted in parallel.

      (3) The hierarchy also does not affect all features of the dorsal or ventrolateral pathway equally. The hawkmoths still regulate their perpendicular distance to ventral gratings with dorsal gratings present, to same degree as with only ventral grating - because perpendicular distance regulation is not a feature of the dorsal response. And while the hawkmoths show a significant reduction in their position adjustment to dorsal contrast when it is in conflict with lateral gratings (Fig. 4C), they show exactly the same amount of lateral movement and speed adjustment as for dorsal gratings alone, when not combined with lateral ones (Fig. 4D and Fig. S3A). So even for one particular setup geometry and stimulus combination, there clearly is not one integration weight for all features of the responses.

      We extended the discussion section to clarify these points “The benefit of our study system is that the same cues activate different control pathways in different regions of the visual field, so that the resulting behaviour can directly be interpreted in terms of integration weights” (l. 448-451)

      l. 391-417, we also updated the former Fig. 5, now Fig. 6 to reflect this discussion.

      The authors do explain the choice of specific stimuli in the context of their very nice natural scene analysis in Fig. 1 and there is an excellent discussion of the ecological context for the behaviors. However, I struggled to directly map the results from the natural scenes to the conclusions of the paper. How do they directly inform the methods and conclusions for the laboratory experiments? Most important is the discussion in the middle paragraph of page 12, which suggests a relationship with Figure 1B, but seems provocative but lacking a quantification with respect to the laboratory stimuli.

      We show that contrast cues and translational optic flow are not homogeneously distributed in the natural environments of hawkmoths. This directly related to our laboratory findings, when it comes to responses to these stimuli in different parts of their visual field. In order to interpret the results of these behavioural experiments with respect to the visual stimuli, we did perform measurements of translational optic flow and contrast cues in the laboratory setup. As a result, we make several predictions about the animals’ use of translational optic flow and contrast cues in natural settings:

      a) Hawkmoths in the lab responded strongest to ventral optic flow, even though it was not stronger in magnitude, given our measurements, than lateral optic flow. Thus, we propose that the stronger response to ventral optic flow might be an evolutionary adaptation to the natural distribution of translational optic flow cues.

      b) In the natural habitats of hawkmoths, dorsal coverage is much less frequent that ventrolateral structures generating translational optic flow, yet the hawkmoths responded with a much higher weight to the former. Moreover, in our flight tunnel experiments, the animals responded with the same or higher weights to dorsal cues, which had a lower magnitude of translational optic flow and contrast than the same cues in the ventrolateral visual field. So we showed, combining behavioural experiments and stimulus measurements in the lab that the weighting of dorsal and ventrolateral cues did not follow their stimulus magnitude in the lab. Moreover, comparing to the natural cue distributions, we suggest that the integration weights also did not evolve to match the prevalence of these cues in natural habitats.

      We integrated the measurements of natural visual scene statistics in the new Fig. 6, to relate the behavioural findings to the natural context also in the figure structure, and sequence logic of the text, as they are discussed here.

      The central conclusion of the first section of the results is that there are likely two different pathways mediating the dorsal and the ventrolateral response. This seems reasonable given the data, however, this was also the message that I got from the authors' prior paper (ref 11). There are certainly more comparisons being done here than in that paper and it is perfectly reasonable to reinforce the conclusion from that study but I think what is new about these results needs to be highlighted in this section and differentiated from prior results. Perhaps one way to help would be to be more explicit with the open hypotheses that remain from that prior paper.

      We appreciate the suggestion to highlight more clearly what the open questions that are addressed in this study are. As a result, we have entirely restructured the introduction, added sections to the discussion and fundamentally changed the graphical result summary in Fig. 6, to reflect the following new findings (and differences to the previous paper):

      The previous paper demonstrated that there are two different pathways in hummingbird hawkmoths that mediate visual flight guidance, and newly described one of them, the dorsal response. This established flight guidance in hummingbird hawkmoths as a model for the questions asked in the current study, which are very different in nature from the previous paper.  

      The main question addressed in the current study is how these two flight guidance pathways interact to generate consistent behaviour? Throughout the literature of parallel sensory and motor pathways guiding behaviour, there are different solutions – from winner-takes-all to equal mixed responses. We tested this fundamental question using the hummingbird hawkmoth flight guidance systems as a model.

      This is the main question addressed in the various conflict experiments in this study, and we show that indeed, the two systems operate in parallel. As long as the animals can enact both dorsal and optic-flow responses, they do so at the original strengths of the responses. Only when this is not possible, hierarchies become visible. We carefully measured the optic flow and contrast cues generated by the different stimuli to ensure that the hierarchies we observed were not generated by imbalances of the external stimuli.

      - Does the interaction hierarchy of the two pathways follow the statistics of natural environments?  We did show qualitatively previously how optic flow and contrast cues are distributed across the visual field in natural habitats of the hummingbird hawkmoth. In this study, we quantitatively analysed the natural image data, including a new analysis for the contrast edges, and statistically compared the results across conditions. This quantitative analysis supported the previous qualitative assessment that the prevalence of translational optic flow was highest in the ventral and lowest in the dorsal visual field in all natural habitat types. The distribution of contrast edges across the visual field did depend on habitat type much stronger than visible in the qualitative analysis in the previous paper. When compared to the magnitude of the behavioural responses, and considering that the hummingbird hawkmoth is predominantly found in open and semi-open habitats, the natural distributions of optic flow and contrast edges did not align with the response hierarchy observed in our laboratory experiments. Dorsal cues elicited much stronger responses relative to ventrolateral optic flow responses than would be expected.

      To provide a more complete picture of the dorsal pathway, which will be important to understand its nature, and also compare to other species, we conducted additional experiments that were specifically set up to test for response features known from the translational optic flow response. To compare and contrast the two systems. These experiments here allowed us to show that the dorsal response is not simply a translational optic flow reduction response that creates much stronger output than the ventrolateral optic flow response. We particularly show that the dorsal response was lacking the perpendicular distance regulation of the optic flow response, while it did provide alignment with prominent contrasts (possibly to reduce the perceived translational optic flow), which is not observed in the ventrolateral optic flow response. The strong avoidance of any dorsal contrast cues, not just those inducing translational optic flow, is another feature not found in the ventrolateral pathway.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Many comparisons between visual conditions are made and it was confusing at times to know which conditions the authors were comparing. Thinking of a way to label each condition with a letter or number so that the authors could specify which conditions are specifically being compared would greatly enhance comprehension and readability.

      We appreciate this concern. To be able to refer to the individual stimulus conditions in the analysis and results description, we gave each stimulus a unique identifier (see table S1), and provided these identifiers in the respective figures and throughout the text. We hope that this makes the identification of the individual stimuli easier.

      Consider adding in descriptive words to the y-axis labels for the position graphs that would help the reader quickly understand what a positive or negative value means with respect to the visual condition.

      We did now change the viewpoint on the example tracks in Figs. 2-5, to take a virtual viewpoint from the top, not as the camera recorded from below, which requires some mental rotation to reconcile the left and right sides. Moreover, we noticed that the example track axes were labelled in mm, while the axes for the plots showing median position in the tunnel were labelled in cm. We reconciled the units as well. This will make it easier to see the direct equivalent of the axis (as well as positive and negative values) in the example tracks in those figures, and the median positions, as well as the cross-index.

      There are no line numbers provided so it is a bit challenging to provide feedback on specific sentences but there are a handful of typos in the manuscript, a few examples:

      (1) Cue conflict section, first paragraph: "When both cues were presented to in combination, ..." (remove to)

      (2) The ecological relevance section, first paragraph, first sentence: "would is not to fly"

      (3) Figure S3 legend: explanation for C is labeled as B and B is not included with A

      We apologise for the missing line numbers. We added these and resolved the issues 1-3.

      Reviewer #2 (Recommendations for the authors):

      - The pictograms in Fig. 1a were at first glance not clear to me, maybe adding l, r, d, v to the first pictogram could make the figure more immediately accessible.

      We added these labels to make it more accessible.

      - I would suggest noting in the main text that the red patterns were chosen for technical reasons (see Methods), if this is correct.

      We added this information and a reference to the methods in the main text (lines 100-102).

      - "Thus, hawkmoths are currently the only insect species for which a partitioning of the visual field has been demonstrated in terms of optic-flow-based flight control [33-35]." I think that is a bit too strong and maybe it would be more interesting to connect the current data to connected data in other insects to perhaps discuss important similarities. Ref 32 for example shows that fruit flies weigh ventral translational optic flow considerably more than dorsal translational optic flow. Reichardt 1983 (Naturwissenschaften) showed that stripe fixation in large flies (a behaviour relying in part on the motion pathway) is confined to the ventral visual field, etc...

      We have changed this sentence to acknowledge partitioning in other insects, and motivating the use of our model species for this study: While fruit flies weight ventral translational optic flow stronger than dorsal optic flow, the most extreme partitioning of the visual field in terms of  optic-flow-based flight control has been observed in hawkmoths [33-35]. (lines 60-62)

      - I think the statistical differences group mean differences could be described in more detail at least in Fig. 2 (to me the description was not immediately clear, in particular with the double letters).

      We added an explanation of the letter nomenclature to all respective figure legends:

      Black letters show statistically significant differences in group means or median, depending on the normality of the test residuals (see Methods, confidence level: 5%). The red letters represent statistically significant differences in group variance from pairwise Brown–Forsythe tests (significance level 5%). Conditions with different letters were significantly different from each other. The white boxplots depict the median and 25% to 75% range, the whiskers represent the data exceeding the box by more than 1.5 interquartile ranges, and the violin plots indicate the distribution of the individual data points shown in black.

      - "When translational optic flow was presented laterally" I would use a more wordy description, since it is the hawkmoth that is controlling the optic flow and in addition to translational optic flow, there might also be rotational components, retinal expansion etc.

      We extended the description to explain that the moths were generating the optic flow percept based on stationary gratings in different orientations, by way of their flight through the tunnel. Lines 127-129

      - While it is clearly stated that the measure of the perpendicular distance from the ventral and dorsal pattern via the size of the insect as seen by the camera is indirect, I would suggest to determine the measurement uncertainty of distance estimate.

      - Connected to above - is the hawkmoth area averaged over the entire flight and is the variance across frames similar in all the stimuli conditions? Is it, in principle, conceivable that the hawkmoths' pitch (up or down) is different across conditions, e.g. with moths rising and falling more frequently in a certain condition, which could influence the area in addition to distance?

      There are a number of sources that generate variance in the distance estimate (which was based on the size of the moth in each video frame, after background subtraction): the size of the animal, the contrast with which the animal was filmed (which also depended on the type of pattern in the tunnel – it was lower with ventral or dorsal patterns as a background than with lateral ones), and the speed of the animal, as motion blur could impact the moth’s image on the video. The latter is hard to calibrate, but the uncertainty related to animal size and pattern types could theoretically be estimated. However, since we moved between finishing the data acquisition for this study and publishing the paper, the original setup has been dismantled. We could attempt to recreate it as faithfully as possible, but would be worried to introduce further noise. We therefore decided to not attempt to characterise the uncertainty, to not give a false impression of quantifiability of this measure. For the purpose of this study, it will have to remain a qualitative, rather than a quantitative measure. If we should use a similar measure again, we will make sure to quantify all sources of uncertainty that we have access to.

      The variance in area is different between conditions. Most likely, the animals vary their flight height different for different dorsal and ventral patterns, as they vary their lateral flight straightness with different lateral visual input. For the reasons mentioned above, we cannot disentangle the effects of variations in flight height and other sources of uncertainty relating to animal size in the video frames. We therefore averaged the extracted area across the entire flight, to obtain a coarse measure of their flight height. Future studies focusing specifically on the vertical component or filming in 3D will be required to determine the exact amount of vertical flight variation.

      - Results second paragraph, suggestion: pattern wavelength or spatial frequency instead of spatial resolution.

      - Same paragraph, suggestion: For an optimal wavelength/spatial frequency of XX

      We corrected these to spatial frequency.

      - Above Fig 3- "this strongly suggests a different visual pathway". In my opinion it would be better to say sensory-motor /visuomotor pathway or to more clearly define visual pathway? Could one in principle imagine a uniform set of local motion sensitive neurons across the entire visual field that connect differentially to descending/motor neurons.

      We appreciate this point and changed this, and further instances in the manuscript to visuomotor pathway.

      - If I understood correctly, you calculated the magnitude of optic flow in the different tunnel conditions based on the image of a fisheye camera moving centrally in the tunnel, equidistant from all walls. I did not understand why the magnitude of optic flow should differ between the four quadrants showing the same squarewave patterns. Apologies if I missed something, but maybe it is worth explaining this in more detail in the manuscript.

      We recognize that this point may not have been immediately clear and have therefore provided additional clarification in the Methods and results section (lines 106-111, 543-549). We anticipated differences in the magnitude of optic flow due to potential contrast variations arising from the way the stimuli were generated—being mounted on the inner surfaces of different tunnel walls while the light source was positioned above. On the dorsal wall, light from the overhead lamps passed through the red material. For laterally mounted patterns, the animals perceived mainly reflected light, as these tunnel walls were not transparent.

      A similar principle applied to the background, which consisted of a white diffuser allowing light to pass through dorsally, but white non-transmissive paper laterally, with a 5% contrast random checkerboard patterns. The ventral side presented a more complex scenario, as it needed to be partially transparent for the ventrally mounted camera. Consequently, the animals perceived a combination of light reflections from the red patterns and the white gauze covering the ventral tunnel side, against the much darker background of the surrounding room.

      To ensure that the observed flight responses were not artifacts of deviations in visual stimulation from an ideal homogeneous environment, we used the camera to quantify the magnitude of optic flow and contrast patterns under these real experimental conditions. This approach also allowed us to directly relate the optic flow measurements taken indoors to those recorded outdoors, as we employed the same camera and analytical procedures for both datasets.

      Reviewer #3 (Recommendations for the authors):

      In addition to the considerations above I had a few minor points:

      There are so many different directions of stimuli and response that it is quite challenging to parse the results. Can this be made a little easier for the reader?

      We appreciate this concern. To be able to refer to the individual stimulus conditions in the analysis and results description, we gave each stimulus a unique identifier (see table S1), and provided these identifiers in the respective figures and throughout the text. We hope that this makes the identification of the individual stimuli easier.

      One suggestion (only a suggestion): I found myself continuously rotating the violin plots in my head so that the lateral position axis lined up with the lateral position of the tunnel icons below. Consider if rotating the plots 90 degs would help interpretability. It was challenging to keep track of which side was side.

      We did discuss this with a number of test-readers, and tried multiple configurations. They all have advantages and drawbacks, but we decided that the current configuration for the majority of testers was the current one. To help the mental transformations from the example flight tracks in the figures, we now present the example flight tracks in Figs. 2-5 in the same reference frame as the figures showing median position (so positive and negative values on those axes correspond directly), and changed the view from a below the tunnel to an above the tunnel view, as this is the more typical depiction. We hope that this enhances readability.

      Are height measurements sensitive to the roll and pitch of the animal? I suspect this is likely small but worth acknowledging.

      They are indeed. These effects are likely small but contribute to the overall inaccuracy, which we could not quantify in this particular setup (see also response to reviewer 2 on that point), which is why the height measurements have to be considered a qualitative approximation rather than a quantification of flight height. We added text to acknowledge the effects of roll and pitch specifically (lines 657-658)

      The Brown-Forsythe test was reported as paired but this seems odd because the same moths were not used in each condition. Maybe the authors meant something different by "paired" than a paired statistical design?

      Indeed, the data was not paired in the sense that we could attribute individual datapoints to individual moths across conditions. We applied the Brown-Forsythe test in a pairwise manner, comparing the variance of each condition with another one in pairs each, to test if the variance in position differed across conditions. We did phrase this misleadingly, and have corrected it to „The variance in the median lateral position (in other words, the spread of the median flight position) was statistically compared between the groups using the pairwise Brown–Forsythe tests“ l. 187-188

      There is some concern about individual moth preferences and bias due to repeated measures. I appreciate that the individual moth's identity was not likely known in most cases, but can the authors provide an approximate breakdown of how many individual moths provided the N sample trajectories?

      This is a very valid concern, and indeed one we did investigate in a previous study with this setup. We confirmed that the majority of animals (70%, 68% and 53% out of 40 hawkmoths, measured on three consecutive days) crossed the tunnel within a randomly picked window of 3h (Stöckl et al. 2019). We now state this explicitly in the methods section (lines 594-597). Thus, for the sample sizes in our study, statistically, each moth would have contributed a small number of tracks compared to the overall number of tracks sampled.

      The statistics section of the methods said that both Tukey-Kramer (post-hoc corrected means) and Kruskal-Wallis (non-parametric medians) were done. It is sometimes not clear which test was done for which figure, and where the Kruskal-Wallis test was done there does not seem to be a corrected statistical significance threshold for the many multiple comparisons (Fig. 2). It is quite possible I am just missing the details and they need to be clarified. I think there also needs to be a correction for the Brown-Forsythe tests but I don't know this method well.

      We first performed an ANOVA, and if the test residuals were not normally distributed, we used a Kruskal-Wallis test instead. For the post-hoc tests of both we used Tukey-Kramer to correct for multiple comparisons. The figure legends did indeed miss this information. We added it to clarify our statistical analysis strategy and refer to the methods section for more details (i.e. l. 185-186). All statistical results, including the type of statistical test used, have been uploaded to the data repository as well.

      The connection to stimulus reliability in the discussion seems to conflate reliability with prevalence or magnitude.

      We have rephrased the respective discussion sections to clearly separate the prevalence and magnitude of stimuli, which was measured, from an implied or hypothesized reliability (lines 510-511).

      Line numbers would be helpful for future review.

      We apologize for missing the line numbers and have added them to the revised manuscript.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1 (Public review):

      Summary:

      In a previous work Prut and colleagues had shown that during reaching, high frequency stimulation of the cerebellar outputs resulted in reduced reach velocity. Moreover, they showed that the stimulation produced reaches that deviated from a straight line, with the shoulder and elbow movements becoming less coordinated. In this report they extend their previous work by addition of modeling results that investigate the relationship between the kinematic changes and torques produced at the joints. The results show that the slowing is not due to reductions in interaction torques alone, as the reductions in velocity occur even for movements that are single joint. More interestingly, the experiment revealed evidence for decomposition of the reaching movement, as well as an increase in the variance of the trajectory.

      Strengths:

      This is a rare experiment in a non-human primate that assessed the importance of cerebellar input to the motor cortex during reaching.

      Weaknesses:

      None

      Reviewer #1 (Recommendations for the authors):

      The authors have answered my questions adequately and I have no further comments.

      Reviewer #2 (Public review):

      This manuscript asks an interesting and important question: what part of 'cerebellar' motor dysfunction is an acute control problem vs a compensatory strategy to the acute control issue? The authors use a cerebellar 'blockade' protocol, consisting of high frequency stimuli applied to the cerebellar peduncle which is thought to interfere with outflow signals. This protocol was applied in monkeys performing center out reaching movements and has been published from this laboratory in several preceding studies. I found the takehome-message broadly convincing and clarifying - that cerebellar block reduces muscle activation acutely particularly in movements that involve multiple joints and therefore invoke interaction torques, and that movements progressively slow down to in effect 'compensate' for these acute tone deficits. The manuscript was generally well written, data were clear, convincing and novel. The key strengths are differentiating acute from subacute (within session but not immediate) kinematic consequences of cerebellar block.

      Reviewer #2 (Recommendations for the authors):

      I think the manuscript is good as is. That said, it would have been nice to see more of the behavioral outcomes in Figure 5 (e.g. decomposition and trajectory variability) analyzed longitudinally like the velocity measurements in Fig. 4. This would clearly strengthen the insight into acute and compensatory components of cerebellar motor deficits.

      The two behavioral measures of motor noise used in our study are movement decomposition and trajectory variability (Figure 5). Since trajectory variability is measured across trials we could not analyze this measure longitudinally as a function of trial number. However, following the reviewer’s advice, we examined movement

      decomposition for successive trials in control vs. cerebellar block for movements to targets 2-4 similar to the analysis of  hand velocity in figure 4. We found no interaction effect between trial sequence x cerebellar block on movement decomposition. This result is consistent with our conclusion that noisy joint activation occurs independently of adaptive slowing of multi-joint movements. We have updated our main text (lines 293-299) and supplementary information (supplementary figure S5 and supplementary table S8) to include this result.  

      Reviewer #3 (Public review):

      Summary:

      In their revised manuscript, Sinha and colleagues aim to identify distinct causes of motor impairments seen when perturbing cerebellar circuits. This goal is an important one, given the diversity of movement related phenotypes in patients with cerebellar lesion or injury, which are especially difficult to dissect given the chronic nature of the circuit damage. To address this goal, the authors use high-frequency stimulation (HFS) of the superior cerebellar peduncle in monkeys performing reaching movements. HFS provides an attractive approach for transiently disrupting cerebellar function previously published by this group. First, they find a reduction in hand velocities during reaching, which was more pronounced for outward versus inward movements. By modeling inverse dynamics, they find evidence that shoulder muscle torques are especially affected. Next, the authors examine the temporal evolution of movement phenotypes over successive blocks of HFS trials. Using this analysis, they find that in addition to the acute, specific effects on torques in early HFS trials, there was an additional progressive reduction in velocity during later trials, which they interpret as an adaptive response to the inability to effectively compensate for interaction torques during cerebellar block. Finally, the authors examine movement decomposition and trajectory, finding that even when low velocity reaches are matched to controls, HFS produces abnormally decomposed movements and higher than expected variability in trajectory.

      Strengths:

      Overall, this work provides important insight into how perturbation of cerebellar circuits can elicit diverse effects on movement across multiple timescales.

      The HFS approach provides temporal resolution and enables analysis that would be hard to perform in the context of chronic lesions or slow pharmacological interventions. Thus, this study describes an important advance over prior methods of circuit disruption in the monkey, and their approach can be used as a framework for future studies that delve deeper into how additional aspects of sensorimotor control are disrupted (e.g., response to limb perturbations).

      In addition, the authors use well-designed behavioral approaches and analysis methods to distinguish immediate from longer-term adaptive effects of HFS on behavior. Moreover, inverse dynamics modeling provides important insight into how movements with different kinematics and muscle dynamics might be differentially disrupted by cerebellar perturbation.

      In this revised version of the manuscript, the authors have provided additional analyses and clarification that address several of the comments from the original submission.

      Remaining comments:

      The argument that there are acute and adaptive effects to perturbing cerebellar circuits is compelling, but there seems to be a lost opportunity to leverage the fast and reversible nature of the perturbations to further test this idea and strengthen the interpretation. Specifically, the authors could have bolstered this argument by looking at the effects of terminating HFS - one might hypothesize that the acute impacts on joint torques would quickly return to baseline in the absence of HFS, whereas the longer-term adaptive component would persist in the form of aftereffects during the 'washout' period. As is, the reversible nature of the perturbation seems underutilized in testing the authors' ideas. While this experimental design was not implemented here, it seems like a good opportunity for future work using these approaches.

      We agree with the reviewer that examining the effect of the cerebellar block on immediate post-block washout trials in future studies will be insightful.    

      The analysis showing that there is a gradual reduction in velocity during what the authors call an adaptive phase is convincing. While it is still not entirely clear why disruption of movement during the adaptive phase is not seen for inward targets, despite the fact that many of the inward movements also exhibit large interaction torques, the authors do raise potential explanations in the Discussion.

      The text in the Introduction and in the prior work developing the HFS approach overstates the selectivity of the perturbations. First, there is an emphasis on signals transmitted to the neocortex. As the authors state several times in the Discussion, there are many subcortical targets of the cerebellar nuclei as well, and thus it is difficult to disentangle target-specific behavioral effects using this approach. Second, the superior cerebellar peduncle contains both cerebellar outputs and inputs (e.g., spinocerebellar). Therefore, the selectivity in perturbing cerebellar output feels overstated. Readers would benefit from a more agnostic claim that HFS affects cerebellar communication with the rest of the nervous system, which would not affect the major findings of the study. In the revised manuscript, the authors do provide additional anatomical and evolutionary context and discuss potential limitations in the selectivity of HFS in the Materials and Methods. However, I feel that at least a brief mention of these caveats in the Introduction, where it is stated, "we then reversibly blocked cerebellar output to the motor cortex", would benefit the reader.

      Following the advice of the reviewer, we have now revised the introduction section of our manuscript in the following way (lines 61-67):

      “…We then reversibly disrupted cerebellar communication with other neural structures using high-frequency stimulation (HFS) of the superior cerebellar peduncle, assessing the impact of this perturbation on subsequent movements. Although our approach primarily affects cerebellar output to the motor cortex, it also disrupts fibers carrying input signals (e.g., spinocerebellar) and pathways to various subcortical targets (e.g., cerebellorubrospinal). Thus, our manipulation broadly interferes with cerebellar communication…”

      Reviewer #3 (Recommendations for the authors):

      Typo on line 102; "subs-sessions"

      We have corrected this typographical error in our revised manuscript (line 106).

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Flowers et al describe an improved version of qFit-ligand, an extension of qFit. qFit and qFit-ligand seek to model conformational heterogeneity of proteins and ligands, respectively, cryo-EM and X-ray (electron) density maps using multi-conformer models - essentially extensions of the traditional alternate conformer approach in which substantial parts of the protein or ligand are kept in place. By contrast, ensemble approaches represent conformational heterogeneity through a superposition of independent molecular conformations.

      The authors provide a clear and systematic description of the improvements made to the code, most notably the implementation of a different conformer generator algorithm centered around RDKit. This approach yields modest improvements in the strain of the proposed conformers (meaning that more physically reasonable conformations are generated than with the "old" qFit-ligand) and real space correlation of the model with the experimental electron density maps, indicating that the generated conformers also better explain the experimental data than before. In addition, the authors expand the scope of ligands that can be treated, most notably allowing for multi-conformer modeling of macrocyclic compounds.

      Strengths:

      The manuscript is well written, provides a thorough analysis, and represents a needed improvement of our collective ability to model small-molecule binding to macromolecules based on cryo-EM and X-ray crystallography, and can therefore have a positive impact on both drug discovery and general biological research.

      Weaknesses:

      There are several points where the manuscript needs clarification in order to better understand the merits of the described work. Overall the demonstrated performance gains are modest (although the theoretical ceiling on gains in model fit and strain energy are not clear!).

      We thank the reviewer for their thoughtful review. To address comments, we have added clarifying statements and discussion points around the extent of performance gains, our choice of benchmarking metrics, and the “standards” in the field for significance. We expanded our analysis to highlight how to use qFit ligand in “discovery” mode, which is aimed at supporting individual modeling efforts. As we now write in the discussion:

      “It is advisable to employ qFit-ligand selectively, focusing on cases with a moderate correlation between your input model and the experimental data, strong visual density in the binding pocket, high map resolution, or when your single-conformer ligand model is strained.”

      Additionally, we note in the discussion:

      “qFit-ligand primarily serves as a “thought partner” for manual modeling. Modelers still must resolve many ambiguities, including initial ligand placement, to fully take advantage of qFit capabilities. In active modeling workflows or large scale analyses, the workflow would only accept the output of qFit-ligand when it improves model quality. In cases where qFit-ligand degrades map-to-model fit and/or strain, we can simply revert to the input model. In practice, users can easily remove poorly fitting conformations using molecular modeling software such as COOT, while keeping the well modeled conformations, which is an advantage of the multiconformer approach over ensemble refinement methods.”

      Reviewer #2 (Public review):

      Summary:

      The manuscript by Flowers et al. aimed to enhance the accuracy of automated ligand model building by refining the qFit-ligand algorithm. Recognizing that ligands can exhibit conformational flexibility even when bound to receptors, the authors developed a bioinformatic pipeline to model alternate ligand conformations while improving fitting and more energetically favorable conformations.

      Strengths:

      The authors present a computational pipeline designed to automatically model and fit ligands into electron density maps, identifying potential alternative conformations within the structures.

      Weaknesses:

      Ligand modeling, particularly in cases of poorly defined electron density, remains a challenging task. The procedure presented in this manuscript exhibits clear limitations in low-resolution electron density maps (resolution > 2.0 Å) and low-occupancy scenarios, significantly restricting its applicability. Considering that the maps used to establish the operational bounds of qFit-ligand were synthetically generated, it's likely that the resolution cutoff will be even stricter when applied to real-world data.

      We thank Reviewer #2 for their comments on the role of conformational flexibility and how our tool addresses the complexity involved in modeling alternative conformations. We agree that there are limitations at low resolution, limiting the application of our algorithm. That is the case with all structural biology tools. Automatically finding alternative conformations of ligands in high-resolution structures is an enhancement to the toolbox of ligand fitting. Expanding the algorithm to work with fragment screening data is important in this realm, as almost all of this data fits in the high-resolution range where qFit-ligand works best.

      The reported changes in real-space correlation coefficients (RSCC) are not substantial, especially considering a cutoff of 0.1. Furthermore, the significance of improvements in the strain metric remains unclear. A comprehensive analysis of the distribution of this metric across the Protein Data Bank (PDB) would provide valuable insights.

      We agree that the changes are small, partially because the baseline (manually modeled ligands) is very high. To provide additional evidence, we added evaluations using EDIAm, which is a more sensitive metric. In Figure 2 (page 10), representing the development dataset, we see more improvements above 0.1. With this being said, it is unclear what constitutes a ‘substantial’ improvement for either of these metrics, especially considering alternative conformations may only change the coordinates of a subset of ligands, just slightly improving the fit to density.

      We agree that looking across the PDB on strain would provide valuable insight. To explore this, we looked to see how qFit-ligand could improve the fitting of deposited ligands with high strain (see section: Evaluating qFit-ligand on a set of structures known to be highly strained, Page 15). While only a subset of these structures had alternative conformers placed (24.6%), we observed that in this subset, the ligands often improved the RSCC and strain. This figure also demonstrates that while RSCC may not change much numerically, the alternative conformers explain previously unexplained density with lower energy conformers than what is currently deposited.

      To mitigate the risk of introducing bias by avoiding real strained ligand conformations, the authors should demonstrate the effectiveness of the new procedure by testing it on known examples of strained ligand-substrate complexes.

      See above.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      A - Specific comments:

      (1) It appears necessary to provide qFit-ligand with an initial model with the ligand already placed. This is not clear from the start of the introduction on page 3. It appears that ligand position is only weakly adjusted fairly late in the process, in step F of Figure 1. It seems, therefore, that the accuracy of initial placement is rather critical (see the example discussed on page 21). At the same time, in my experience, ambiguous cases are quite common, for example with flat ligands with a few substituents sticking out or with ligands with highly mobile tails. It would be helpful for the authors to comment on the sensitivity to initial ligand placement, either in the discussion or, better yet, in the form of an analysis in which the starting model position is randomly perturbed.

      In our revised version, we have modified the introduction to clarify the necessity of including an initial ligand model (page 4).

      “The qFit-ligand algorithm takes as input a crystal or cryo-EM structure of an initial protein-ligand complex with a single conformer ligand in PDBx/mmCIF format, a density map or structure factors (encoded by a ccp4 formatted map or an MTZ), and a SMILES string for the ligand.”

      We also describe our sampling algorithm more clearly (see: Biasing Conformer Generation, page 6). Steps A-E generate many conformations (using RDKit), which are then selected/fit into experimental density (using quadratic programming). To help with additional shifting issues in the input ligand, after the first selection, we do additional rotation/translation of the generated conformers that are kept. We then do another round of fitting to the density (quadratic programming followed by mixed integer quadratic programming).

      Given this sampling, we have not elected to do an additional computational experiment to test the “radius of convergence” or dependence on initial conditions. However, we outline the fundamental procedure here so that someone can build on the work and test the idea:

      - Create single conformer models as we currently do

      - randomly perturb the coordinates of the ligand by 0.1-0.3Å

      - refine to convergence, creating a series of “perturbed, modified true positives” for each dataset

      - Run qFit ligand

      - Evaluate the variability in the resulting multi-conformer models

      (2) Top of page 6 ("Biasing Conformer Generation"): the authors say "as we only want to generate ligands that physically fit within the protein binding pocket, we bias conformation generation towards structures more likely to fit well within the receptor's binding site". Apart from the odd redundancy of this sentence, I am confused: at the stage that seems to be referred to here (A-C in Figure 1) is the fit to the electron density already taken into account, or does this only happen later (after step E)?

      Thank you for pointing this out. We have edited the statement to clarify it:

      “To guide the conformation generation from the Chem.rdDistGeom based on the ligand type and protein pocket, we developed a suite of specialized sampling functions to bias the conformational search towards structures more likely to fit well into the receptor’s binding site.”

      We do not consider the electron density during conformer generation (only selection from the generated conformers). The sampling is additionally biased by the type of ligand and the size of the binding pocket.

      (3) qFit-ligand appears to be quite slow. Are there prospects for speedup? Can the code take advantage of GPUs or multi-CPU environments?

      We agree with this. We have made some algorithmic improvements, most notably removing duplicate conformers based on root mean squared distance. This, along with parallelization, decreased the average runtime from ~19 minutes to ~8 minutes (see additional details: qFit-ligand runtime, page 8). We do not currently take advantage of GPU specific code.

      (4) Section: Detection of experimental true positive multi-conformer ligands:

      a) Why are carbohydrate ligands excluded? This seems like an important class of ligands that one would like qFit to be able to treat! Which brings me to a related question: can covalently attached groups (e.g., glycosylation sites!) be modeled using qFit-ligand, or is qFit-ligand restricted to non-covalently bound groups?

      Currently, qFit-ligand does not support covalently bound ligands, but this is an area of interest we are hoping to expand into. In the revised version, we added the non-covalently attached carbohydrates back into the true positive dataset. In Figure 4 (page 14), we show that qFit-ligand is able to improve fit to the experimental density in around 80% of structures, while also often reducing torsion strain (see additional details: qFit-ligand applied to unbiased dataset of experimental true positives, page 14).

      b) "as well as 758 cases where the ligand model's deposited alternate conformations (altlocs) were not bound in the same chain and residue number" - I do not understand what this means, or why it leads to the exclusion of so many structures. Likewise, a number of additional exclusions are described in Figure S3. Some more background on why these all happened would be helpful. Are you just left with the "easy" cases?

      Sometimes modelers will list the multiple conformations of a bound ligand as a separate residue within the PDB file, rather than as a single multiconformer model. For example, rather than writing a multiconformer LIG bound at A, 201 with altlocs ‘A’ and ‘B’, a modeler might write this instead as LIG, A, 201 and LIG A, 301. We initially excluded these kinds of structures. However, we agree that this choice resulted in the removal of many potentially valid true positives. We have since updated our data processing pipeline to include these cases, and they are examined in the updated manuscript.

      c) I do not follow the argument made at the end of this section (last two paragraphs on page 9): "when using a single average conformation to describe density from multiple conformations, the true low-energy states may be ignored". I get that, but the conformations in the "modified true positives" dataset derive directly from models in which two conformations were modeled, so this cannot be the explanation for why qFit-ligand models result in somewhat lower average strain. It would seem that the paper could be served by providing examples where single conformations were modeled in deposited structures, but qFit detects multiple conformations.

      We agree with this comment that the strain obtained from the modified true positives is likely higher than the deposited models. However, the modified structure is refined with a single conformation, and therefore changed from the deposited “A” conformation. Thus, the reduced strain observed in our qFit-ligand models relative to the modified true positives is not unexpected.

      To expand our dataset, we also looked at deposited structures with high strain, all of which were modeled as single conformers. Here, we saw a decrease in strain when alternative conformers were placed (see section: Evaluating qFit-ligand on a set of structures known to be highly strained, page 15). Further, we provide an example from the XGen macrocycle dataset where a ligand initially modeled as a single conformer exhibited relatively high strain. After qFit‐ligand modeled a second conformation, the overall strain was reduced (Figure 6C, page 19; Figure 6—figure supplement 1C, page 59).

      (5) Section: qFit-ligand applied to an unbiased dataset of experimental true positives Bottom of page 14: The paragraph starting with "qFit-ligand shows particular strength in scenarios with strong evidence..." is enigmatic: there's no illustration (unless it directly relates to the findings in Figure 4, in which case this should be more explicit). Since this points out when the reader will and will not benefit from using qFit-ligand, it should be clear what the authors are talking about.

      This claim considers all the evidence presented in the manuscript, not necessarily one particular aspect of it. We advise using qFit-ligand when there is a moderate correlation between the input model and the experimental data, strong visual density in the binding pocket, high map resolution, and/or when your single conformer ligand model is strained. We have made all of these points clearer in the updated manuscript.

      B  - Section: qFit-ligand can automatically detect and model multiple conformations of macrocycles:

      This is an exciting extension of qFit-ligand, but some aspects of the analysis strike me as worrisome. Of the initial dataset of 150 structures, fewer than half make it all the way through analysis. It's hard to believe that this is a fully representative subset. Why, for example, could 29 structures not be refined against the deposited structure factors? Why does strain calculation (in RDKit?) fail on 30 ligands? What about the other 18 cases--why did these fail (in PHENIX?).

      We agree that this is a striking number of failures, however, we note that they are not specific shortcomings of qFit-ligand (in fact, most are because standard structural biology and/or cheminformatics software fail on many PDB depositions). Therefore, these failures reflect broader limitations in standard bioinformatics and refinement restraint files when handling macrocycles. The strain calculator we used was not built for macrocycles, and after consulting with many experts in the field, the consensus was that no method works well with macrocycles. We discuss these issues in additional detail in the discussion (page 27):

      “Additionally, our algorithm’s placement within the larger refinement and ligand modeling ecosystem highlighted other areas that need improvement. We note that macrocycles, due to their complicated and interconnected degrees of freedom, suffer acutely from the refinement issues, as demonstrated by the failure of approximately one-third of datasets in our standard preparation or post-refinement pipelines due to ligand parameterization issues. Many of these stemmed from problematic ligand restraint files, highlighting the difficulty of encoding the geometric constraints of macrocycles using standard restraint libraries. Improved force-field or restraints for macrocycles are desperately needed to improve their modeling.”

      C  - Minor issues:

      (1) "Fragment-soaked event maps" - this is a semantically strange section title!

      We have updated the section title in our revised manuscript. The new title is ‘qFit-ligand recovers heterogeneity in fragment-soaked event maps’.

      (2) Too many digits! All over the manuscript, percentages are displayed with 0.01% precision, while these mostly refer to datasets with ~150 structures. Shifting just one structure from one category to another changes these percentages by nearly 1%.

      We have updated the sig figs in our revised manuscript.

      (3) The authors are keen to classify decreases in RSCC as significant only when these changes exceed 0.1, but do not apply the same standard for increases. For instance, in Figure 4B if we were to classify improvements as significant if ΔRSCC > 0.1, there would be fewer significant improvements than decreases in performance (although it is visually clear that for most datasets things get better. Similarly, in Figure 5A if we were to classify improvements as significant if ΔRSCC > 0.1, qFit-ligand would only yield significant improvements for two out of 73 cases-not a lot).

      We agree with the reviewer that there needs to be more consistency in our analysis of improvements/deteriorations. However, we note that operationally, when the decreases in model quality are observed, the modeler would simply reject the new model in favor of the input model. We have added to the discussion:

      “In active modeling workflows or large scale analyses, the workflow would only accept the output of qFit-ligand when it improves model quality. In cases where qFit-ligand degrades map-to-model fit and/or strain, we can simply revert to the input model. In practice, users can easily remove poorly fitting conformations using molecular modeling software such as COOT, while keeping the well modeled conformations, which is an advantage of the multiconformer approach over ensemble refinement methods.”

      There is generally no consensus in the field as to what might indicate a ‘significant’ change in RSCC, and any threshold we choose would be arbitrary. We note that in our manuscript, we had previously characterized a decrease in RSCC to be ‘significant’ if it exceeded 0.1. However, as there is no real scientific justification for this cutoff, or any cutoff, we moved away from this framing in the revised manuscript. Therefore, we just classify if we improve RSCC. For example, on page 9:

      “qFit-ligand modeled an alternative conformation in 72.5% (n=98) of structures. Compared with the modified true positive models, 83.7% (n=113) of qFit-ligand models have a better RSCC and 77.0% (n=104) structures saw an improvement in EDIAm, representing an improved fit to experimental data in the vast majority of structures.”

      In addition, we have conducted additional experiments using more sensitive metrics (EDIAm) to further illustrate qFit-ligand’s performance.

      (4) Small peptides are not discussed as a class of ligands, although these are quite common.

      Canonical peptides can be modeled with standard qFit. Non-canonical peptides present failure modes similar to the macrocycles discussed above, with a mix of ATOM and HETATM records and the need for custom cif definitions and link records. For these reasons we have not included an analysis outside of the macrocycle section. We have noted this caveat in the discussion:

      “We note that even linear non-canonical peptides present similar failure modes to macrocycles, with a mix of ATOM and HETATM records and the need for custom cif definitions and link records. For these reasons, we did not include analysis on small peptide ligands; however, canonical peptides can be modeled with standard qFit [8].”

      (5) Top of page 10: "while refinement improves": what kind of refinement does this refer to?

      This refers to refinement with Phenix. We have updated this language to reflect this (page 8). “We refer to these altered structures as our ‘modified true positives’, which we use as input to qFit-ligand, and subsequent refinement using Phenix.”

      (6) Bottom of page 11: "they often did" -> "it often did"

      We have made this change in the revised version.

      (7) Top of page 14: RMSDs and B factors do have units.

      We have added the units in our revision.

      (8) Top of page 24. In the generation of a composite omit map, why are new Rfree flags being generated? Did I misunderstand that?

      r_free_flags.generate=True only creates R-free flags if they are not present in the input file as is the case for many (especially older) PDB depositions.

      (9) Bottom of page 27: how large is the mask? Presumably when alt confs of the ligand are possible, it would be helpful for the mask to cover those?

      We agree that this mask should be updated. In our revision, we define the mask around the coordinates of the full qFit-ligand ensemble. The same mask is used to calculate the RSCC of the input (single conformer) model versus the qFit-ligand model.

      (10) Middle of page 29: "These structure factors are then used to compute synthetic electron density maps." - It is not clear whether the following three sentences are an explanation of the details of that statement or rather things that are done afterwards.

      We clarify this in the manuscript (page 36).

      “These structure factors are then used to compute synthetic electron density maps. To each of these maps, we generate and add random Gaussian noise values scaled proportionally to the resolution. This scaling reflects the escalation of experimental noise as resolution deteriorates, a common occurrence in real-life crystallographic data.”

      (11) Chemical synthesis: I am not qualified to assess this and am surprised to see some much detail here rather than in some other manuscript. Are the corresponding structures deposited anywhere?

      All of the structures we discuss in this manuscript are deposited in the PDB and listed in Supplementary Table 5.

      Reviewer #2 (Recommendations for the authors):

      The data should consistently present the number of structures that exhibit improvements or deterioration in particular metrics, like RSCC and strain, using a cutoff that should be significant. For instance, stating that "85.93% (n=116) of structures having a better RSCC in the qFit-ligand models compared to the modified true positive models" without clarifying the magnitude of improvement (e.g., a marginal increase of 0.01 in RSCC) lacks meaningful context. The figures should clearly indicate the specific cutoff values used for each metric. The accompanying text should provide a detailed explanation for the selection of these cutoff values, justifying their significance in the context of the study.

      Currently, there is no established consensus within the field on what constitutes a 'significant' improvement in RSCC or strain values. As such, we chose not to impose an arbitrary cutoff and just look at which structures improve RSCC. We also removed all language stating significance, as there isn’t a good standard in the field to assess significance. This is especially important as only improvements would be considered in an active modeling project. In cases where qFit ligand degrades the RSCC (or strain) to a large extent, the modeler would simply revert to the input model.

      In the first section of Results: "First, for all ligands, we perform an unconstrained search function allowing the generated conformers to only be constrained from the bounds matrix (Figure 1A). This is particularly advantageous for small ligands that benefit from less restriction to fully explore their conformational space. We then perform a fixed terminal atoms search function (Figure 1B)." It is unclear whether a fixed terminal atom search was conducted for each conformer generated in the initial step to further explore the conformational space. This aspect should be clarified to provide a more comprehensive understanding of the methodology.

      Each independent conformer generation function (A-E) is initialized with only the input ligand model and runs in parallel with the other functions. These functions do not build on each other, but rather perturb the input molecule independently of one another. In our updated manuscript, we have clarified the methodology (page 6).

      “First, in all cases, we perform an unconstrained search function (Figure 1A), a fixed terminal atoms search function (Figure 1B), and a blob search function (Figure 1C).”

      Phrase: "We randomly sampled 150 structures and, after manual inspection of the fit of alternative conformations, chose 135 crystal structures as a development set for improving qFit-ligand." The authors should explain why they filtered 10% of the structures.

      To develop qFit-ligand, we wanted to use a very high-quality dataset. We needed to know with some degree of certainty that if qFit-ligand failed to produce an alternate conformation (or generated conformations low in RSCC or high in strain), the failure was due to an algorithmic limitation rather than poor-quality input data. Therefore, after selection based on numerical metrics, we manually examined each ligand in Coot to observe if we believed the alternative conformers fit well into the density.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1:

      Reviewer #1 (Recommendations For The Authors):

      (1) At several places in the reply to reviewers and the manuscript, when discussing the new simulations conducted, the authors mention they break the 180 trials into a train/test split of 108/108 - is this value correct? If so, how? (pg 19 of updated manuscript)  

      Thank you for pointing this out; it was not clearly explained. We have now added the explanation to the Methods section: 

      “For each iteration, we randomly selected 108 responses from the full set of 180 for training, and then independently sampled another 108 from the same full set for testing. This ensured that the same orientation could appear in both sets, consistent with the structure of the original experiment.”

      (2) I appreciate the authors have added the variance explained of principal components to the axes of Fig. 3, though it took me a while to notice this, and this isn't described in the figure caption at all. It would likely help readers to directly explain what the % means on each axis of Fig. 3.

      Thank you, we have now added a description in both Fig. 2 and 3:

      “The axes represent the first two principal components, with labels indicating the percent of total explained variance.”

      (3) I believe there is a typo/missing word in the new paragraph on pg 15: "neural visual WM representations in the early visual cortices are [[biased]] towards distractors" (I think the bracketed word may be omitted as a typo)

      Thank you - fixed.

    1. Author response:

      We would like to thank the editors and reviewers for their time and their helpful feedback. We largely agree with the reviewer recommendations and comments, which we will address for the next Version on Record of this manuscript. We plan to address reviewer comments in the following ways.

      Reviewers requested a more comprehensive analysis of our RNA-seq experiment comparing vehicle treatment to enoxolone treatment over time. We will improve our analysis by providing clear, accessible, and organized tables defining differentially expressed genes at each time point, gene set lists that comprise our gene ontology analysis, and the lists of shared differentially expressed genes from enoxolone treatment and HNF4⍺ knockout. While some of this data was provided in the supplementary files, we recognize that it should be more accessible for the reader. Furthermore, as suggested by the Reviewer, we will enhance our transcriptomic analysis by utilizing bioinformatic tools such as Enrichr.

      The Reviewers noted that we identified a number of lipoprotein-lowering compounds through our drug screen, but limited the impact of our manuscript by focusing on enoxolone, a known inhibitor of HNF4⍺ and modulator of lipid metabolism. While we understand with the sentiment that other novel compounds would be interesting to study, we aimed to demonstrate proof of concept in this manuscript. We view the characterization of novel compounds as beyond the direct scope of this manuscript. We did not perform LipoGlo imaging and electrophoresis experiments on each drug because these experiments are low-throughput given the number of drugs and doses we examined. In light of the Reviewer’s comments, we will add some additional characterizations of our validated hits with LipoGlo imaging and electrophoresis studies.

      The reviewers also identified a number of typos in text and figures that will be addressed in the next Version on Record. We believe that the recommended changes will strengthen our manuscript and broaden its appeal. We are grateful for the opportunity to improve our work based on the reviewers’ valuable suggestions.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1:

      We thank the reviewer for highlighting the strength in our manuscript  as quote: “Overall, this work not only deepens our understanding of PRMT1's role in leukemia progression but also opens new avenues for targeting metabolic pathways in cancer therapy.”

      Weakness :

      (1) The findings rely heavily on a single AMKL cell line, with no validation in patient-derived samples to confirm clinical relevance or even another type of leukemia line. Adding the discussion of PRMT1's role in other leukemia types will increase the impact of this work.

      We mentioned in the introduction that PRMT1 is known to be the driver for leukemia with diverse types of mutations. In a related paper published in Cell Reports (Su et al. 2021), we demonstrated that PRMT1 is upregulated in MDS myeloid dysplasia syndrome patient samples and that the inhibition of PRMT1 promotes megakaryocytic differentiation of a few MDS samples. AMKL is very rare. Via Children’s Oncology group consortium, we have obtained five AMKL samples with Down’s syndrome and AMKL with RBM15-MKL1 translocation out of 32 samples in the bank over the last 20 years. Interestingly, these patient samples also contain trisomy 19. As PRMT1 is localized on chromosome 19, we speculate that PRMT1 is the significant driver for AMKL leukemia, although we have very limited genetic evidence. However, these human frozen samples derived from peripheral blood cannot be grown in a cell culture system. Although we did not perform metabolic analysis for other AMKL cell lines, we did validate in our unpublished studies that PRMT1 drives down CPT1A expression in normal bone marrow cells and platelets in mice and in human leukemia cell line called MEG-01, which can be differentiated into megakaryocytes upon PMA (phorbol 12-myristate 13-acetate) treatment. Therefore, we expect that the PRMT1-mediated metabolic reprogramming we described here should apply to other types of hematological malignancies.

      (2) The observed heterogeneity in Prmt1 expression is noted but not further investigated, leaving gaps in understanding its broader implications.

      The expression level of PRMT1 is heterogeneous within leukemia cell populations, making it intriguing to study. We can sort the cells based on high versus low PRMT1 expression using a fluorescent dye called E84. However, we have not conducted transcriptome analysis on these two populations, mainly due to resource constraints. Theoretically, the E84 high-expression population may transiently utilize glucose more efficiently, as these cells do not ectopically express PRMT1. Therefore, when nutrient levels decline, these cells might switch to the low PRMT1 expression population. It will be interesting to see whether endogenous leukemia cells transiently expressing high levels of PRMT1 take advantage of their efficient usage of glucose and thus adapt to the niche environment successfully, as we observed in the Figure 1. I agree that this would be an interesting direction to pursue in the future.

      (3) Some figures and figure legends didn't include important details or had not matching information.

      We would like to thank the reviewer for pointing out these mistakes. Now we have corrected.

      (4) Some wording is not accurate, such as line 80 "the elevated level of PRMT1 maintains the leukemic stem cells", the study is using the cell line, not leukemia stem cells.

      Leukemic stem cells are often referred to as cells that can initiate leukemia when transplanted into recipient mice, a concept first proposed by John Dick. In this study, we found that even the 6133 cell line displays heterogeneity in terms of PRMT1 expression levels. We identified a subgroup of 6133 cells as leukemia stem cells due to their ability to initiate leukemia.

      (5) In the disease model, histopathology of blood, spleen, and BM should be shown.

      We did not conduct histopathology analysis. 6133 cells associated histopathology has been published in Mercher et al JCI 2009 and a recent preprint by Diane Krause’s group.

      (6) Can MS023 treatment reverse the metabolic changes in PRMT1 overexpression AMKL cells?

      Yes, We demonstrated in figure 4 in the seahorse assays that prmt1 inhibitor can increase the oxygen consumption.

      It would be helpful to provide a summary graph at the end of the manuscript.

      Yes, we now provide a graphic abstract.

      Reviewer #2 (Public review):

      We would like to thank the reviewer for finding the manuscript novel and important.

      Weaknesses:

      (1) The manuscript lacks detailed molecular mechanisms underlying PRMT1 overexpression, particularly its role in enhancing survival and metabolic reprogramming via upregulated glycolysis and diminished oxidative phosphorylation (OxPhos). The findings primarily report phenomena without exploring the reasons behind these changes.

      In the introduction, we highlighted that numerous studies have demonstrated how PMT1 directly interacts with several key enzymes involved in glycolysis. These studies provide a mechanism for the observed upregulation of PMT1 in leukemia. Additionally, our previous research published in eLife 2015 {Zhang, 2015 #5031} demonstrated that PRMT1 methylates the RNA-binding protein RBM15, which can bind to the 3' UTR of mRNAs encoding various metabolic enzymes. Therefore, we propose that PMT1 may also regulate metabolism indirectly through the RBM15 protein.

      (2) The article shows that PRMT1 overexpression leads to augmented glycolysis and low reliance on the OxPhos. However, the manuscript also shows that PMRT1 overexpression leads to increased mitochondrial number and mitochondrial DNA content and has an elevated NADPH/NAD+ ratio. Further, these overexpressing cells have the ability to better survive on alternative energy sources in the absence of glucose compared to low PMRT1-expressing parental cells. Surprisingly, the seashores assay in PRMT1 overexpressing cells showed no further enhancement in the ECAR after adding mitochondrial decoupler FCCP, indicating the truncated mitochondrial energetics. These results are contradicting and need a more detailed explanation in the discussion.

      We have explained the metabolic changes in more detail now. Increasing mitochondria number is not equivalent to increasing fatty acid oxidation and oxygen consumption, as the mitochondria have many other functions. PRMT1 only downregulates CPT1A, which is a rate-limiting step for long-chain fatty acid oxidation. The data suggest that PRMT1 promotes the biogenesis of mitochondria maybe via PGC1alpha as published by Stallcup’s group. The seahorse assays were performed in the high concentration of glucose instead of alternative carbon sources.  FCCP treatment under high glucose conditions did not increase the ECR and OCR, which is normal for leukemia cells as shown in other people’s publications {Sriskanthadevan, 2015 #3944}{Kreitz, 2019 #2133}. PRMT1 could dampen the activities of TCA cycle and the electron transportation chain as the proteomic data from our unpublished data and published data {Fong, 2019 #1185} suggested. The elevated NADPH/NAD+ ratio is another indication that glycolysis and anabolism are enhanced by PRMT1.

      (3) How was disease penetrance established following the 6133/PRMT1 transplant before MS023 treatment?

      Yes, the data was in figure 1f, demonstrating that the penetrance is 100%.  

      (4) The 6133/PRMT1 cells show elevated glycolysis compared to parental 6133; why did the author choose the 6133 cells for treatment with the MS023 and ECAR assay (Fig.3 b)? The same is confusing with OCR after inhibitor treatment in 6133 cells; the figure legend and results section description are inconsistent.

      Sorry for the mistakes while we are preparing the manuscript.  We used 6133/PRMT1 cells to be treated with MS023 in figure 4.

      (5) The discussion is too brief and incoherent and does not adequately address key findings. A comprehensive rewrite is necessary to improve coherence and depth.

      We agree with the reviewer. Now we added comprehensive review of PRMT1-mediated metabolism. The PRMT1 homolgous in yeast is called hmt1. In yeast, hmt1 is upregulated by glucose and enhance glycolysis. So PRMT1 enhanced glycolysis is a conserved pathway in eukaryocytic cells.

      (6) The materials and methods section lacks a description of statistical analysis, and significance is not indicated in several figures (e.g., Figures 1C, D, F; Figures 2D, E, F, I). Statistical significance must be consistently indicated. The methods section requires more detailed descriptions to enable replication of the study's findings.

      We have added extra details on the methods and statistical analysis for the figures.

      (7) Figures are hazy and unclear. They should be replaced with high-resolution images, ensuring legible text and data.

      We have prepared separate figure files with high resolution.

      (8) Correct the labeling in Figure 2I by removing the redundant "D."

      We would like to thank the reviewer and fixed the figure.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review):

      Strengths:

      The genetic approaches here for visualizing the recombination status of an endogenous allele are very clever, and by comparing the turnover of wildtype and mutant cells in the same animal the authors can make very convincing arguments about the effect of chronic loss of pu.1. Likely this phenotype would be either very subtle or nonexistent without the point of comparison and competition with the wildtype cells.

      Using multiple species allows for more generalizable results, and shows conservation of the phenomena at play.

      The demonstration of changes to proliferation and cell death in concert with higher expression of tp53 is compelling evidence for the authors' argument.

      Weaknesses:

      This paper is very strong. It would benefit from further investigating the specific relationship between pu.1 and tp53 specifically. Does pu.1 interact with the tp53 locus? Specific molecular analysis of this interaction would strengthen the mechanistic findings.

      We agree with the reviewer’s assessment regarding the significance of the relationship between PU.1 and TP53. To investigate the potential interaction between Pu.1 and Tp53 in zebrafish, we analyzed the promoter region of zebrafish tp53. Indeed, we found three PU.1 binding sites (GAGGAA) on tp53 promoter, which locate on the antisense strand from position -1047 to -1042, -1098 to -1093 and -1423 to -1418 relative to the transcriptional start site (Fig. S10). These potential Pu.1 binding sites indicate a direct interaction between Pu.1 and tp53 locus. Furthermore, a previous study by Tschan et al. (2008) elucidated the mechanism by which PU.1 attenuates the transcriptional activity of the P53 tumor suppressor family through direct binding to the DNA-binding and/or oligomerization domains of p53/p73 proteins. We have also cited this study (Line 399-401) and included all above information in the discussion of the revised manuscript (Line 399-405).

      Reviewer #2 (Public review):

      Strengths:

      Generation of an elegantly designed conditional pu.1 allele in zebrafish that allows for the visual detection of expression of the knockout allele.

      The combination of analysis of pu.1 function in two model systems, zebrafish and mouse, strengthens the conclusions of the paper.

      Confirmation of the functional significance of the observed upregulation of tp53 in mutant microglia through double mutant analysis provides some mechanistic insight.

      Weaknesses:

      (1) The presented RNA-Seq analysis of mutant microglia is underpowered and details on how the data was analyzed are missing. Only 9-15 cells were analyzed in total (3 pools of 3-5 cells each). Further, the variability in relative gene expression of ccl35b.1, which was used as a quality control and inclusion criterion to define pools consisting of microglia, is extremely high (between ~4 and ~1600, Figure S7A).

      We feel sorry for the unclearness of RNAseq procedures and have accordingly added the details about RNA-seq data analysis in the “Material and methods” section (Line 491-501). Briefly, reads were aligned to the zebrafish genome using the STAR package. Original counts were calculated with featureCounts package. Differential expression genes (DEGs) were identified with the DESeq2 package. Owing to the technical challenge of unambiguously distinguishing microglia from dendritic cells (DCs) in brain cell suspensions, we employed a strategy of isolating 3-5 cells per pool and quantifying the relative expression of the microglia-specific marker ccl34b.1 normalized to the DC-specific marker ccl19a.1. This approach aimed to reduce DC contamination in downstream analyses. Across all experimental groups subjected to RNA-seq analysis, the ccl34b.1/ccl19a.1 expression ratios exceeded 5, confirming microglia as the dominant cell population. Nonetheless, residual DC contamination in the RNA-seq data cannot be entirely ruled out. We have discussed this technical constraint in the revised manuscript to ensure methodological transparency (Line 498-501).

      (2) The authors conclude that the reduction of microglia observed in the adult brain after cKO of pu.1 in the spi-b mutant background is due to apoptosis (Lines 213-215). However, they only provide evidence of apoptosis in 3-5 dpf embryos, a stage at which loss of pu.1 alone does lead to a complete loss of microglia (Figure 2E). A control of pu.1 KI/d839 mutants treated with 4-OHT should be added to show that this effect is indeed dependent on the loss of spi-b. In addition, experiments should be performed to show apoptosis in the adult brain after cKO of pu.1 in spi-b mutants as there seems to be a difference in the requirement of pu.1 in embryonic and adult stages.

      We apologize for the omission of data regarding conditional pu.1 knockout alone in the embryos in our manuscript, which may have led to ambiguity. We would like to clarify that conditional pu.1 knockout alone at the embryonic stage does not induce microglial death (Fig S2). Microglial death occurs only in both embryonic and adult brains when Pu.1 is disrupted in the spi-b mutant background. The blebbing morphology of some microglia after pu.1 conditional knockout in adult spi-b mutant indicated microglia undergo apoptosis at both embryonic and adult stages (Figure S4 and Fig. S5). The reviewer’s concern likely arises from the distinct outcomes of global pu.1 knockout (Fig. 2) versus conditional pu.1 ablation (Fig. S2). Global knockout eliminates microglia during early development due to Pu.1’s essential role in myeloid lineage specification. We have included this clarification in the revised manuscript (Line 208-211).

      (3) The number of microglia after pu.1 knockout in zebrafish did only show a significant decrease 3 months after 4-OHT injection, whereas microglia were almost completely depleted already 7 days after injection in mice. This major difference is not discussed in the paper.

      We propose that zebrafish Pu.1 and Spi-b function cooperatively to regulate microglial maintenance, analogous to the role of PU.1 alone in mice. This cooperative mechanism likely explains the observed difference in microglial depletion kinetics between zebrafish and mice following pu.1 conditional knockout. Specifically, the compensatory activity of Spi-b in zebrafish may buffer the immediate loss of Pu.1, whereas in mice, the absence of Spi-b expression in microglia eliminates this redundancy, resulting in rapid microglial depletion. Furthermore, during evolution, SPI-B appears to have acquired lineage-specific roles, becoming absent in microglia. We have included the clarification in the revised manuscript (Line 302-305).

      (4) Data is represented as mean +/-.SEM. Instead of SEM, standard deviation should be shown in all graphs to show the variability of the data. This is especially important for all graphs where individual data points are not shown. It should also be stated in the figure legend if SEM or SD is shown

      We have represented our data as mean ± SD in the revised manuscript.

      Recommendations for the authors:

      Reviewing Editor:

      To further strengthen the manuscript, we ask the authors to address the reviewers' comments through additional experiments where necessary. In cases where certain experiments may be challenging, we encourage the authors to address these concerns within the text, such as by referencing any prior evidence of pu.1 and tp53 interactions or incorporating in silico analyses that support such interaction.

      As suggested, we have performed in-silico analysis of Pu.1 binding sites in zebrafish tp53 promoter and also cited previous paper showing how PU.1 attenuates the transcriptional activity of the P53 tumor suppressor family (Line 399-405).

      Reviewer #1 (Recommendations for the authors):

      It would be useful to investigate the relationship between pu.1 and tp53. The data presented here show that pu.1 deficient cells have higher expression of tp53, but this could be an indirect effect. However, since pu.1 has known DNA binding motifs, it would be worthwhile to investigate if there are any direct interactions between pu.1 and the tp53 locus -- does pu.1 directly bind and repress tp53 expression? This could be directly investigated with Cut & Run or an EMSA.

      The interaction between Pu.1 and Tp53 has been discussed in the public review section.

      The paper would likely also benefit from a more in-depth discussion of the relationship of the zebrafish alleles and their relationship to mammalian Pu.1 -- as presented here, the authors are implicitly arguing that zebrafish pu.1 and spi-b are both more closely related to mammalian Pu.1 than to mammalian Spi-b. A clear argument, perhaps backed up by sequence alignment and homology matching, would help readers, especially those less familiar with zebrafish genome duplications.

      We have conducted detailed sequence alignment in our previous work (Yu et al., 2017, Blood) and found zebrafish Spi-b shares the highest similarity with the mammalian SPI-B among Ets family transcription factors in zebrafish. A unique P/S/T-rich region known to be essential for mammalian SPI-B transactivation activity is present in zebrafish Spi-b. Our data do not support the interpretation that Spi-b is more closely related to mammalian Pu.1 than to Spi-b. Instead, functional compensation between pu.1 and spi-b in microglia maintenance likely reflects their shared role as Ets-family transcriptional regulators, rather than ortholog-driven redundancy.

      Reviewer #2 (Recommendations for the authors):

      (1) The nomenclature of the genes in the SPI family in zebrafish is somewhat confusing as genes were renamed several times. It would make it easier for the reader to understand if in the abstract and the main text, spi-b would be referred to as the zebrafish orthologue of mouse SPI-B (as determined by the authors in previous work) rather than the paralogue of zebrafish pu.1. To clarify which genes were analyzed in both zebrafish and mouse, Gene accession numbers should be added.

      Thanks for the recommendations. We have changed “the paralogue of zebrafish pu.1” to “the orthologue of mouse Spi-b” in the abstract (Line 22) and added gene accession numbers for both zebrafish and mouse gene (Line 105-106 and 301-302).

      (2) Methods RNA-seq: Details on how the aligned reads were analyzed to detect differentially expressed genes are missing and should be added. In addition, a table with read counts, fold changes and adjusted p values should be added.

      We have added details of RNA-seq analysis in the Material and Methods part (Line 491-501). A table generated by Deseq2 has been included as a supplemental file to show read counts, fold changes and adjusted p values (Supplemental file 2).

      (3) Figure 2H: It would be helpful to the reader if the KO splicing would be shown in comparison to WT splicing.

      Thank you for your suggestion. We have added the sequence result between exon 3 and exon 4 of pu.1 from wildtype cDNA to show WT splicing in Figure 2H.

      (4) Legend Figure 5C. Relative expression should be replaced with transcripts per million (TPM).

      We have corrected it in the figure legend of Figure 5C (Line 786-787).

      (5) In Figure S3. the label on the y-axis in panel B is not visible.

      We apologize for the mistake during figures assembling. We have corrected it and now the y-axis is visible.

      (6) In Figure S7B an explanation for the colors in the heat map is missing and should be added.

      Colors represent scaled TPM values. The red color represents high expression while the blue color represents low expression. We have added the information in the figure legend.

      (7) A justification for the use of male mice only should be added or additional experiments in female mice should be performed.

      Female mice were excluded to avoid variability associated with estrous cycle-dependent hormonal changes, which are known to influence microglial behavior (Habib P et al., 2015). We have added a justification in the revised manuscript (Line 547-548).

      (8) The manuscript would benefit from some language editing. A few examples are listed below:

      a) line 97: the rostral blood (RBI) should read the rostral blood island.

      b) line 373 typo: nucleus translocation should read nuclear translocation.

      c) line 393 typo: pu.1-dificent should read pu.1-deficient.

      We apologize for the typos or grammar mistakes in the manuscript. We have checked the manuscript thoroughly and revised those typos or grammar mistakes.

      Reference:

      Tschan MP, Reddy VA, Ress A, Arvidsson G, Fey MF, Torbett BE (2008) PU.1 binding to the p53 family of tumor suppressors impairs their transcriptional activity. Oncogene 27: 3489-93

      Yu T, Guo W, Tian Y, Xu J, Chen J, Li L, Wen Z (2017) Distinct regulatory networks control the development of macrophages of different origins in zebrafish. Blood 129: 509-519

      Habib P, Beyer C (2015) Regulation of brain microglia by female gonadal steroids. J Steroid Biochem Mol Biol 146: 3-14

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Tubert C. et al. investigated the role of dopamine D5 receptors (D5R) and their downstream potassium channel, Kv1, in the striatal cholinergic neuron pause response induced by thalamic excitatory input. Using slice electrophysiological analysis combined with pharmacological approaches, the authors tested which receptors and channels contribute to the cholinergic interneuron pause response in both control and dyskinetic mice (in the L-DOPA off state). They found that activation of Kv1 was necessary for the pause response, while activation of D5R blocked the pause response in control mice. Furthermore, in the L-DOPA off state of dyskinetic mice, the absence of the pause response was restored by the application of clozapine. The authors claimed that 1) the D5R-Kv1 pathway contributes to the cholinergic interneuron pause response in a phasic dopamine concentration-dependent manner, and 2) clozapine inhibits D5R in the L-DOPA off state, which restores the pause response.

      Strengths

      The electrophysiological and pharmacological approaches used in this study are powerful tools for testing channel properties and functions. The authors' group has well-established these methodologies and analysis pipelines. Indeed, the data presented were robust and reliable.

      Weaknesses:

      Although the paper has strengths in its methodological approaches, there is a significant gap between the presented data and the authors' claims.

      The authors answered the most of concerns I raised. However, the critical issue remains unresolved.

      I am still not convinced by the results presented in Fig. 6 and their interpretation. Since Clozapine acts as an agonist in the absence of an endogenous agonist, it may stimulate the D5R-cAMP-Kv1 pathway. Stimulation of this pathway should abolish the pause response mediated by thalamic stimulation in SCINs, rather than restoring the pause response. Clarification is needed regarding how Clozapine reduces D5R-ligand-independent activity in the absence of dopamine (the endogenous agonist). In addition, the author's argued that D5R antagonist does not work in the absence of dopamine, therefore solely D5R antagonist didn't restore the pause response. However, if D5R-cAMP-Kv1 pathway is already active in L-DOPA off state, why D5R antagonist didn't contribute to inhibition of D5R pathway? Since Clozapine is not D5 specific and Clozapine experiments were not concrete, I recommend testing whether other receptors, such as the D2 receptor, contribute to the Clozapine-induced pause response in the L-DOPA-off state.

      Thank you for the opportunity to clarify this point. It seems there may have been a misunderstanding regarding our proposal about clozapine's mechanism of action. We are not suggesting that clozapine acts as an agonist, but rather as an “inverse agonist”. Unlike classical agonists, inverse agonists produce a pharmacological effect opposite to that of an agonist. Although clozapine is best known for its antagonistic effects on dopamine and serotonin receptors, under conditions where no endogenous agonist is present, it has been shown to reduce the constitutive activity of D1 and D5 receptors (PMID: 24931197). This is explained in lines 240-254 in the Results section.

      In contrast, the prototypical and selective D1/D5 receptor antagonist SCH23390 does not exhibit inverse agonist properties and would not be expected to produce effects in the absence of an agonist (PMID: 7525564). The observation that SCH23390 blocks the effects of clozapine in dopamine-depleted animals strongly supports the idea that clozapine acts through D1/D5 receptors. This is now clarified in lines 257264.

      To further address your comments, we now include a new figure (Figure 6) presenting experiments that show D2-type receptor agonists do not restore the pause response in dyskinetic mice in the off-L-DOPA condition. These results are described in a new subsection of the Results section and discussed in a newly added paragraph in the Discussion (lines 369-380).

      Finally, to exclude a potential contribution of serotonin receptors to clozapine’s effects, we have expanded what is now Figure 7 (formerly Figure 6) to show that clozapine continues to restore the pause response even in the presence of a serotonin receptor antagonist in the bath.

      All these results are further discussed in lines 342-360.

      Reviewer #2 (Public review):

      Summary:

      This manuscript by Tubert et al. presents the role of D5 receptors (D5R) in regulating the striatal cholinergic interneuron (CIN) pause response through D5R-cAMP-Kv1 inhibitory signaling. Their findings provide a compelling model explaining the "on/off" switch of the CIN pause, driven by the distinct dopamine affinities of D2R and D5R. This mechanism, coupled with varying dopamine states, is likely critical for modulating synaptic plasticity in cortico-striatal circuits during motor learning and execution. Furthermore, the study bridges their previous finding of CIN hyperexcitability (Paz et al., Movement Disorder 2022) with the loss of the pause response in LID mice and demonstrates the restore of the pause through D1/D5 inverse agonism.

      Strengths:

      The study presents solid findings, and the writing is logically structured and easy to follow. The experiments are well-designed, properly combining ex vivo electrophysiology recording, optogenetics, and pharmacological treatment to dissect / rule out most, if not all, alternative mechanisms in their model.

      Weaknesses:

      While the manuscript is overall satisfying, one conceptual gap needs to be further addressed or discussed: the potential "imbalance" between D2R and D5R signaling due to the ligand-independent activity of D5R in LID. Given that D2R and D5R oppositely regulate CIN pause responses through cAMP signaling, investigating the role of D2R under LID off L-DOPA (e.g., by applying D2 agonists or antagonists, even together with intracellular cAMP analogs or inhibitors) could provide critical insights. Addressing this aspect would strengthen the manuscript in understanding CIN pause loss under pathological conditions.

      Thank you for your comments. Although our primary focus is on the role of D5 receptors, we have also investigated the effects of two D2-type receptor agonists in dyskinetic mice in the off-L-DOPA condition. We found that neither quinpirole nor sumanirole was able to restore the pause response. These results are presented in Figure 6 and related text in the Results and Discussion sections.

      Understanding why D2 agonists fail to restore the pause response—despite their expected effect of reducing cAMP levels—is an important question that warrants further investigation. Interestingly, previous studies have reported paradoxical effects of D2 receptor stimulation in SCINs in animal models of dystonia (PMID: 16934985, PMID: 21912682), as well as under conditions where the SCIN’s constitutively active integrated stress response is diminished (PMID: 33888613). This is now discussed in lines 369-380.

      Reviewer #3 (Public review):

      Summary:

      Tubert et al. investigate the mechanisms underlying the pause response in striatal cholinergic interneurons (SCINs). The authors demonstrate that optogenetic activation of thalamic axons in the striatum induces burst activity in SCINs, followed by a brief pause in firing. They show that the duration of this pause correlates with the number of elicited action potentials, suggesting a burst-dependent pause mechanism. The authors demonstrated this burst-dependent pause relied on Kv1 channels. The pause is blocked by a SKF81297 and partially by sulpiride and mecamylamine, implicating D1/D5 receptor involvement. The study also shows that the ZD7288 does not reduce the duration of the pause, and that lesioning dopamine neurons abolishes this response, which can be restored by clozapine.

      Weaknesses:

      While this study presents an interesting mechanism for SCIN pausing after burst activity, there are several major concerns that should be addressed:

      (1) Scope of the Mechanism: It is important to clarify that the proposed mechanism may apply specifically to the pause in SCINs following burst activity. The manuscript does not provide clear evidence that this mechanism contributes to the pause response observed in behavioral animals. While the thalamus is crucial for SCIN pauses in behavioral contexts, the exact mechanism remains unclear. Activating thalamic input triggers burst activity in SCINs, leading to a subsequent pause, but this mechanism may not be generalizable across different scenarios. For instance, approximately half of TANs do not exhibit initial excitation but still pause during behavior, suggesting that the burstdependent pause mechanism is unlikely to explain this phenomenon. Furthermore, in behavioral animals, the duration of the pause seems consistent, whereas the proposed mechanism suggests it depends on the prior burst, which is not aligned with in vivo observations. Additionally, many in vivo recordings show that the pause response is a reduction in firing rate, not complete silence, which the mechanism described here does not explain. Please address these in the manuscript.

      Thank you for the opportunity to clarify these points. We acknowledge that the response of SCINs to optogenetic stimulation of thalamic afferents in brain slices represents a model system that may not capture all aspects of TAN responses to behaviorally salient events. Nevertheless, this approach allows us to test mechanistic hypotheses that are difficult to address in behaving animals with current technologies. This is now stated in lines 311-314.

      Importantly, our ex vivo preparation reproduces, for the first time, the loss of TAN responses observed in non-human primates with parkinsonism, enabling investigation of the underlying mechanisms. In line with your suggestion, we have expanded the Discussion (third and fourth paragraphs) to address the sources of variability in pause responses.

      (2) Terminology: The use of "pause response" throughout the manuscript is misleading. The pause induced by thalamic input in brain slices is distinct from the pause observed in behavioral animals. Given the lack of a clear link between these two phenomena in the manuscript, it is essential to use more precise terminology throughout, including in the title, bullet points, and body of the manuscript.

      Thank you for raising this important point. We agree that it is essential to be precise in describing the nature of the pause observed in our ex vivo model. While we believe that readers would recognize from the abstract and methods that our study focuses on a model of the pause response, we understand your concern about potential confusion. In response, we have revised the terminology in the abstract, bullet points, and throughout the manuscript to more clearly reflect that we are describing an ex vivo model of the pause observed in behaving animals.

      (3) Kv1 Blocker Specificity: It is unclear how the authors ruled out the possibility that the Kv1 blocker did not act directly on SCINs. Could there be an indirect effect contributing to the burst-dependent pause?

      Clarification on this point would strengthen the interpretation of the results.

      This issue is addressed in lines 147-150.

      (4) Role of D1 Receptors: While it is well-established that activating thalamic input to SCINs triggers dopamine release, contributing to SCIN pausing (as shown in Figure 3), it would be helpful to assess the extent to which D1 receptors contribute to this burst-dependent pause. This could be achieved by applying the D1 agonist SKF81297 after blocking nAChRs and D2 receptors.

      Figure 3C shows that the D1/D5 receptor antagonist SCH23390 does not modify the pause, while the full D1/D5 agonist SKF81297 abolishes it, indicating that in our slice preparation, baseline dopamine levels are not contributing to the pause through D1/D5 receptor stimulation.

      (5) Clozapine's Mechanism of Action: The restoration of the burst-dependent pause by clozapine following dopamine neuron lesioning is interesting, but clozapine acts on multiple receptors beyond D1 and D5. Although it may be challenging to find a specific D5 antagonist or inverse agonist, it would be more accurate to state that clozapine restores the burst-dependent pause without conclusively attributing this effect to D5 receptors.

      As explained in our response to Reviewer #1, the effect of clozapine is blocked by the D1/D5-selective antagonist SCH23390. Additionally, new data presented in Figure 7C show that clozapine's ability to restore the pause response is maintained even in the presence of a broad-spectrum serotonin receptor antagonist. Since SCINs do not significantly express D1 receptors, we believe that these findings strongly support a role for D5 receptors in SCINs.

      Comments on revisions:

      The authors have addressed many of my concerns. However, I remain unconvinced that adding an 'ex vivo' experiment fully resolves the fundamental differences between the burst-dependent pause observed in slices - defined by the duration of a single AHP - and the pause response in CHINs observed in vivo, which may involve contributions from more than one prolonged AHP. In vivo, neurons can still fire action potentials during the pause, albeit at a lower frequency. Moreover, in behaving animals, pause duration does not vary with or without initial excitation. The mechanism proposed demonstrates that the pause duration, defined by the length of a single AHP, is positively correlated with preceding burst activity.

      As discussed in paragraphs 3 and 4 of the Discussion (starting at line 285), and illustrated in Figure 1J–K, our data show that the duration of the pause can be modulated by rebound excitation from thalamic input. The absence of this rebound allows us to observe a longer pause when more spikes are elicited during the initial excitatory phase, providing a clearer readout of the contribution of intrinsic membrane mechanisms. We do not claim that intrinsic mechanisms alone account for the entire phasic response of SCINs in behaving animals (lines 295-303 in Discussion).

      To improve clarity, I recommend using the term 'SCIN pause' to describe the ex vivo findings, distinguishing them more explicitly from the 'pause response' observed in behaving animals. This distinction would help contextualize the ex vivo findings as potentially contributing to, but not fully representing, the pause response in vivo.

      We did changes in the abstract, bullet points, and main text to clarify that we are not studying the in vivo response.

      Again, it would be helpful to present raw data for pause durations rather than relying solely on ratios. This approach would provide the audience with a clearer understanding of the absolute duration of the burst-dependent pause and allow for better comparison to the ~200 ms pause observed in behaving animals.

      Thank you for your comment. Following your suggestion, we provide the average pause durations for the data shown in Figure 1H (lines 127–130). We opted not to include raw pause durations in the main text for all figures, as this would make the manuscript more difficult to read and, in our view, is unnecessary. The figures already allow readers to estimate absolute durations: in each case, pause durations are shown relative to baseline ISIs in one panel, while the corresponding absolute ISIs are shown side-by-side. This provides a clearer understanding of pause magnitude relative to the cell’s spontaneous firing, which is more informative than absolute values alone, since one would expect a pause to be longer than the average ISI. Please note that baseline ISI are significantly shorter in dyskinetic mice (Figure 5l). Showing the pause duration relative to baseline ISI allows readers to readily compare results across figures regardless of changes in SCIN baseline firing rate.

      Additionally, it is important to note that, in vivo, pause durations are typically inferred from perievent time histograms (PETHs), which represent population averages across many trials. In contrast, in our ex vivo studies, we measured pause duration on a trial-by-trial basis. This approach enables us to analyze how the pause duration varies as a function of the initial burst size in the same neuron—something not typically reported in in vivo studies. As described in the first two paragraphs of the Results, the same SCIN may respond with a different number of spikes in successive trials, and this variability is influenced by factors such as the timing of the last spontaneous spike relative to stimulation onset (Figure 1D–F). We are not aware of studies reporting trial-by-trial analyses of pause duration in behaving animals, particularly in relation to the strength of initial excitation. Therefore, while our slice preparation may yield pause durations that are longer than those observed in vivo, direct comparison to PETH-derived pause durations from behaving animals is not straightforward.

    1. Author response:

      The following is the authors’ response to the previous reviews

      We are appreciative of the reviewers’ and editors’ constructive suggestions of manuscript, which have helped us to improve our manuscript. We have made considerable revisions to our details of data analyses.

      The reason that the reviews did not change is that there were really three central points that led to the "incomplete". These were (1) the fact that there was potentially a selection bias due to double dipping, and (2) there was potentially a time-confound due to the lack of counterbalancing (3) There is confusion about how the modeling was done, but it seems like the modelling was of the complete block (rather than tied to specific events in that block).

      (1) Double dipping

      We appreciate the opportunity to explain our robust safeguards against double-dipping and have provided detailed clarifications regarding the data analyses (pp.11-14).Our study ensures statistical independence between task-related region selection and hypothesis testing through three orthogonal mechanisms:

      (1) Regressor Orthogonality:Statistical Independence Between Selection and Testing

      The selection regressor (group mean activation) was mathematically independent from test regressors (group differences, behavioral scores). This was confirmed through our GLM implementation: First-level: Task vs. rest contrast (β values) for each participant; Second-level: One-sample t-tests (selection) vs. independent group/behavioral tests.

      (2) Multimodal Validation: Complementary Neural and Behavioral Measures

      We employed multiple distinct metrics to provide convergent yet independent validation of effects.

      Neural Measures: Three orthogonal indices assessed different neural dimensions.

      A. Single-brain activation examines neural activity patterns within individual decision-makers,

      B. while within-group neural synchronization (GNS) quantifies the temporal alignment of neural activity across interacting group members during shared decision processes.

      C. Functional connectivity (FC) analyses, by contrast, measure correlated activity between different brain regions within individual participants.

      Behavioral Safeguards: Behavioral metrics were analyzed in independent regressions, avoiding circularity.

      A. Individual performance was based on personal accuracy,

      B. collective performance represented the group-level average accuracy across raters, and

      C. their similarity was quantified as the Euclidean distance between individual and collective scores.

      (3) Statistical Safeguards

      We further ensured independence by applying strict FDR correction at both selection (p < 0.05) and testing stages (p < 0.05). Besides, permutation test was conducted, we tested 1,000 pseudo-group iterations for GNS null distributions.

      Drawing on both classic and latest NIRS (e.g., Jiang et al., 2015; Liu et al., 2023; Stolk et al., 2016; Xie et al., 2023) and NIRS hyperscanning studies (e.g., Liu et al., 2019; P’arnamets et al., 2020; Reinero et al., 2021; Számadó et al., 2021; Solansky, 2011), we performed the data analyses. Below, we provide the details of our data analysis:

      Single-brain activation. To identify task-related brain regions (channels), we used a one-sample t-test based on brain activation data from all participants during the task compared to the baseline (resting state).

      (1)  Data Collection: Each participant had brain activation data (HbO signals measured by fNIRS) during the task (the entire process of reading, sharing, discussing, and decision-making) and the resting state (baseline).

      (2)  Pre-processing: We sought to explore the neural mechanisms that manipulated group identification and its effect on collective performance. Data were preprocessed using the Homer2 package in MATLAB 2020b (Mathworks Inc., Natick, MA, USA). First, motion artifacts were detected and corrected using a discrete wavelet transformation filter procedure. After that, the raw intensity data were converted to optical density (OD) changes. Then, kurtosis-based wavelet filtering (Wav Kurt) was applied to remove motion artifacts with a kurtosis threshold of 3.3 (Chiarelli, Maclin, Fabiani, & Gratton, 2015). Based on a prior multi-brain study of social interactions (Cheng et al., 2022), the output was bandpass filtered using a Butterworth filter with order 5 and cut-offs at 0.01 and 0.5 Hz to remove longitudinal signal drift and instrument noise. Finally, OD data were converted to HbO concentrations.

      (3) Individual-Level Analysis: First, a GLM was used to compute the "task vs. rest" brain activation contrast for each participant [0,1], obtaining each individual's "task effect" value (β value, representing task activation strength).

      (4) Group-Level Analysis: These "task effect" values from all participants were then aggregated, and a one-sample t-test was performed for each brain region (or channel) to determine whether the average activation in that region was significantly greater than 0 (i.e., significantly more active during the task compared to the resting state).

      (5) Task-Related Regions: If the t-test result for a brain region was significant (p < 0.05, FDR-corrected), we considered that region "task-related" and suitable for further analysis.

      (6) Subsequent Tests:

      - Group Comparisons: We examined differences in activation between groups (e.g., high vs. low group identification) using independent t-tests on the same task vs. baseline contrast.

      - Behavioral Correlations: We analyzed relationships between task-related activation (β values) and behavioral scores (e.g., individual performance) using Pearson analyses.

      - Mediation model: We examined the relationship between an individual's perceived group identification and individual performance, which was mediated by task-related activation (β values).

      Within-Group Neural Synchronization (GNS).

      (1) Data Collection and Pre-processing as above

      (2) Calculation: WTC was applied to generate the brain-to-brain coupling of each pair in each triad (Coherence1&2, Coherence 1&3, and Coherence 2&3). Then, three coherence values from three pairs were averaged as the GNS for each triad, that is, GNS = (Coherence 1&2 + Coherence 1&3 + Coherence 2&3) / 3.

      (3) Task-Related Regions: Time-averaged GNS (also averaged across channels in each group) was compared between the baseline session (i.e., the resting phase) and the task session (from reading information to making decisions) using a series of one-sample t-tests. When determining the frequency band of interest, the time-averaged GNS was also averaged across channels. After that, we analyzed the time-averaged GNS of each channel. Then, channels showing significant GNS were regarded as regions of interest and included in subsequent analyses.

      (4) Permutation test: The nonparametric permutation test was conducted on the observed interaction effects on GNS of the real group against the 1,000 permutation samples.

      (5) Subsequent Tests:

      - Group Comparisons: We examined differences in activation between groups (e.g., high vs. low group identification) using independent t-tests on the same task vs. baseline contrast.

      - Behavioral Correlations: The Pearson’s correlation between GNS and collective performance (i.e., calculated by averaging the individual scores assigned by the three raters for each group) was performed.

      -  Mediation model: We examined how GNS mediated the relationship between group identification and collective performance.

      The brain activation connectivity.

      (1) Data Collection and Pre-processing as above

      (2) Calculation: Exploratory Pearson’s correlations between individual performance related HbO and collective performance-related HbO.

      (3) Moderation analysis: Single-brain activation × connectivity → GNS.

      (2) Counterbalancing.

      We sincerely appreciate this valuable methodological insight. Building on prior group decision-making research (De Wilde et al., 2017; Stasser et al., 1992), we refined all stages to enhance experimental control and procedural clarity throughout the process (i.e., a. Reading information, b. Sharing private information, c. Discussing information, d. Decision) (Xie et al., 2023). Importantly, we maintained a fixed task sequence to preserve ecological validity, as this progression mirrors natural group decision-making dynamics.

      While this design choice precludes sequential counterbalancing, several factors mitigate potential temporal confounds: (1) random assignment and uniform task timing across conditions minimize systematic between-group differences; (2) our whole-block GLM approach captures sustained decision-related neural activity rather than phase-specific effects; and (3) We fully acknowledge this limitation and will incorporate a detailed discussion of temporal considerations in the revised manuscript, while noting that our design provides unique advantages for studying naturalistic decision-making processes.

      (3) The modelling was of the complete block

      In our revised manuscript, we have explicitly stated that the analysis was performed at the block level rather than the event level, for the following reasons:

      (1) The hidden profile task is inherently a “group decision-making process” that unfolds dynamically across multiple stages (reading, sharing, discussing, and deciding). Prior research in this paradigm (De Wilde et al., 2017; Stasser & Titus, 1985; Xie et al., 2023) has consistently treated these phases as integrated blocks because the key cognitive and social processes (e.g., information integration, deliberation, and consensus formation) occur over extended interactions rather than discrete events.

      (2) Methodologically, our fNIRS hyperscanning approach requires longer blocks to reliably capture the slow hemodynamic response and the gradual emergence of inter-brain neural synchronization during naturalistic social exchanges (Cui et al., 2012; Liu et al., 2019). Event-related designs, while useful for transient stimuli, are less suited for studying prolonged, interactive decision-making where neural coupling develops over time. Thus, our block-based analysis aligns with both the cognitive demands of the task and the neuroimaging constraints, ensuring robust detection of group-level neural dynamics.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Prior research indicates that NaV1.2 and NaV1.6 have different compartmental distributions, expression timelines in development, and roles in neuron function. The lack of subtype-specific tools to control Nav1.2 and Nav1.6 activity however has hampered efforts to define the role of each channel in neuronal behavior. The authors attempt to address the problem of subtype specificity here by using aryl sulfonamides (ASCs) to stabilize channels in the inactivated state in combination with mice carrying a mutation that renders NaV1.2 and/or NaV1.6 genetically resistant to the drug. Using this innovative approach, the authors find that action potential initiation is controlled by NaV1.6 while both NaV1.2 and NaV1.6 are involved in backpropagation of the action potential to the soma, corroborating previous findings. Additionally, NaV1.2 inhibition paradoxically increases the firing rate, as has also been observed in genetic knockout models. Finally, the potential anticonvulsant properties of ASCs were tested. NaV1.6 inhibition but not NaV1.2 inhibition was found to decrease action potential firing in prefrontal cortex layer 5b pyramidal neurons in response to current injections designed to mimic inputs during seizure. This result is consistent with studies of loss-of-function Nav1.6 models and knockdown studies showing that these animals are resistant to certain seizure types. These results lend further support for the therapeutic promise of activity-dependent, NaV1.6-selective, inhibitors for epilepsy.

      Strengths:

      (1) The chemogenetic approaches used to achieve selective inhibition of NaV1.2 and NaV1.6 are innovative and help resolve long-standing questions regarding the role of Nav1.2 and Nav1.6 in neuronal electrogenesis.

      (2) The experimental design is overall rigorous, with appropriate controls included.

      (3) The assays to elucidate the effects of channel inactivation on typical and seizure-like activity were well selected.

      Weaknesses:

      (1) The potential impact of the YW->SR mutation in the voltage sensor does not appear to have been sufficiently assessed. The activation/inactivation curves in Figure 1E show differences in both activation and inactivation at physiologically relevant membrane voltages, which may be significant even though the V1/2 and slope factors are roughly similar.

      We have performed new experiments testing how YW->SR mutations affect spiking on their own. The reviewer’s intuition was correct; the small changes in voltage-dependence in NaV1.6 identified in heterologous expression systems translated into a ~2 mV hyperpolarization in threshold in neurons.

      (2) Additional discussion of the fact that channels are only partially blocked by the ASC and that ASCs act in a use-dependent manner would improve the manuscript and help readers interpret these results.

      We have updated text extensively to address this concern. Details are found in the author suggestions below.

      (3) NaV1.6 was described as being exclusively responsible for the change in action potential threshold, but when NaV1.6 alone was inactivated, the effect was significantly reduced from the condition in which both channels were inactivated (Figure 4E). Similarly, Figure 6C shows that blockade of both channels causes threshold depolarization prior to the seizure-like event, but selective inactivation of NaV1.6 does not. As NaV1.2 does not appear to be involved in action potential initiation and threshold change, what is the mechanism of this dissimilarity between the NaV1.6 inactivation and combined NaV1.6/ NaV1.2 inactivation?

      We believe the dissimilarity is due to interactions between NaV1.2 and other channel classes (e.g., potassium channels) throughout the cell, including the somatodendritic domain. NaV1.6 that initiates APs, localized to the AIS, do not live in isolation, and AP threshold can be affected by the recent membrane potential history. Loss of NaV1.2-mediated depolarization in the dendrites begets less potassium channel-mediated repolarization, as described in Figure 4.

      (4) The idea that use-dependent VGSC-acting drugs may be effective antiseizure medications is well established. Additional discussion or at least acknowledgement of the existing, widely used, use-dependent VGSC drugs should be included (e.g. Carbamazepine, Lamotrigine, Phenytoin). Also, the idea that targeting NaV1.6 may be effective for seizures is established by studies using genetic models, knockdown, and partially selective pharmacology (e.g. NBI-921352). Additional discussion of how the results reported here are consistent with or differ from studies using these alternative approaches would improve the discussion

      We agree; the concept of use-dependent block as a means to treat seizure is not new, and we have updated the discussion to include commentary on other medications currently in use. What is new here is our ability to explore the role of NaV1.2 and NaV1.6 in electrogenesis with a level of drug selectivity that could not be achieved without the addition of the YW->SR mutations. This approach in itself will not be useful in the clinic, but it may help guide drug design in the future. One major interpretation of this work is that NaV1.6 block is more effective than NaV1.2 block in general, and may even be effective for non-SCN8A genetic conditions. This is indeed one of the reasons that we believe that drugs like NBI-921352, itself an aryl-sulfonamide, is being tested in seizure models.

      Reviewer #2 (Public review):

      The authors used a clever and powerful approach to explore how Nav1.2 and Nav1.6 channels, which are both present in neocortical pyramidal neurons, differentially control firing properties of the neurons. Overall, the approach worked very well, and the results show very interesting differences when one or the other channel is partially inhibited. The experimental data is solid and the experimental data is very nicely complemented by a computational model incorporating the different localization of the two types of sodium channels.

      In my opinion the presentation and interpretation of the results could be improved by a more thorough discussion of the fact that only incomplete inhibition of the channels can be achieved by the inhibitor under physiological recording conditions and I thought the paper could be easier to digest if the figures were re-organized. However, the key results are well-documented.

      This is a concern raised by multiple reviewers, and we thank you all for your help in improving the way in which we discuss the results. We have revised the manuscript extensively, moving figures around per your advice and the advice of R1 in their comments to authors.

      Reviewer #3 (Public review):

      Summary:

      The authors used powerful and novel reagents to carefully assess the roles of the voltage gated sodium channel (NaV) isoforms in regulating the neural excitability of principal neurons of the cerebral cortex. Using this approach, they were able to confirm that two different isoforms, NaV1.2 and NaV1.6 have distinct roles in electrogenesis of neocortical pyramidal neurons.

      Strengths:

      Development of very powerful transgenic mice in which NaV1.2 and/or NaV1.6 were modified to be insensitive to ASCs, a particular class of NaV blocker. This allowed them to test for roles of the two isoforms in an acute setting, without concerns of genetic or functional compensation that might result from a NaV channel knockout.

      Careful biophysical analysis of ASC effects on different NaV isoforms.

      Extensive and rigorous analysis of electrogenesis - action potential production - under conditions of blockade of either NaV1.2 or NaV1 or both.

      Weaknesses:

      Some results are overstated in that the representative example records provided do not directly support the conclusions.

      We have swapped out example records to better capture the median effect observed and to better capture our discussion of these results. Please see below, in recommendations for authors, for details.

      Results from a computational model are provided to make predictions of outcomes, but the computational approach is highly underdeveloped.

      Modeling has been elaborated upon extensively, with more detail in methods, a new sensitivity analysis supplemental figure, and a deposition into ModelDB.  Please see below, in recommendations for authors, for details.

      Reviewer #1 (Recommendations for the authors):

      Regarding the concern about the potential impact of the YWàSR mutation: All results in Figures 2-6 report only within-subject changes before and after drug-activating protocols. These results show that the drug has no effect on the mutant channel, but whether the mutant channel itself has any effect on neuronal properties is not clear. This deficiency could be rectified by reporting raw values for AP threshold, spike rate, etc. in the pre-drug condition and statistically analyzing the apparent differences in the activation/inactivation curves.

      Data in our original submission only included data in the presence of GNE-4076. We now present new data showing how the YWàSR mutation affects baseline activity of neurons. These data are in Supplemental Figure 1. Compared to wildtype (no drug control) neurons, we observe no change in peak dV/dt. However, threshold is hyperpolarized by approximately 2 mV in dual knockin neurons (median values: -57.4 mV for dual knockin and -55 mV for wildtype). This is consistent with measures from heterologously expressed channels, where we observed somewhat subtle shifts in voltage-dependence of inactivation and activation in NaV1.6 as a result of YWàSR incorporation. 

      In addition to these data, we also include the baseline dataset from Figure 3, where GNE-4076 is present throughout recording, and report that neither threshold nor peak dV/dt are influenced by the presence of GNE at baseline. This suggests that any drug binding at baseline (i.e., before firing APs via somatic current injection) is negligible, consistent with the concept that GNE-4076 has low affinity for the closed channel state.

      Minor Comments:

      While the single-cell response to "seizure-like" input aptly demonstrates the change in action potential threshold and firing rate induced by NaV1.6 inhibition, this component of the paper could be enhanced by a network-level assay that assesses the impact of this drug on an actual seizure-like event in acute slices or on seizure susceptibility in vivo.

      This is an excellent thought, and the work near the end of this manuscript is an effort to mimic network-like activity in a controlled way in single cells. To expand this to bona fide seizure-like activity in acute slices or in vivo is something that we are considering for future studies. To do this properly requires extensive validation of dosing and seizure induction that will require several years’ effort.

      Fig 1e caption says "circles" but the markers are squares

      This has been corrected, thank you for catching it.

      Color scheme in S2B is not intuitive to me

      We’ve now updated the caption to better describe the color scheme used within.

      Fig S2: graph or show change in threshold

      Empirical threshold data are in main figure 3D. Changes in threshold related to modeling are now included in a new sensitivity analysis that is in a new Supplemental Figure 2.

      Fig 3A example of NaV1.6 inhibition does not show change in AP threshold apparent in the aggregate data

      We have updated the representative example to better illustrate the change in AP threshold for NaV1.6 inhibition.

      "AP initiation is mediated exclusively by NaV1.6" not corroborated by data; APs still occur when NaV1.6 is inhibited

      This was an over-interpretation of our data, indeed. We have updated the language to be more accurate to the following: “AP threshold and AP initiation appears to be initiated in an NaV1.6-rich region in control conditions; when NaV1.6 is inhibited, APs can occur at more depolarized potentials, likely mediated predominately by NaV1.2.”

      Fig S3C missing WT/Scn8aSR/SR significance marking. Chosen example makes it look like there is a small decrease.

      Please note that there is no difference between these two conditions when in delta dV/dt for AIS inflection point (p = 0.4344).

      Reviewer #2 (Recommendations for the authors):

      This manuscript presents a clever and powerful approach to examining differential roles of Nav1.2 and Nav1.6 channels in excitability of pyramidal cell excitability, by engineering mice in which a sulfonamide inhibitor of both channels has reduced affinity for one or the other. Overall, the results in the manuscript are interesting and give important information about differential roles of Nav1.6 and Nav1.2 channels.

      The paper makes an important contribution to better understanding distinct roles of Nav1.2 and Nav1.6 channels. This improved understanding could help guide design of anti-seizure drugs targeted to sodium channels.

      Having made it clear that I think this is an important and impressive piece of work for which the authors should be congratulated, I found reading and interpreting the manuscript a frustrating experience. I will be blunt about the ways in which I found the presentation and discussion to be frustrating and even annoying, in the spirit of frank feedback by one interested and appreciative reader that the authors can consider or reject as they wish.

      From the start, I had the feeling that the authors were presenting and discussing the results in a sanitized "never-mind-about the details" fashion such as might be appropriate for a seminar to a general audience not interested in details, but not appropriate for a research paper.

      Our intent certainly was not to frustrate or annoy readers. We are very grateful that you have provided these comments, which have certainly improved the manuscript, hopefully mitigating some of the frustration for future readers. We appreciate that there are complex drug and voltage effects occurring within these studies, and in an effort to distill these effects into digestible prose, we appear to have been too earnest. We have expanded on the requested topics below and please note that, for the aficionados, every figure displays individual data. Further, we have made a special effort to ensure that features of excitability are presented throughout the drug and manipulation timecourse, including time-points before and after periods subject to statistical comparison, so that the reader may draw their own conclusions.

      General:

      There were two major ways in which I found the presentation and discussion frustrating and even annoying: First, not clearly discussing early in the presentation the fact that it is impossible to achieve complete inhibition with this agent during measurements of physiological firing and second, presenting so much of the effects as deltas of various parameters rather than showing effects on absolute values of the parameters.

      Our response to the first issue will follow the next comment, as it relates to this statement. Regarding use of deltas and absolute values for changes in threshold and dV/dt across figures. Every cell has a unique AP threshold and peak dV/dt, and we found that displaying data zeroed to baseline values best illustrated the effects of GNE-4076. Without this, GNE-based effect could be buried within the cell-to-cell variability. This helped most when trying to make the case that threshold was unaffected in 2a/8a YWàSR knockin animals. We continue to believe that this is the best way to display the data in the primary figures, but to provide a more complete account, we now present absolute values in supplemental tables and supplemental figures.

      The first issue, the incomplete inhibition by the agent, was the most annoying because the authors obviously thought a lot about this and even closed the paper by proposing this as a positive feature of this class of inhibitors, yet discussed it only piecemeal - and with most of the key experimental data in the Supplement. There are two fundamental characteristics of this (and other) sulfonamide inhibitors that complicate interpretation of experiments, especially when applied in a slice experiment: they only bind to the channel when the channel is depolarized, and even when the channel is depolarized for many seconds, bind very slowly to the channel.

      That makes it almost impossible to know exactly what fraction of channels is being inhibited during measurements of firing. Obviously, the authors are well-aware of this issue and they allude to it and even make use of it in some of the protocols, but they never really discuss it in a very clear manner.

      We agree that it is impossible to know the precise fraction of channels inhibited in acute slice preparations. But the reason for this is likely different than what has been interpreted by this reviewer. To state that ASMs “only bind to the channel when the channel is depolarized, and even when the channel is depolarized for many seconds, bind very slowly to the channel.” is not consistent with prior data on ASM–channel interactions. Clarification on these points may help the reviewer and a broader audience better understand the effects occurring here, and we appreciate being able to both address this concept here and by revising the manuscript.

      First, ASMs bind activated channels and stabilize the inactivated state. It is correct that channels are more likely to enter these states when subject to voltage depolarization, but channel state is stochastic and can enter activated states near resting membrane potentials. The on-rate is fast enough that channels are blocked immediately in recordings in heterologous systems (Figure 1C). It is more likely that channel biophysical state stochasticity, along with drug concentration used herein, are likely dictating the rate at which channels accumulate block during repetitive spiking.

      To address this in text, we have revised the 3rd paragraph of the introduction to better incorporate these ideas. This also helps with comments in the reviewer paragraph below.

      The key experimental data on this is relegated to the Supplemental Figures. When the reader is first shown results of the effects of the inhibitor on firing in Fig 2, the presentation has been set up as if everything is perfect, and the inhibitor will be completely inhibiting either both or only one channel according to the mouse. With this presentation, it is then exceptionally striking that the cell in the middle panel of Fig 2A, labeled "Nav1.2/1.6 Inhibited" is firing action potentials very nicely even with both channels "inhibited". For a reader not already aware that there is likely only partial inhibition of each channel, the reaction will be "Huh? Shouldn't blocking both channels simply completely block excitability?". The authors do preface Fig 2 by a very brief allusion to the incomplete inhibition: "In spiking neurons, ASCs would therefore be predicted to exhibit use-dependence, progressively blocking channels in proportion to a neuron's activity rate" but this comes out of nowhere after the over-simplified picture of complete inhibition up to that point, and without any estimation of how much inhibition there is likely to be before activity, or how much induction of inhibition there is likely to be during the activity. Without this, interpreting the data in Fig 2 is basically impossible.

      The key experimental data on this issue is really in Supplemental Figures 1-2 and Fig 4, and I found myself immediately ping-ponging back and forth between the Supplemental figures and the main text trying to understand what is going on with the partial inhibition. This was frustrating.

      Thank you for these suggestions; they help with readability appreciably. We have re-organized the figures presented in the manuscript and emphasized details about ASCs to ensure readers can discern between near-complete blockade of channels (Figures 1-4) and activity-dependent ASC onboarding (Figures 5-7). We now present near-complete block experiments first, detailing the current clamp-> voltage clamp (-12 mV)-> current clamp experiments. We incorporated Supp. Fig. 1 into main Figure 1 and moved Supp. Fig. 2 into main Fig. 2.

      As the reviewer notes, there are clear time-dependent effects on channel function when stepping to -12 mV, independent of GNE-4076 block. As stated previously, “We therefore focused on the 12-20 sec after voltage-clamp offset for subsequent analysis, as it is a period in which most channel-intrinsic recovery has occurred, but also a period in which we would still expect significant block from GNE-4076.” We hope that reordering the manuscript as suggested and placing these results near the beginning will help with discerning between near-complete block and activity depending onboarding. By beginning with these experiments, which underscore that 100% block cannot be studied without “contamination” from native slow inactivation, we hope that the readers can better understand why data was done as presented.

      In my opinion, the paper would be greatly improved by a detailed discussion of the voltage- and time-dependence of the inhibitor at the very beginning of the paper. For me, reading and digesting the paper would have been far easier if Fig 1 included a discussion of the voltage- and time-dependence of inhibition, and next Figs were then Supplemental Figs 1-2, and main Fig 4. The key questions are: how much inhibition is there before a 10-s current injection from the resting potential, and how much additional inhibition is there produced during either the 10-s bout of firing or the "on-boarding" depolarization protocol, and how long does that additional inhibition last? The most direct information on that is in the plots in Fig. 4D and Fig 4F in combination with Supplemental Fig 1, which shows that the on-boarding depolarization reduces current to about 30% of current before on-boarding. This is so central to the interpretation of all the results that I think Supp Fig 1 should be in the main paper as the first piece of data in neurons.

      We originally had the nucleated patch data in supplement due to space constraints in an already large figure 1. Based on your recommendation we have moved it to the main figure. We have also changed the ordering of the paper and related figures to present data as suggested. Hopefully this better guides readers through the questions you are raising above, which are addressed in the (now reordered) figures mentioned above.

      Specific:

      (1) Fig.1 I can find no information on the voltage protocol used to generate the dose-response curves. In the literature characterizing sulfonamide blockers, most protocols use very unphysiological strong, long depolarization to induce inhibition, usually with equally unphysiological short hyperpolarizations to produce recovery from inactivation. One assumes something like that was used here. Obviously, the protocol needs to be explained.

      We updated the methods section to better describe the voltage protocol used to generate the dose response curves. In contrast to the literature characterizing sulfonamide blockers, we used pulses that closely mimic physiological activation from -80 mV (rest) to 0 mV (depolarized) for 20 msec. GNE-4076 was perfused onto cells at increasing concentrations throughout the experiment. At each successive dose, cells were held at 0 mV to allow adequate GNE-4076 onboarding.

      (2) Supp Fig1. This shows the effect of depolarization to enhance inhibition, but not how much inhibition there was before the depolarization. Presumably, there were measurements during the application of drug? How much inhibition is there before the depolarization? Why does the time only go to 20-s, when the times in Figs 4 go to 10 minutes?

      Nucleated patch recordings are notoriously difficult to maintain for long durations, especially when subjecting the patch to large voltage deflections. These recordings extend to 20s recovery periods because that is the duration for which we maintained all recordings, though some exhibited rather impressive longevity and allowed for several minutes of recording thereafter. Regardless, the goal here was to assess block within the 12-20 sec recovery window we utilized in current clamp recordings from intact neurons. This was achieved.

      Please note that GNE-4076 was present throughout all recordings. This was in part due to time constraints, as we could not maintain patches long enough to also perform wash-in. The degree of inhibition can be inferred by comparing peak dV/dt and threshold of cells in the absence and presence of GNE-4076. These data are presented in a new Supplemental figure 1, showing no difference in threshold or peak dV/dt.

      (3) Fig. 4. Similar question here - this is a very nice and informative figure, but we see only the delta in threshold and dv/dt, but how were the initial absolute values different in the drug compared to control?

      These data are presented in a new Supplemental Figure 1, showing no difference in threshold or peak dV/dt.

      (4) Fig 2. As far as I can tell, we have no idea how much inhibition there is at rest, before the current injection -what is the dv/dt in the drug compared to in the control? Were there experiments in which the current injections were delivered before and after applying drug? If not, at least it would be useful to see population data on dv/dt of the first spike in control and with drug.

      These data are presented in a new Supplemental Figure 1, showing no difference in threshold or peak dV/dt.

      (5). Fig. 2. Do the authors have any quantitative information on how much extra inhibition would be produced at 200 nM drug using physiological waveforms of firing?

      These types of analyses are part of later figures using EPSC-like waveforms to evoke spiking.

      I was unconvinced that the changes in threshold and dv/dt during the firing in the drug necessarily represent time-dependent use-dependent effects of drug. Partial inhibition by TTX would probably produce greater progressive changes in spike shape and reduced ability to fire robustly.

      TTX is not use-dependent, so it is a good contrast to GNE-4076. We experimented with a few cells at 2 and 10 nM TTX concentrations and found that concentrations required to mimic the block of spiking that occurs with 200 nM GNE-4076 in WT cells was associated with a marked use-independent elevation in AP threshold, with an inability to maintain ~10 Hz spiking rates with the baseline EPSC-like stimulation pattern. These effects are very different from those produced by GNE-4076, but were expected given the use-independence of TTX. We did not pursue this line of inquiry fully, so we present these data only as individual examples in the reviewer figure below:

      Author response image 1.

      Data from Figure 6B, D, E are replicated here with individual lines of 2 nM and 10 nM TTX shown in dashed lines. Note marked changes in threshold not observed with GNE-4076. TTX sourced from Alomone Labs.

      Minor:

      p. 5 and elsewhere: it seems unnecessary to give values of threshold and dv/dt to three decimal places, especially when the precision is not better than a single decimal place.

      We have reduced unnecessary precision throughout.

      Reviewer #3 (Recommendations for the authors):

      The computational model is highly underdeveloped. Without more rigorous development the results of the computational model appear to provides little additional insight beyond that expected from the known axodendritic localizations of NaV 1.2 and 1.6. If the authors wish to use the computational results to make rigorous predictions, then this section needs to be either be expanded to be more complete and promoted to a regular figure, with full details of the model, and how it was evaluated for accuracy. Alternatively, this point regarding computational insight could be de-emphasized and or removed from the paper.

      Modeling:

      (1) I don't see any methods describing the precise model parameters that were used.

      Apologies, this is a model that we have built and tested extensively over the years (PMID: 38290518, 35417922, 34348157, 31995133, 31230762, 28256214), though there have been some small updates over these works. We have deposited this model at ModelDB and provide data there regarding model construction (access #2019342).

      (2) There appears to be no robustness test to assess whether the particular results/conclusions were unduly dependent on particular model construction decisions.

      We have now generated a new supplemental figure 2 that explores the robustness of these observations to changes in NaV1.2 and NaV1.6 position within the AIS and changes in relative density of NaV1.2 and NaV1.6. As shown there, the model is tolerant to all but extreme, non-physiological manipulations to these parameters.

      (3) Figure S2 does not really provide convincing evidence of a biologically relevant model. Probably the model itself needs to be redesigned to better replicate the biological response and be validated by testing parameter sensitivity.

      a) All of the results in S2C show that there is a huge reduction in the first action potential (black?) followed by relatively little change in subsequent spikes. This is not seen in any of the models. The progressive changes in threshold as predicted by the model for dual and NaV1.6 block are not at all evident in the results of C, except perhaps for the the very first and the very last spikes.

      b) The baseline action potential in B is different than the recorded action potentials. In particular, the somatic depolarization occurs much later and over a more extended time frame than the real neuron, and the phase plot shows an actual dip in depolarization at the transition to the somatic spike, which is not representative of naturally occurring action potentials.

      To address both (a) and (b), please note that in empirical experiments there are two parallel processes occurring: block by GNE-4076 and channel recovery from inactivation. In the model we can isolate the effects of block to test that parameter fully and in isolation. This is something that we could never achieve biologically. The important take home here in both cases is to observe that with NaV1.6 block there is a change in threshold, whereas with NaV1.2 block there is none.

      (4) The one finding that seems to be robust is that the changes in NaV1.2 have little effect on threshold.

      Yes! This is a major take-home message from both the model and the use of these knockin mice in combination with GNE-4076. In mature pyramidal cells, NaV1.6 is the major determinant of AP threshold. And to editorialize on this observation, changes in threshold are a useful metric to test if other pharmacology are truly selective for NaV1.2 over NaV1.6. We note that phrixotoxin-3, which is described as NaV1.2 specific in multiple papers, was never tested for specificity over NaV1.6 in its original description, and we find that it fails this test in our hands.

      Data presentation:

      (1) The phase plots in Figure 3B (left and right) appear to be visually identical, and as such don't strongly support any particular conclusion.

      We changed the representative example record (specifically for Fig. 3A-B) to more directly support the conclusions.

      (2) It is unclear to me what is meant by AP speed (title of Figure 3 legend). Do the authors mean propagation speed along the axon, or perhaps the rate of action potential firing?

      Apologies, we are referencing dV/dt when we mention AP speed. We updated AP speed to AP velocity throughout the manuscript.

    1. Author response:

      Reviewer 1:

      The selection of heavy metal stress as the condition to investigate is not speculative. The elucidation of the genome from the Palomero toluqueño maize landrace revealed heavy metal effects during domestication (Vielle-Calzada et al., 2009). Differences concordant with its ancient origin identified chromosomal regions of low nucleotide variability that contained the three domestication loci included in this study; all three are involved in heavy-metal detoxification. Results presented in Vielle-Calzada et al 2009 indicated that environmental changes related to heavy metal stress were important selective forces acting on maize domestication. Our study expands those results by starting to elucidate the function of these heavy metal response genes and their role in the evolutionary transition from teosinte parviglumis to maize.

      Although the paper presents some interesting findings, it is difficult to distinguish which observations are novel versus already known in the literature regarding maize HM stress responses. The rationale behind focusing on specific loci is often lacking. For example, a statistically significant region identified via LOD score on chromosome 5 contains over 50 genes, yet the authors focus on three known HM-related genes without discussing others in the region. It is unclear why ZmHMA1 was selected for mutagenesis over ZmHMA7 or ZmSKUs5.

      We appreciate the value of this comment. We will modify the manuscript to clearly show which phenotypic observations are novel and which were previously reported for maize grown under HM stress. The rationale for focusing on three specific loci is related to results from Vielle-Calzada et al. 2009 (see comment above). Although we demonstrated that these three loci show unusual reduction in genetic variability when compared to the rest of chromosome 5 – including a separate class of genes previously identified as being affected by domestication (Hufford et al., 2012) -, we will expand the genetic and expression analysis to all genes included in a region precisely defined via LOD scores of five QTL 1.5-LOD support intervals that overlap with ZmHMA1.Within this region of 1.5 to 2 Mb, we will compare nucleotide variability and gene expression in response to HMs. Contrary to major domestication loci showing a single highly pleiotropic gene responsible for important domestication traits, in this chr.5 genomic region phenotypic effects are due to multiple linked QTLs (Lemmon and Doebley, 2014). The mutagenic analysis of ZmHMA7 and ZmSKUs5 will be included in a different publication; we can anticipate that the results reinforce the conclusions of this study.

      The idea that HM stress impacted gene function and influenced human selection during domestication is of interest. However, the data presented do not convincingly link environmental factors with human-driven selection or the paleoenvironmental context of the transition. While lower nucleotide diversity values in maize could suggest selective pressure, it is not sufficient to infer human selection and could be due to other evolutionary processes. It is also unclear whether the statistical analysis was robust enough to rule out bias from a narrow locus selection. Furthermore, the addition of paleoclimate records (Paleoenvironmental Data Sources as a starting point) or conducting ecological niche modeling or crop growth models incorporating climate and soil scenarios would strengthen the arguments.

      We agree that lower nucleotide diversity values in maize are not sufficient to infer human selection and could be due to other evolutionary processes. As a matter of fact, since these same HM response loci also show unusually low nucleotide variability in teosinte parviglumis (Fig 2), we cannot discard the possibility that natural selection forces related to environmental changes could have affected native teosinte parviglumis populations in the early Holocene, before maize emergence. This possibility supports a speculative model suggesting that phenotypic changes caused by HM stress could have preceded human selection and its consequences, contributing to initial subspeciation; the model is proposed in the “Ideas and Speculation” section of the manuscript. Fortunately, as suggested by the reviewer, a large body of paleoclimatic records and paleoenvironmental data is available for the Trans-Mexican Volcanic Belt  in the Holocene, including geographic regions where the emergence of maize presumably occurred. We will include an extensive analysis of available paleoenvironmental data and discuss it at the light of our current results regarding the effects of HM stress. We are also expanding the physical range of our statistical analysis to cover at least 60 Kb per locus - including neighboring genes for all three loci - to determine if our results could be due to narrow locus selection.

      Despite the interest in examining HM stress in maize and the presence of a pleiotropic phenotype, the assessment of the impact of gene expression is limited. The authors rely on qPCR for two ZmHMA genes and the locus tb1, known to be associated with maize architecture. A transcriptomic analysis would be necessary to 1- strengthen the proposed connection and 2- identify other genes with linked QTLs, such as those in the short arm of chromosome 5.

      Although real-time qPCR is an accurate and reliable approach to assess the expression of specific genes such as ZMHMA1 and Tb1, we will explore the possibility of complementing our analysis with available RNA-seq results that are pertinent for this study (see for example Li et al., 2022 and Zhang et al., 2024) and further explore causative effects between HM stress, Tb1 and ZmHMA1 expression. As also pointed by Reviewer#1, TEs are known to influence gene expression under abiotic stress and RNA-Seq analysis would allow to determine if TE activity could lead to similar outcomes.

      Reviewer #2:

      The authors explored Cu/Cd stress but not a more comprehensive panel of heavy metals, making the implications of this study quite narrow. Some techniques used, such as end-point RT-PCR and qPCR, are substandard for the field. The phenotypic changes explored are not clearly connected with the potential genetic mechanisms associated with them, with the exception of nodal roots. If teosintes in response to heavy metal have phenotypic similarity with modern landraces of maize, then heavy metal stress might have been a confounding factor in the selection of maize and not a potential driving factor. Similar to the positive selection of ZmHMA1 and its phenotypic traits. In that sense, there is no clear hypothesis of what the authors are looking for in this study, and it is hard to make conclusions based on the provided results to understand its importance. The authors do not provide any clear data on the potential influence of heavy metals in the field during the domestication of maize. The potential role of Tb-1 is not very clear either.

      Thank you for these comments. We will clearly emphasize our hypothesis that HM stress was an important factor driving the emergence of maize from teosinte parvglumis through action of HM response genes. A comprehensive panel of heavy metals would not be more accurate in terms of simulating the composition of volcanic soils evolving across 9,000 years in the region where maize presumably emerged. Copper (Cu) and cadmium (Cu) correspond each to a different affinity group for proteins of the ZmHMA family. ZmHMA1 has preferential affinity for Cu and Ag (silver), whereas ZmHMA7 has preferential affinity to Cd, Zn (zinc), Co (cobalt), and Pb (lead). Since these P1b-ATPase transporters mediate the movement of divalent cations, their function remains consistent regardless of the specific metal tested, provided it belongs to the respective affinity group. By applying sublethal concentrations of Cd (16 mg/kg) and Cu (400 mg/kg), we caused a measurable physiological response while allowing plants to complete their life cycle, including the reproductive phase, facilitating a comprehensive analysis of metal stress adaptation.

      Although real-time qPCR is an accurate and reliable approach to assess gene expression, we agree that RNA-Seq results would improve the scope of the analysis and better assess the role of Tb1 in relation to HM response (see comments for Reviewer#1). There are two phenotypic changes clearly connected with the genetic mechanisms involved in the parviglumis to maize transition: plant height and the number of seminal roots (not nodal roots). We will emphasize these phenotypic changes in a modified version of the manuscript. There is a possibility for HM stress to represent a confounding factor in the selection of maize and not a driving factor; however, if such is the case, we think it is rather unlikely that the real driving factor could have acted through mechanisms not related to abiotic stress or HM response. To address the possibility that HM stress was a cofounding factor, we will extensively analyze genetic diversity and gene expression in all loci containing genes mapping in close proximity to peak LOD scores of all 1.5-LOD support intervals located in chromosome 5 and showing pleiotropic effects on domestication traits (Lemmon and Doebley, 2014). These will also include those mapping in close proximity to ZmHMA1. The potential influence of heavy metals in the field is being investigated through the analysis of paleoenvironmental data (see response to Reviewer#1); we will include our results in a modified version of the manuscript.

      We thank both reviewers for their detailed revision the manuscript and their pertinent recommendations to improve its presentation and reading.

      References:

      Hufford, Matthew B., Xun Xu, Joost Van Heerwaarden, Tanja Pyhäjärvi, Jer-Ming Chia, Reed A. Cartwright, Robert J. Elshire, et al. 2012. Comparative population genomics of maize domestication and improvement. Nature Genetics 44(7): 808-11.

      Lemmon Zachary H., Doebley John F. 2014. Genetic dissection of a genomic region with pleiotropic effects on domestication traits in maize reveals multiple linked QTL. Genetics 198(1): 345-353.

      Lin Kaina, Zeng Meng, Williams Darron V., Hu Weimin, Shabala Sergey, Zhou Meixue, Cao Fangbin, et al. 2022. Integration of transcriptome and metabolome analyses reveals the mechanictic basis for cadmium accumulation in maize. iScience 25(12): 105484.

      Vielle-Calzada JP, De La Vega OM, Hernández-Guzmán G, Ibarra-LacLette E, Alvarez-Mejía C, Vega-Arreguín JC, Jiménez-Moraila B, Fernández-Cortés A, Corona-Armenta G, Herrera-Estrella L, Herrera-Estrella A. 2009. The Palomero genome suggests metal effects on domestication. Science 326: 1078.

      Zhang Mengyan, Zhao Lin, Yun Zhenyu, Wu Xi, Wu Qi, et al. 2024. Comparative transcriptome analysis of maize (Zea mays L.) seedlings in response to copper stress. Open Life Sciences 19(1): 20220953.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      The authors build on their previous study that showed the midgut microbiome does not oscillate in Drosophila. Here, they focus on metabolites and find that these rhythms are in fact microbiome-dependent. Tests of time-restricted feeding, a clock gene mutant, and diet reveal additional regulatory roles for factors that dictate the timing and rhythmicity of metabolites. The study is well-written and straightforward, adding to a growing body of literature that shows the time of food consumption affects microbial metabolism which in turn could affect the host.

      We thank the reviewer for the positive comments.

      Some additional questions and considerations remain:

      (1) The main finding that the microbiome promotes metabolite rhythms is very interesting. Which microbiota are likely to be responsible for these effects? The author's previous work in this area may shed light on this question. Are specific microbiota linked to some of the metabolic pathways investigated in Figure 5?

      This is a good question. Although the Drosophila microbiome shows limited diversity, comprised largely of two major families (Acetobacteraceae and Lactobacillaceae), effects on the host could arise from just a subset of species within these families. However, identifying these would require inoculating microbiome-free flies with single and mixed combinations of species and conducting metabolomics to examine cycling of each of the three categories of metabolites we studied-- primary, lipids and biogenic amines (each of these may respond differently to different species). We believe this is beyond the scope of this manuscript, which is focused on how cycles in these different types of metabolites change in the context of the microbiome, the circadian clock and different diets.

      (2) TF increases the number of rhythmic metabolites in both microbiome-containing and abiotic flies in Figure 1. This is somewhat surprising given that flies typically eat during the daytime rather than at night, very similar to TF conditions. I would have assumed that in a clock-functioning animal, the effect of restricting food availability should not make a huge difference in the time of food consumption, and thus downstream impacts on metabolism and microbiome. Can the authors measure food intake directly to compare the ad-lib vs TF flies to see if there are changes in food intake? Would restricting feeding to other times of day shift the timing of metabolites accordingly?

      Previous studies have indicated that there is no significant difference in food consumption between ad-lib and TF flies (Gill et al., 2015; Villaneuva et al 2019). We also found that the presence of a microbiome does not alter total food consumption when compared with germ-free flies (Zhang et al, 2023, and current manuscript). Though flies primarily feed during the day, some food consumption occurs at night (i.e the feeding rhythm is not tight) and so restricting food to the daytime can increase metabolite cycling. Restricting feeding to other times of day is expected to shift metabolite cycling. We previously showed that this shifts transcript cycling (Xu et al, Cell Metabolism 2011)

      (3) In Figure 2, Per loss of function reveals a change in the phase of rhythmic metabolites. In addition, the effect of the microbiome on these is very different = The per mutants show increased numbers of rhythmic metabolites when the microbiome is absent, unlike the controls. Is it possible that these changes are due to altered daily feeding rhythms in per mutants? Testing the time and amount of food consumed by the per mutant flies would address this question. Would TF in the per mutants rescue their metabolite rhythms and make them resemble clock-functioning controls?

      We previously showed that per<sup>01</sup> flies lose feeding rhythms in DD and LD conditions, but consume a lot more food (Barber et al, 2021). Given that locomotor rhythms are maintained in per<sup>01</sup> in LD (Konopka and Benzer 1971), these rhythms or other rhythms driven by LD cues likely account for the maintenance of metabolite rhythms. And the increased food consumption may contribute to the changes observed. To address the reviewer’s question about the microbiome, we assayed feeding rhythms in per<sup>01</sup> in the absence/presence of a microbiome on the diets that haven’t been tested before (high sugar and high protein diet). Surprisingly, feeding was rhythmic on a high protein diet, regardless of whether a microbiome was present (new Figure S10). On a high sugar diet, feeding appears to be somewhat rhythmic in the presence of a microbiome (although not significant) and not when the microbiome is absent. The same is true in iso31 controls, and in all cases, the phase is the same. Despite the similar effect of the microbiome on feeding rhythms in wild type and per<sup>01</sup>, the effect on cycling is very different. Thus, feeding rhythms do not appear to explain the effects of the microbiome on metabolite cycling in per<sup>01</sup>.

      (4) The calorie content of each diet-normal vs high protein vs high-sugar are different. The possibility of a calorie effect rather than a difference in nutrition (protein/carbohydrate) should be discussed. Another issue worth considering is the effect of high protein/sugar on the microbiome itself. While the microbiome doesn't seem to affect rhythms in the high-protein diet, the high-sugar diet seems highly microbiome-dependent in Supplementary Fig 8C vs D. Does the diet impact the microbiome and thus metabolite rhythmicity downstream?

      Thank you for these good suggestions. We have added to the discussion the possibility that caloric content, rather than nutrition (protein/carbohydrate), affects metabolite cycling in flies fed normal vs. high-protein vs. high-sugar diets. We have also discussed the possibility that effects of different diets on metabolite cycling are mediated by changes in the microbiome. We cite papers that show effects of diet on microbiomes.

      (5) It would be good if a supplementary table was provided outlining the specific metabolites that are shown in the radial plots. It is not clear if the rhythms shown in the figures refer to the same metabolites peaking at the same time, or rather the overall abundance of completely different metabolites. This information would be useful for future research in this area.

      We have added a supplementary Table 1-21 which includes all the raw metabolites.

      Reviewer #2 (Public Review):

      Summary:

      The paper addresses several factors that influence daily changes in concentration of metabolites in the Drosophila melanogaster gut. The authors describe metabolomes extracted from fly guts at four time-points during a 24-hour period, comparing profiles of primary metabolites, lipids, and biogenic amines. The study elucidates that the percentage of metabolites that exhibit a circadian cycle, peak phases of their increased appearance, and the cycling amplitude depends on the combination of factors (microbiome status, composition or timing of the diet, circadian clock genotype). Multiple general conclusions based on the data obtained with modern metabolomics techniques are provided in each part of the article. Descriptive analysis of the data supports the finding that microbiome increases the number of metabolites for which concentration oscillates during the day period. Results of the experiments show that timed feeding significantly enhanced metabolite cycling and changed its phase regardless of the presence of a microbiome. The authors suggest that the host circadian rhythm modifies both metabolite cycling period and the number of such metabolites.

      Strengths:

      The obvious strength of the study is the data on circadian cycling of the detected 843, 4510, and 4330 total primary metabolites, lipids, and biogenic amines respectively in iso31 flies and 623, 2245, and 2791 respective metabolites in per<sup>01</sup> mutants. The comparison of the abundance of these metabolites, their cycling phase, and the ratio of cycling/non-cycling metabolites is well described and illustrated. The conditions tested represent significant experimental interest for contemporary chronobiology: with/without microbiota, wild-type/mutant period gene, ad libitum/time-restricted feeding, and high-sugar/high-protein diet. The authors conclude that the complex interaction between these factors exists, and some metabolic implications of combinations of these factors can be perceived as reminiscent of metabolic implications of another combination ("...the microbiome and time-restricted feeding paradigms can compensate for each other, suggesting that different strategies can be leveraged to serve organismal health"). Enrichment analysis of cycling metabolites leads to an interesting suggestion that oscillation of metabolites related to amino acids is promoted by the absence of microbiota, alteration of circadian clock, and time-restricted feeding. In contrast, association with microbiota induces oscillation of alpha-linolenic acid-related metabolites. These results provide the initial step for hypothesising about functional explanations of the uncovered observations.

      We thank the reviewer for summarizing the contributions made by this manuscript.

      Weaknesses:

      Among the weaknesses of the study, one might point out too generalist interpretations of the results, which propose hypothetical conclusions without their mechanistic proof. The quantitative indices analysed are obviously of particular interest, however are not self-explaining and exhaustive. More specific biological examples would add valuable insights into the results of this study, making conclusions clearer. More specific comments on the weaknesses are listed below:

      (1) The criterion of the percentage of cycling metabolites used for comparisons has its own limitations. It is not clear, whether the cycling metabolites are the same in the guts with/without microbiota, or whether there are totally different groups of metabolites that cycle in each condition. GO enrichment analysis gives only a partial assessment, but is still not quantitative enough.

      Microbiome-containing flies and germ-free flies do share some cycling metabolites. Figure 6 provides GO analysis for the pathways enriched in each condition, and Figure S6 shows quantitative data on the number that overlap between different conditions. We have also expanded discussion of specific cycling groups (e.g. amino acid metabolism) to indicate that different metabolites of the same pathway may cycle under different conditions. In addition, we have added detailed information for all cycling metabolites in Supplemental Tables 1-21.

      (2) The period of cycling data is based on only 4 time points during 24 hours in 4 replicates (>200 guts per replicate) on the fifth day of the experiment (10-12-day-old adults). It does not convincingly prove that these metabolites cycle the following days or more finely within the day. Moreover, it is not clear how peaks in polar histogram plots were detected in between the timepoints of ZT0, ZT6, ZT12, and ZT18.

      We acknowledge these limitations, but note that these experiments are very challenging because of the amount of tissue/guts needed for each data point and the time it takes to dissect each gut. Thus, getting more closely spaced time points is difficult. And we believe the detection of daily peaks with four biological replicates provides good evidence for cycling. The peaks in polar histogram plots are based on the parameter of JTK_adjphase when conducting JTK cycle analysis; as the data are averaged across replicates, the average can sometimes fall in between two assayed time points. Details can be found in the attached Supplementary Tables.

      (3) Average expression and amplitude are analysed for groups of many metabolites, whereas the data on distinct metabolites is hidden behind these general comparisons. This kind of loss of information can be misleading, making interpretation of the mentioned parameters quite complicated for authors and their readers. Probably more particular datasets can be extracted to be discussed more thoroughly, rather than those general descriptions.

      We analyzed groups of metabolites, dividing them into primary metabolites, lipids and biogenic amines, to extract general take-home messages and also to simplify the presentation. Figure 6 demonstrates specific pathways whose cycling is affected in each condition assayed. And Figure S11 shows examples of cycling metabolites under different conditions. To highlight a dataset that is altered under different conditions, we expanded our discussion of amino acid metabolism, and show how the specific metabolites that cycle in this pathway may vary from one condition to another (Figure S11). For more quantitative data on individual metabolites, we now provide supplementary tables that display all the cycling metabolites. These include those uniquely cycling in one group, those shared between both two groups, and those uniquely cycling in the other group.

      (4) The metabolites' preservation is crucial for this type of analysis, and both proper sampling plus normalisation require more attention. More details about measures taken to avoid different degradation rates, different sizes of intestines, and different amounts of microbes inside them will be beneficial for data interpretation.

      We were careful to control for gut size and to preserve the samples so as to minimize degradation (We placed all the fly samples on ice during collection, and the entire dissection process was also conducted on ice. Once the gut sample collection was completed, we immediately transferred the samples to dry ice for storage. After we finished collecting all the samples, we stored them at -80°C). In general, gut sizes varied in the following order: females fed high-protein diets >females fed normal chow diets> female flies fed high-sugar diets. As the metabolomic facility suggested 10mg samples for each biological repeat, we dissected at least 180 female guts from flies fed high-protein diets, 200 female guts from flies fed normal chow diets, and at least 250 female guts from flies fed high-sugar diets. Also, as gut sizes were smaller in sterile flies, relative to microbiome-containing flies, on a high protein diet, we collected 200 guts from sterile flies under these conditions. Finally, the service that conducted the metabolomics (UC Davis) provided three detailed files to describe the extraction process for primary metabolites, lipids, and biogenic amines, respectively. We have submitted these files as supplemental materials in the revised manuscript.

      (5) The data in the article describes formal phenomena, not directly connected with organism physiology. The parameters discussed obviously depend on the behavior of flies. Food consumption, sleep, and locomotor activity could be additionally taken into account.

      These are very interesting suggestions. Previous results indicated that microbiome-containing flies do not change their total food consumption or exhibit changes in feeding rhythms when compared with germ-free flies (Zhang et al., 2023), which indicates that microbiome-mediated metabolite cycling is independent of feeding rhythms. As noted above, we examined the contribution of feeding to metabolite cycling in per<sup>01</sup> flies, and did not see an obvious link. We also assayed feeding rhythms and overall food consumption in wild type under AS and AM conditions and on different diets, and likewise could not account for changes in metabolite cycling based on altered food intake (new Figure S10). We acknowledge that behavior, including locomotor activity and sleep, could indeed influence metabolite cycling. We have added discussion of this.

      (6) Division of metabolites into three classes limits functional discussion of found differences. Since the enrichment analysis provided insights into groups of metabolites of particular interest (for example, amino acid metabolism), a comparison of their cycling characteristics can be shown separately and discussed.

      The intent of this work was to provide an overall account of changes in metabolite cycling that occur under different conditions/diets/genotypes. We have expanded the discussion of amino acid metabolism and show how different metabolites of this pathway cycle under different conditions (Figure S11). We believe that discussion/analysis of other specific groups would be good follow-up studies, which can build upon this work. Detailed datasets about all cycling metabolites are provided in Table S1-12.

      Reviewer #3 (Public Review):

      Summary:

      The authors. sought to quantify the influence of the gut microbiome on metabolite cycling in a Drosophila model with extensive metabolomic profiling over a 24-hour period. The major strength of the work is the production of a large dataset of metabolites that can be the basis for hypothesis generation for more specific experiments. There are several weaknesses that make the conclusions difficult to evaluate. Additional experiments to quantify food intake over time will be required to determine the direct role of the microbiome in metabolite cycling.

      Strengths:

      An extensive metabolomic dataset was collected with treatments designed to determine the influence of the gut microbiome on metabolite circadian cycling.

      Weaknesses:

      (1) The major strength of this study is the extensive metabolomic data, but as far as I can tell, the raw data is not made publicly available to the community. The presentation of highly processed data in the figures further underscores the need to provide the raw data (see comment 3).

      The raw data have been submitted to the public metabolite database. https://www.ebi.ac.uk/metabolights/. (ID: MTBLS8819)

      In addition, the normalized metabolite data have been added in the supplemental materials.

      (2) Feeding times heavily influence the metabolome. The authors use timed feeding to constrain when flies can eat, but there is no measurement of how much they ate and when. That needs to be addressed.

      Since food is the major source of metabolites, the timing of feeding needs to be measured for each of the treatment groups. In the previous paper (Zhang et al 2023 PNAS), the feeding activity of groups of 4 male flies was measured for the wildtype flies. That is not sufficient to determine to what extent feeding controls the metabolic profile of the flies. Additionally, timed feeding opportunities do not equate to the precise time of feeding. They may also result in dietary restriction, leading to the loss of stress resistance in the TF flies. The authors need to measure food consumption over time in the exact conditions under which transcriptomic and metabolomic cycling are measured. I suggest using the EX-Q assay as it is much less effort than the CAFE assay and can be more easily adapted to the rearing conditions of the experiments.

      As noted above, we have now added considerable additional data on feeding and feeding rhythms in microbiome-containing and sterile wild type and per<sup>01</sup> flies on different diets (Figure S10). Our previous study, using the EX-Q assay method, found no differences in either total food consumption or feeding rhythms between microbiome-containing flies and germ-free flies (Zhang et al., 2023). Also, previous work has demonstrated that there is no significant difference in food consumption between ad-lib and TF flies (Villaneuva et al 2019).

      (3) The data on the cycling of metabolites is presented in a heavily analyzed form, making it difficult to evaluate the validity of the findings, particularly when a lack of cycling is detected. The normalization to calculate the change in cycling due to particular treatments is particularly unclear and makes me question whether it is affecting the conclusions. More presentation of the raw data to show when cycling is occurring versus not would help address this concern, as would a more thorough explanation of how the normalization is calculated - the brief description in the methods is not sufficient.

      For instance, the authors state that "timed feeding had less effect on flies containing a microbiome relative to germ-free flies." One alternative interpretation of that result is that both treatments are cycling but that the normalization of one treatment to the other removes the apparent effect. This concern should be straightforward to address by showing the raw data for individual metabolites rather than the group.

      We have added Supplement Table1-21 that includes detailed information on metabolite identity and data processing. Also, we have included the raw data, encompassing all the cycling metabolites, in the Supplement Table1-21.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) The abstract could be rewritten to clarify. I found the last part of the introduction better but struggled to understand the abstract.

      We apologize for this. The abstract was indeed quite dense; we have revised it for clarity.

      (2) Supplementary Figure 8 could be moved to the main text. Since all the comparisons are on one page it is much easier to see the similarities and differences in the conditions tested.

      We have moved Supplementary Figure 8 to main Figure 5.

      (3) The sex and age of the flies used in all experiments should be clarified. The authors mention female guts are collected in the methods (line 111) but it is not clear if this is throughout.

      All guts used in this study were female. We have clarified this in the manuscript.

      Reviewer #2 (Recommendations For The Authors):

      Some minor notes that might be improved:

      (1) The order of obtaining eggs without microbiota might be different (first - bleaching, second - sterilisation with ethanol). Otherwise, it is not clear why dechorionating is needed after sterilisation.

      Protocols for generating axenic flies vary. We used the method Feltzin et al reported in 2019: “For newborn fly embryos (<12 hours). First, cleanse and sterilize any leftover agar from collection plates using 100% ethanol, second, dechorionate the fly embryos with 10% bleach, and then immediately rinse three times in germ-free PBS”.

      (2) References for the resources used might be provided (MetaboAnalyst5.0, JTK_CYCLEv3.1).

      We have added the reference for MetaboAnalyst5.0, JTK_CYCLEv3.1 (Pang et al., 2022)

      (3) References or justification for the chosen composition of the diets might be useful (standard diet, high-protein diet, high-sugar diet).

      We have added the references (Bedont et al, 2021, Morris et al, 2021).

      (4) Justification of the choice of iso31 line and per<sup>01</sup> mutant might be important.

      iso31 is the standard wild type line we use in the laboratory. To understand the role of the endogenous clock in microbiome-mediated metabolite cycling, we chose the classical canonical clock mutant per<sup>01</sup> as this displays fewer non-circadian phenotypes seen. For instance, loss of transcriptional activators of the clock produces additional effects (e.g. hyperactivity), likely because of the effect it has on overall expression of many genes. We have added this explanation to the manuscript.  

      (5) Abbreviation decoding might be introduced when it is used for the first time in the text (line 240 - TM, TS).

      We apologize for this omission and have rectified it. Thanks

      TM (timed feeding microbiome-containing flies)

      TS (timed feeding germ-free flies)

      (6) The term "germ-free" is recommended to be avoided in the context of the paper (germ-free = infertile for animals). It might be replaced with the terms "without microbiota" or "germ-free" for example.

      Given that the reviewer recommends use of the word “germ-free” in the second sentence, we assume that the first sentence was intended to say we should avoid “sterile” (and not “germ-free”). We have edited to “germ-free” in the manuscript.

      (7) When only one diet is assumed, it might be better to say so (line 324 - "the protein diet" instead of "protein diets").

      Sorry, we have edited accordingly.

      (8) Too many speculative conclusions are confusing (line 476 - what does it mean for "just as” - how exactly similar; line 477 - what kind of "compensation"; line 503 - how exactly it is related to "metabolic homeostasis" and to which kind of homeostasis).

      “just as” was not intended to refer to any degree of similarity but only to the fact that amino acid cycling occurs in the absence of a clock, as it does in the absence of a microbiome. We speculate that this “compensates” for something that is normally conferred by the clock and the microbiome, for instance maybe the clock drives cycling of a microbiome component that is important for protein metabolism. In the absence of either the clock or the microbiome, this is compensated for by amino acid cycling. We have clarified in the text.

      We used the term "metabolic homeostasis" to reflect steady maintenance of metabolic health via interaction and modulation of different factors. As in the case of the example given above for amino acid metabolism, a perturbation of one process might produce a change in another to optimize metabolism. We have changed the wording in the text to better convey our message (lines 576-579)

      (9) Particular examples of metabolites might be beneficial for supporting conclusions (a figure which shows, for instance, the specific data on linolenic acid: in which conditions it cycles, in which not, what is the period of cycling, what are the exact expression and JTK_amplitude values).

      All cycling metabolites, including linolenic acid, are now included in the supplemental tables.

      Reviewer #3 (Recommendations For The Authors):

      (1) The level of biological replication is unclear for the metabolomic experiments. I see that 200 guts per sample were collected and 4 repeat samples were made at each timepoint. Are these 4 biological replicates for each treatment (AS, AM, TS, TM) at each timepoint? 5 replicates are standard in metabolomics. Please be more explicit in the methods.

      There are 4 biological replicates for each time point of each of the 4 treatments. The metabolomics service recommended 4-6 replicates, so we prepared 4 replicates for each sample. As noted above, these preparations are quite difficult. We found that in general the biological replicates do not differ significantly from each other.

      (2) Wolbachia can have a significant influence on fly physiology. How was this variable addressed? Were flies checked for Wolbachia?

      All the flies are Wolbachia-free, as in our previous study (Zhang et al., 2023). Initially, we treated the flies with 1 mM kanamycin (11815024, ThermoFisher) to remove bacteria. Afterwards, we repopulated the flies with a Wolbachia-free microbiome containing Lactobacillus and Acetobacter bacteria from a medium previously occupied by other flies.

      (3) In Results section 1, the authors report changes in the percentages of metabolites that are cycling, but no statistical test is presented to show that these changes are indeed significant. The authors need to report statistics on the percentages of cycling metabolites.

      We used statistical tests, specifically JTK cycle, to determine cycling of each metabolite. The P value for cycling of each metabolite in this test is computed on the basis of all the biological replicates and all time points. Metabolites that showed a significant P value contribute to the percent cycling. As a result, there is only one value for the percentage cycling in each condition. Thus, statistical analysis cannot be done.

      (4) The authors report that the species proportions in the gut microbiome don't cycle, but do absolute CFU counts? By many accounts (see e.g. Blum et al 2013 mBio), the gut microbiome in lab flies is what they recently ate from the food. The abundance of bacteria in the gut would then be directly tied to the timing of feeding. Timed feeding should produce oscillations in individual flies, so individual flies should be analyzed.

      We assume the reviewer is suggesting that rhythmic feeding could result in rhythmic abundance of the microbiome, which could contribute to cycling. This is indeed a possibility and one we now discuss in the manuscript. Thanks! Analysis of the gut microbiome in individual flies would require quantitation of CFUs from single guts. We do not believe a single gut would yield enough material.

      (5) Line 252: the ZT9 peak could just be due to feeding and digestion.

      This is possible. We now acknowledge this

      (6) What is the expectation for metabolite cycling in per mutant flies? Shouldn't per mutant flies have no cycling on average? Does the cycling suggest there is an external factor causing cycling?

      Under light-dark conditions, metabolite cycling in per mutant flies may be driven by light: dark cues, either directly or through other light-driven rhythms e,g. locomotor activity is rhythmic in per<sup>01</sup> flies maintained in LD.

      (7) Performing food intake analysis on each of the treatments would provide critical data to address the direct role of the microbiome in metabolite cycling.

      As noted above, we now provide considerable additional data on food intake at different times of day in microbiome-containing and germ-free wild type and per<sup>01</sup> flies on different diets (Figure S11). Overall, our data indicate that food intake or feeding rhythms do not account for the effects we report here.

      (8) Please be more explicit about replication in the methods and figure legends.

      We have added n=4 for each condition in the methods and figure legends.

      (9) There are numerous minor grammatical errors such as incorrect verb tenses and usage of articles. Additional proofreading could correct these.

      Sorry! We have done a thorough proofreading and made corrections.

    1. Author response:

      Reviewer #1 (Public Review):

      Insects, such as bees, are surprisingly good at recognizing visual patterns. How they achieve this challenging task with limited computational resources is not fully understood. Based on the actual bee's behaviour and visual circuit structure, MaBouDi et al. constructed a biologically plausible model where the circuit extracts essential visual features from scanned natural scenes. The model successfully discriminated a variety set of visual patterns as the actual bee does. By implementing a type of Hebb's rule for non-associative learning, an early layer of the model extracted orientational information from natural scenes essential to pattern recognition. Throughout the paper, the authors provided intuitive logic for how the relatively simple circuit could achieve pattern recognition. This work could draw broad attention not only in visual neuroscience but also in computer vision.

      We appreciate your positive feedback.

      However, there are a number of weaknesses in the manuscript. 1) The authors claim that the model is inspired by micromorphology, yet it does not rigorously follow the detailed anatomy of the insect brain revealed as of now. 2) Some claims sound a bit too strong compared to what the authors demonstrated with the model. For example, when the authors say the model is minimal, the authors simply investigated how many lobula neurons are required for pattern discrimination in the model. However, the manuscript appears to use this to claim that the presented model is the minimal one required for visual tasks. 3) It lacks explanations of what mechanisms in the model could discriminate some patterns but not others, making the descriptions very qualitative. 4) The authors did not provide compelling evidence that the algorithm is particularly tuned to natural scenes.

      We appreciate the reviewer's constructive feedback and have revised the manuscript to clarify and strengthen our claims. Below, we address each of the concerns raised:

      (1) The model does not rigorously follow the detailed anatomy of the insect brain

      We acknowledge that our model is an abstraction rather than a direct reproduction of the full micromorphology of the insect brain. The goal of our study was not to replicate every anatomical feature but rather to extract the core computational principles underlying active vision, based on the functional activity of insect brain. Although the recent connectome studies provide detailed structural maps, they do not fully capture the functional dynamics of sensory processing and behavioural outcomes. Our model integrates key neurobiological insights, including the hierarchical structure of the optic lobes, lateral inhibition in the lobula, and non-associative learning mechanisms shaping spatiotemporal receptive fields.

      However, to address this concern, we have revised the introduction and discussion to explicitly acknowledge the model’s level of abstraction and its relationship to the known anatomy of the insect visual system. Furthermore, we highlight future directions in which connectomic data could refine our model.

      (2) Strength of claims regarding minimality of the model

      We appreciate the reviewer’s concern regarding the definition of a "minimal" model. Our intention was not to claim that this model represents the absolute minimal neural architecture for visual learning task but rather that it identifies a minimal set of necessary computational elements that enable pattern discrimination in insects. To clarify this, we have refined the text to ensure that our conclusions about minimality are explicitly tied to the specific constraints and assumptions of our model. For instance, in the revised manuscript, we emphasise that our findings demonstrate how the number of lobula neurons, inhibitory lateral connection, non-associative learning model, affect neural representation and discrimination performance, rather than establishing an absolute lower bound on the complexity required for visual processing in insects.

      (3) Mechanistic explanations for pattern discrimination

      Thank you for highlighting this point. We have conducted a more detailed analysis of the model’s response to different patterns and expanded our discussion of the underlying mechanisms. To address this, we have refined our explanation of how different scanning strategies and temporal integration mechanisms contribute to neural selectivity in the lobula and overall discrimination performance. Specifically:

      - Figure 3 illustrates how the model benefits from generating sparse coding in the visual network, leading to improved performance in pattern recognition tasks.

      - Figure 5 now includes a more detailed explanation of how different scanning strategies influence the selectivity and separability of lobula neuron responses. Additionally, we provide further analysis of why the model successfully discriminates certain patterns (e.g., simple oriented bars) but struggles with more complex spatially structured quadrant-based patterns.

      - We elaborate on how sequential sampling, temporal coding, and lateral inhibition collectively shape neural representations, enabling the model to distinguish between visual stimuli effectively.

      These refinements provide a clearer mechanistic explanation of the model’s strengths and limitations, ensuring a more comprehensive understanding of its function.

      (4) Evidence that the model is tuned to natural scenes

      We have revised the manuscript to provide stronger support for the claim that the model is particularly adapted to natural scenes. Specifically:

      - Figure 3 demonstrates that training on natural images leads to sparse, decorrelated responses in the lobula, a hallmark of efficient coding observed in biological systems.

      - Supplementary Figure 2-1B shows that training with shuffled images fails to produce structured receptive fields, reinforcing that the statistical structure of natural images is crucial for efficient learning.

      - We now explicitly discuss how the receptive fields emerging from non-associative learning align with known orientation-selective responses in insect visual neurons, supporting the idea that the model is optimised for processing natural visual inputs (Figures 3, 6) and discussion section.

      Taken together, these revisions clarify how the model captures fundamental principles of insect vision without making overly strong claims about biological fidelity. We thank the reviewer for these insightful comments; addressing them has significantly strengthened the clarity and depth of our manuscript.

      Reviewer #2 (Public Review):

      This study is inspired by the scanning movements observed in bees when performing visual recognition tasks. It uses a multilayered network, representing stages of processing in the visual lobes (lamina, medulla, lobula), and uses the lobula output as input to a model of associative learning in the mushroom body (MB). The network is first trained with short "scanning" sequences of natural images, in a non-associative adaptation process, and then several experimental paradigms where images are rewarded or punished are simulated, with the output of the MB able to provide the appropriate discriminative decisions (in some but not all cases). The lobula receptive fields formed by the initial adaptation process show spatiotemporal tuning to edges moving at particular orientations and speeds that are comparable to recorded responses of such neurons in the insect brain.

      There are two main limitations to the study in my view. First, although described (caption fig 1) as a model "inspired by the micromorphology" of the insect brain, implying a significant degree of accuracy and detail, there are many arbitrary features (unsupported by current connectomics). For example, the strongly constrained delay line structure from medulla to­ lobula neurons, and the use of a single MB0N that has input synapses that undergo facilitation and decay according to different neuromodulators. Second, while it is reasonable to explore some arbitrary architectural features, given that not everything is yet known about these pathways, the presented work does not sufficiently assess the necessity and sufficiency of the different components, given the repeated claims that this is the "minimal circuit" required for the visual tasks explored.

      We appreciate your feedback and have refined the manuscript to clarify model design choices and address concerns regarding minimality.

      (1) Model Architecture and Functional Simplifications<br /> While our model is inspired by insect visual system, it is not intended as an exact anatomical reconstruction but rather a functional abstraction to uncover key computational principles of active vision and visual learning. The delay-line structure and simplified MBON implementation were deliberate choices to enable spatiotemporal encoding and associative learning without overcomplicating the model. As connectome data alone do not fully reveal functional relationships, our approach serves as a hypothesis-generating tool for future neurobiological studies.

      (2) Necessity and Sufficiency of Model Components<br /> We have removed overstatements about minimality and now clarify that our model represents a functional circuit rather than the absolute minimal configuration. Additionally, we conducted new control experiments assessing the influence of different model components, and further justifying key mechanisms such as spatiotemporal encoding and lateral inhibition.

      For a more detailed discussion of these revisions and improvements, please refer to our response to the Journal, above.

      Regarding the mushroom body (MB) learning model, it is strange that no reference is made to recent models closely tied to connectomic and other data in fruit flies, which suggests separate MBONS encode positive vs. negative value; that learning is not dependent on MB0N activity (so is not STDP); that feedback from MBONs to dopaminergic signalling plays an important role, etc. Possibly the MB of the bee operates in a completely different way to the fly, but the presented model relies on relatively old data about MB function, mostly from insects other than bees (e.g. locust) so its relationship to the increasingly comprehensive understanding emerging for the fly MB needs to be clarified. It is implied that the complex interaction of the differential effects of dopamine and octopamine, as modelled here, are required to learn the more complex visual paradigms, but it is not actually tested if simpler rules might suffice. Also, given previous work on models of view recognition in the MB, inspired by bees and ants, it seems plausible that simply using static 25×25 medulla activity as input to produce sparse activity in the KCs would be sufficient for MB0N output to discriminate the patterns used in training, including the face stimulus. Thus it is not clear whether the spatiotemporal input and the lobula encoding are necessary to solve these tasks.

      Thank you for your suggestion. The primary focus of this study was not to uncover the exact mechanisms of associative learning in the mushroom body (MB) but rather to evaluate the role of lobula output activity in active vision. The associative learning component was included as a simplified mechanism to assess how the spatiotemporal encoding in the lobula contributes to visual pattern learning.

      We conducted a detailed analysis of lobula neuron activity, focusing on sparsity, decorrelation, and selectivity to demonstrate how the visual system extracts compact yet relevant signals before reaching the learning centre (see Figure 5). Theoretical predictions based on these findings suggest that such encoding enhances pattern recognition performance. While selecting this possible associative learning mechanism allowed us to explicitly evaluate this capability, it also facilitated comparison with previous active vision experiments and assessed the influence of different components on bee behaviour.

      We acknowledge that recent Drosophila connectomics studies suggest alternative MB architectures, including separate MBONs encoding positive vs. negative values, learning mechanisms independent of MBON activity, and feedback from MBONs to dopaminergic pathways. However, visual learning mechanisms in the MB remain poorly characterised, especially in bees, where the functional relevance of different MBON configurations is still unclear. The decision to simplify the MB learning process was intentional, allowing us to prioritise model interpretability over anatomical replication.

      These simplifications have been explicitly discussed in the revised manuscript, where we suggest future directions for integrating more biologically detailed MB models to enhance our understanding of active visual learning in insects. For a broader discussion of our rationale for prioritising computational simplifications over direct neurobiological replication, please refer to our response to the Journal, above.

      It is also difficult to interpret the range of results in fig 3. The network sometimes learns well, sometimes just adequately (perhaps comparable to bees), and sometimes fails. The presentation of these results does not seem to identify any coherent pattern underlying success or failure, other than that the ability to generalise seems limited. That is, recognition (in most cases) requires the presentation of exactly the same stimulus in exactly the same way (same scanning pattern, distance and speed). In particular, it is hard to know what to conclude when the network appears able to learn some "complex patterns" (spirals, faces) but fails to learn the apparently simple plus vs. multiplication symbol discrimination if it is trained and tested with a scan passing across the whole pattern instead of just the lower half.

      We acknowledge that the variability in the model’s performance across different tasks and conditions required a clearer explanation. In the revised manuscript, we have analysed the underlying factors influencing success and failure in greater detail and have expanded the discussion on the model’s generalisation limitations.

      To address this, we have conducted new control experiments and deeper analyses, now presented in Figure 5, Figure 6F, which illustrate how scanning conditions impact recognition performance. Specifically, we examine why the model can successfully learn complex patterns (e.g., spirals, faces) but struggles with apparently simpler tasks, such as distinguishing between a plus and multiplication symbol when scanning the entire pattern rather than just the lower half. Our results suggest that spatially constrained scanning enhances discriminability, while whole-pattern scanning reduces selectivity due to weaker and less sparse feature encoding in lobula neurons.

      We have also clarified in the Discussion section that while the model demonstrates robust pattern learning under specific conditions, its ability to generalise remains limited when tested with compex patterns (Figure 6F. Further investigation is needed to explore how adaptive scanning strategies or hierarchical processing might improve generalisation.

      In summary, although it is certainly interesting to explore how active vision (scanning a visual pattern) might affect the encoding of stimuli and the ability to learn to discriminate rewarding stimuli, some claims in the paper need to be tempered or better supported by the demonstration that alternative, equally plausible, models of the visual and mushroom body circuits are not sufficient to solve the given tasks.

      There is limited knowledge in the literature regarding the neural correlates of visual-related plasticity in the mushroom body (MB). The majority of our current understanding of the MB is derived from studies on olfactory learning, particularly in Drosophila, which does not provide sufficient data to directly implement or comprehensively compare alternative models for visual learning.

      However, the primary focus of our study is on active vision and how spatiotemporal signals are encoded in the insect visual system. Rather than aiming to replicate a detailed biological model of MB function, we intentionally employed a simplified associative learning network to investigate how neural activity emerging from our visual processing model can support pattern recognition. This approach also allows us to compare model performance with bee behaviour, drawing on insights from previous experimental work on active vision in bees.

      We now discuss the limitations of our approach and the rationale for selectively incorporating specific neural network components in lines 652-677. Additionally, we have provided further justification (see responses above) for prioritising a simplified model, rather than attempting to mimic a highly detailed, yet currently unverified, alternative learning circuit. These clarifications help ensure that our claims are appropriately tempered while still demonstrating the functional relevance of our model.

      Reviewer #3 (Public Review):

      In this manuscript, the authors use the data collected and observations made on bees' scanning behaviour during visual learning to design a bio-inspired artificial neural network. The network follows the architecture of bees visual systems, where photoreceptors project into the lamina, then the medulla, medulla neurons connect to a set of spiking neurons in the lobula. Lobula neurons project to kenyon cells and then to MBON, which controls reward and punishment. The authors then test the performance of the network in comparison with real bee data, finding it to perform well in all tasks. The paper attempts to reproduce a living organism network with a practical application in mind, and it is quite impressive! I appreciate both the potential implications for the understanding of biological systems and the applications in the development of autonomous agents, making the paper absolutely worth reading.

      Thank you for your positive feedback and appreciation of our work.

      However, I believe that the current version somewhat lacks in clarity regarding the methodology and in some of the keywords used to describe the model.

      Definitions:<br /> Throughout the manuscript, the authors use some key terminology that I believe would benefit from some clarification.<br /> The generated model is described in the title and once in the introduction as "neuromorphic". The model is definitely bio-inspired, but at least in some layers of the neural network, the model is built very differently from actual brain connectivity. Generally, when we use the term neuromorphic we imply many advantages of neural tissue, like energy efficiency, that I am not sure the current model is achieving. I absolutely see how this work is going in that direction, and I also fundamentally agree with the choice of terminology, but this should be clearly explained to not risk over-implications

      We appreciate the reviewer’s feedback and acknowledge the importance of clarifying key terminology in our manuscript. As outlined in our response to the Journal, we intentionally simplified the model to focus on understanding the core computational processes involved in active vision rather than precisely replicating the full complexity of insect neural circuits (see other reasons for simplification in the manuscript). This simplification allows us to systematically analyse the influence of specific components underlying active vision mechanisms.

      Despite these simplifications, our model incorporates key neuromorphic principles, including the use of a recurrent neural network architecture and a spiking neuron model at multiple processing levels. These elements enable biologically inspired information processing, aligning with the fundamental characteristics of neuromorphic computing, even if the model does not explicitly focus on hardware efficiency or energy constraints.

      The authors describe this as a model of "active vision". This is done in the title of the article, and in the many paragraph headings (methods, results). In the introduction, however, the term active vision is reserved to the description of bees' behavior. Indeed, the developed model is not a model of active vision, as this would require for the model to control the movement of the "camera". Here instead the stimuli display is given to the model in a fixed progression. What I suspect is that the authors' aim is to describe a model that supports the bees' active vision, not a model of active vision. I believe this should be very clear from the paper, and it may be appropriate to remove the term from the title.

      While our model does not actively control camera movement in the environment, it does simulate the effects of active vision by incorporating scanning dynamics. Our results demonstrate that model responses change significantly with variations in scanning speed and restricted scanning areas, highlighting the importance of movement in shaping visual encoding. However, we acknowledge that true active vision would involve adaptive, real-time control of gaze or trajectory, which the step after the current implementation for make more realistic model of active vison. To address your concern, we have discussed the potential for incorporating dynamic flight behaviours in future studies, allowing the model to actively adjust its scanning strategy based on learned visual cues.

      In the short title, it said that this network is minimal. This is then characterized in the introduction as the minimal network capable of enabling active vision in bees. The authors, however, in their experiment only vary the number of lobula neurons, without changing other parts of the architecture. Given this, we can only say that 16 lobula neurons is the minimal number required to solve the experimental task with the given model. I don't believe that this is generalizable to bees, nor that this network is minimal, as there may be different architectures (for the other layers especially) that require overall less neurons. Moreover, the tasks attempted in the minimal network experiment did not include any of the complex stimuli presented in figure 3, like faces. It may be that 16 lobula neurons are sufficient for the X vs + and clockwise vs counter-clockwise spirals, but we do not know if increasing stimuli complexity would result in a failure of the model with 16 neurons.

      We agree that analysing only the number of lobula neurons is not sufficient to establish a truly minimal model for active vision. To address this, we conducted further control experiments to evaluate the influence of other key components, including non-associative learning, scanning behaviour, and lateral connectivity, on model performance. Our results suggest that the proposed model represents a computationally minimal network capable of implementing a basic active vision process, but a more complex model would be required for higher-order visual tasks.

      However, to avoid potential misinterpretation, we have revised the short title and updated the manuscript to clarify that our model identifies a possible minimal functional circuit rather than the absolute minimal network for active vision. Additionally, we have added further discussion on the simplifications made in the model and emphasised the need for future studies to explore alternative architectures and assess their relevance for understanding active vision in insects.

      Methodology:

      The current explanation of the model is currently a bit lacking in clarity and details. This risks impacting negatively on the relevance of the whole work which is interesting and worth reading! This issue affects also the interpretation of the results, as it is not clear to what extent each part of the network could affect the results shown. This is especially the case when the network under-performs with respect to the best performing scenario (e.g., when varying the speed and part of the pattern that is observed, such as in Fig 2C). Adding a detailed technical scheme/drawing specific to the network architecture could have been a way of significantly increasing the clarity of the Methods section and the interpretation of the results.<br /> On a similar note, the authors make some comparisons between the model and real bees. However, it remains unclear whether these similarities are actually indicative of an optimality in the bees visual scanning strategy, or just deriving from the authors design. This is for me particularly important in the experiments aimed at finding the best scanning procedure. If the initial model training is based on natural images it is performed by presenting left to right moving frames, the highest efficiency of lower-half scanning may be due to how the weights in the initial layers are structured and a low generalizability of the model, rather than to the strategy optimality

      We appreciate the reviewer’s constructive feedback and have taken steps to enhance the clarity, interpretability, and transparency of our model description and results. Below, we address the concerns regarding model explanation, performance interpretation, and the comparison with real bee behaviour.

      (1) Improved Model Explanation and Network Clarity: We apologise that the previous version of the manuscript did not fully detail the architecture and functioning of the model. To address this, we have expanded the Methods section with a more detailed breakdown of the network components, their roles, and their contribution to active vision processing. Additionally, we have summarised the network architecture and its implementation for visual learning tasks at the beginning of the Results section, providing a clearer overview of the information flow from visual input to associative learning. Furthermore, we have explicitly analysed and discussed the role of key model components, including scanning strategies, lateral connectivity, and non-associative learning mechanisms, clarifying how each contributes to the observed results.

      (2) Interpretation of Model Performance Variability: Understanding the factors influencing performance variability is crucial, and to improve clarity, we have conducted further analysis of model performance across different conditions, particularly examining the effects of scanning speed, spatial constraints, and feature encoding (see Figure 2C). Additionally, we have expanded the discussion on how scanning conditions impact performance, providing explanations for why some conditions lead to higher or lower discrimination success. Furthermore, we have clarified why certain stimuli present greater challenges for the model, linking these difficulties to receptive field properties and scanning dynamics.

      (3) Comparison Between Model Behaviour and Real Bees: To address your concern regarding the link between scanning preferences and true biological optimality, we have included further analysis discussing the influence of training conditions on the model’s learned behaviours. Additionally, we propose future experiments to test alternative scanning strategies, including adaptive scanning mechanisms that adjust based on visual task demands. Furthermore, we have expanded the discussion on the simplifications made in this study, explicitly stating the limitations of the model and emphasising the need for future research to explore more flexible and biologically plausible scanning mechanisms.

      We believe these revisions significantly enhance the clarity and interpretability of the study, ensuring that the model’s findings are well contextualised within both computational and biological frameworks.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1 (Public review):

      Specific comments:

      (1) It is difficult to appreciate that there is a "peripheral sub-membrane microtubule array" as it is not well defined in the manuscript. This reviewer assumes that this is in the respective field clear. Yet, while it is appreciated that there is an increased amount of MTs close to the cytoplasmic membrane, the densities appear very variable along the membrane. Please provide a clear description in the Introduction what is meant with "peripheral sub-membrane microtubule array".

      A definition has been added to the Introduction.

      (2) The authors described a "consistent presence of a significant peripheral array in the C57BL/ 6J control mice, while the KO counterparts exhibited a partial loss of this peripheral bundle.

      Specifically, the measured tubulin intensity at the cell periphery was significantly reduced in the KO mice compared to their wild-type counterparts". In vitro "control cells had convoluted nonradial MTs with a prominent sub-membrane array, typical for β cells (Fig. 2A), KIF5B-depleted cells featured extra-dense MTs in the cell center and sparse receding MTs at the periphery (Fig. 2B,C)". Please comment/discuss why in vivo there are no "extra-dense MTs in the cell center".

      We now add a discussion of this point, which we believe could be a manifestation of 3D shape of a beta cell in tissue and/or compensatory mechanisms in organisms.

      (3) Authors should include in the Discussion a paragraph discussing the fact that small changes in MT configuration can have strong effects.

      A paragraph added to the discussion.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Figure 1: Even though the reviewer appreciates that minor changes of MT configuration have severe effects, still the overall effects appear minor (40 vs. <50% or 35% vs. around 28%). Notably, there are no statistically significant differences in the different groups in Fig. 1Suppl-Fig.1 D. This reviewer is not sure if the combination of many not significantly different data points can result in significant changes and this should be checked by a statistician. Authors should include in the Discussion a paragraph discussing the fact that small changes in MT configuration can have strong effects.

      We have now added the requested paragraph to the discussion. Indeed, the differences are small, and the significance is only detected in a data set with a large sample size in Fig. 1J,K (combined data sets with smaller sizes from Fig. 1-Suppl-Fig.1 D), consistent with the fact that a larger sample size generally provides more power to detect an effect.

      (2) Unfortunately, the authors cannot block kinesin-1 resulting in microtubule accumulation in the cell center and then release the block (best inhibiting microtubule formation), to show that the MTs accumulated in the cell center will be transported to the periphery.

      This is indeed the case at the moment, yes.

      Minor comments:

      - Abstract: β-cells vs. β cells (and throughout the manuscript)

      - Page 4: "MTOC, the Golgi, (Trogden et al. 2019), and"

      - Page 5: "β-cell specific"

      - MT-sliding vs. MT sliding

      - Kinesin 1 vs. kinesin-1

      - Page 6, line 1: "β cells. actively"

      - Page 7: "a microtubule probe", should be "MT"

      - Page 9: "1μm" vs. "1 μm"

      - Page 10: "demonstrate a dramatic effect" recommended is: "demonstrate a marked effect"

      - Page 13, line 1: dramatically vs. markedly

      - Page 13, line 5: "50μm" vs. "50 μm" (in general, there should be a space between number and unit?)

      - "37 degrees C" vs. "37{degree sign}C"

      - Animal protocol number?

      - "Mice were euthanized by isoflurane inhalation"? What concentration? How long? More details are needed (no cervical dislocation?).

      - Antibodies: more identifiers are needed.

      - Antibody information in Key reagents and under 5. Reagents and antibodies do not fit (1:500 and 1:1000).

      Thank you, we corrected all relevant information now.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      The manuscript by Hussain and collaborators aims at deciphering the microtubule-dependent ribbon formation in zebrafish hair cells. By using confocal imaging, pharmacology tools, and zebrafish mutants, the group of Katie Kindt convincingly demonstrated that ribbon, the organelle that concentrates glutamate-filled vesicles at the hair cell synapse, originates from the fusion of precursors that move along the microtubule network. This study goes hand in hand with a complementary paper (Voorn et al.) showing similar results in mouse hair cells.

      Strengths:

      This study clearly tracked the dynamics of the microtubules, and those of the microtubule-associated ribbons and demonstrated fusion ribbon events. In addition, the authors have identified the critical role of kinesin Kif1aa in the fusion events. The results are compelling and the images and movies are magnificent.

      Weaknesses:

      The lack of functional data regarding the role of Kif1aa. Although it is difficult to probe and interpret the behavior of zebrafish after nocodazole treatment, I wonder whether deletion of kif1aa in hair cells may result in a functional deficit that could be easily tested in zebrafish?

      We have examined functional deficits in kif1aa mutants in another paper that was recently accepted: David et al. 2024. https://pubmed.ncbi.nlm.nih.gov/39373584/

      In David et al., we found that in addition to a subtle role in ribbon fusion during development, Kif1aa plays a major role in enriching glutamate-filled synaptic vesicles at the presynaptic active zone of mature hair cells. In kif1aa mutants, synaptic vesicles are no longer enriched at the hair cell base, and there is a reduction in the number of synaptic vesicles associated with presynaptic ribbons. Further, we demonstrated that kif1aa mutants also have functional defects including reductions in spontaneous vesicle release (from hair cells) and evoked postsynaptic calcium responses. Behaviorally, kif1aa mutants exhibit impaired rheotaxis, indicating defects in the lateral-line system and an inability to accurately detect water flow. Because our current paper focuses on microtubule-associated ribbon movement and dynamics early in hair-cell development, we have only discussed the effects of Kif1aa directly related to ribbon dynamics during this time window. In our revision, we have referenced this recent work. Currently it is challenging to disentangle how the subtle defects in ribbon formation in kif1aa mutants contribute to the defects we observe in ribbon-synapse function.

      Added to results:

      “Recent work in our lab using this mutant has shown that Kif1aa is responsible for enriching glutamate-filled vesicles at the base of hair cells. In addition this work demonstrated that loss of Kif1aa results in functional defects in mature hair cells including a reduction in evoked post-synaptic calcium responses (David et al., 2024). We hypothesized that Kif1aa may also be playing an earlier role in ribbon formation.”

      Impact:

      The synaptogenesis in the auditory sensory cell remains still elusive. Here, this study indicates that the formation of the synaptic organelle is a dynamic process involving the fusion of presynaptic elements. This study will undoubtedly boost a new line of research aimed at identifying the specific molecular determinants that target ribbon precursors to the synapse and govern the fusion process.

      Reviewer #2 (Public Review):

      Summary:

      In this manuscript, the authors set out to resolve a long-standing mystery in the field of sensory biology - how large, presynaptic bodies called "ribbon synapses" migrate to the basolateral end of hair cells. The ribbon synapse is found in sensory hair cells and photoreceptors, and is a critical structural feature of a readily-releasable pool of glutamate that excites postsynaptic afferent neurons. For decades, we have known these structures exist, but the mechanisms that control how ribbon synapses coalesce at the bottom of hair cells are not well understood. The authors addressed this question by leveraging the highly-tractable zebrafish lateral line neuromast, which exhibits a small number of visible hair cells, easily observed in time-lapse imaging. The approach combined genetics, pharmacological manipulations, high-resolution imaging, and careful quantifications. The manuscript commences with a developmental time course of ribbon synapse development, characterizing both immature and mature ribbon bodies (defined by position in the hair cell, apical vs. basal). Next, the authors show convincing (and frankly mesmerizing) imaging data of plus end-directed microtubule trafficking toward the basal end of the hair cells, and data highlighting the directed motion of ribbon bodies. The authors then use a series of pharmacological and genetic manipulations showing the role of microtubule stability and one particular kinesin (Kif1aa) in the transport and fusion of ribbon bodies, which is presumably a prerequisite for hair cell synaptic transmission. The data suggest that microtubules and their stability are necessary for normal numbers of mature ribbons and that Kif1aa is likely required for fusion events associated with ribbon maturation. Overall, the data provide a new and interesting story on ribbon synapse dynamics.

      Strengths:

      (1) The manuscript offers a comprehensive Introduction and Discussion sections that will inform generalists and specialists.

      (2) The use of Airyscan imaging in living samples to view and measure microtubule and ribbon dynamics in vivo represents a strength. With rigorous quantification and thoughtful analyses, the authors generate datasets often only obtained in cultured cells or more diminutive animal models (e.g., C. elegans).

      (3) The number of biological replicates and the statistical analyses are strong. The combination of pharmacology and genetic manipulations also represents strong rigor.

      (4) One of the most important strengths is that the manuscript and data spur on other questions - namely, do (or how do) ribbon bodies attach to Kinesin proteins? Also, and as noted in the Discussion, do hair cell activity and subsequent intracellular calcium rises facilitate ribbon transport/fusion?

      These are important strengths and as stated we are currently investigating what other kinesins and adaptors and adaptor’s transport ribbons. We have ongoing work examining how hair-cell activity impacts ribbon fusion and transport!

      Weaknesses:

      (1) Neither the data or the Discussion address a direct or indirect link between Kinesins and ribbon bodies. Showing Kif1aa protein in proximity to the ribbon bodies would add strength.

      This is a great point. Previous immunohistochemistry work in mice demonstrated that ribbons and Kif1a colocalize in mouse hair cells (Michanski et al, 2019). Unfortunately, the antibody used in study work did not work in zebrafish. To further investigate this interaction, we also attempted to create a transgenic line expressing a fluorescently tagged Kif1aa to directly visualize its association with ribbons in vivo. At present, we were unable to detect transient expression of Kif1aa-GFP or establish a transgenic line using this approach. While we will continue to work towards understanding whether Kif1aa and ribbons colocalize in live hair cells, currently this goal is beyond the scope of this paper. In our revision we discuss this caveat.

      Added to discussion:

      “In addition, it will be useful to visualize these kinesins by fluorescently tagging them in live hair cells to observe whether they associate with ribbons.”

      (2) Neither the data or Discussion address the functional consequences of loss of Kif1aa or ribbon transport. Presumably, both manipulations would reduce afferent excitation.

      Excellent point. Please see the response above to Reviewer #1 public response weaknesses.

      (3) It is unknown whether the drug treatments or genetic manipulations are specific to hair cells, so we can't know for certain whether any phenotypic defects are secondary.

      This is correct and a caveat of our Kif1aa and drug experiments. In our recently published work, we confirmed that Kif1aa is expressed in hair cells and neurons, while kif1ab is present just is neurons. Therefore, it is likely that the ribbon formation defects in kif1aa mutants are restricted to hair cells. We added this expression information to our results:

      “ScRNA-seq in zebrafish has demonstrated widespread co-expression of kif1ab and kif1aa mRNA in the nervous system. Additionally, both scRNA-seq and fluorescent in situ hybridization have revealed that pLL hair cells exclusively express kif1aa mRNA (David et al., 2024; Lush et al., 2019; Sur et al., 2023).”

      Non-hair cell effects are a real concern in our pharmacology experiments. To mitigate this in our pharmacological experiments, we have performed drug treatments at 3 different timescales: long-term (overnight), short-term (4 hr) and fast (30 min) treatments. The fast experiments were done after 30 min nocodazole drug treatment, and after this treatment we observed reduced directional motion and fusions. This fast drug treatment should not incur any long-term changes or developmental defects as hair-cell development occurs over 12-16 hrs. However, we acknowledge that drug treatments could have secondary phenotypic effects or effects that are not hair-cell specific. In our revision, we discuss these issues.

      Added to discussion:

      “Another important consideration is the potential off-target effects of nocodazole. Even at non-cytotoxic doses, nocodazole toxicity may impact ribbons and synapses independently of its effects on microtubules. While this is less of a concern in the short- and medium-term experiments (30-70 min and 4 hr), long-term treatments (16 hrs) could introduce confounding effects. Additionally, nocodazole treatment is not hair cell-specific and could disrupt microtubule organization within afferent terminals as well. Thus, the reduction in ribbon-synapse formation following prolonged nocodazole treatment may result from microtubule disruption in hair cells, afferent terminals, or a combination of the two.”

      Reviewer #3 (Public Review):

      Summary:

      The manuscript uses live imaging to study the role of microtubules in the movement of ribeye aggregates in neuromast hair cells in zebrafish. The main findings are that

      (1) Ribeye aggregates, assumed to be ribbon precursors, move in a directed motion toward the active zone;

      (2) Disruption of microtubules and kif1aa increases the number of ribeye aggregates and decreases the number of mature synapses.

      The evidence for point 2 is compelling, while the evidence for point 1 is less convincing. In particular, the directed motion conclusion is dependent upon fitting of mean squared displacement that can be prone to error and variance to do stochasticity, which is not accounted for in the analysis. Only a small subset of the aggregates meet this criteria and one wonders whether the focus on this subset misses the bigger picture of what is happening with the majority of spots.

      Strengths:

      (1) The effects of Kif1aa removal and nocodozole on ribbon precursor number and size are convincing and novel.

      (2) The live imaging of Ribeye aggregate dynamics provides interesting insight into ribbon formation. The movies showing the fusion of ribeye spots are convincing and the demonstrated effects of nocodozole and kif1aa removal on the frequency of these events is novel.

      (3) The effect of nocodozole and kif1aa removal on precursor fusion is novel and interesting.

      (4) The quality of the data is extremely high and the results are interesting.

      Weaknesses:

      (1) To image ribeye aggregates, the investigators overexpressed Ribeye-a TAGRFP under the control of a MyoVI promoter. While it is understandable why they chose to do the experiments this way, expression is not under the same transcriptional regulation as the native protein, and some caution is warranted in drawing some conclusions. For example, the reduction in the number of puncta with maturity may partially reflect the regulation of the MyoVI promoter with hair cell maturity. Similarly, it is unknown whether overexpression has the potential to saturate binding sites (for example motors), which could influence mobility.

      We agree that overexpression of transgenes under using a non-endogenous promoter in transgenic lines is an important consideration. Ideally, we would do these experiments with endogenously expressed fluorescent proteins under a native promoter. However, this was not technically possible for us. The decrease in precursors is likely not due to regulation by the myo6a promoter. Although the myo6a promoter comes on early in hair cell development, the promoter only gets stronger as the hair cells mature. This would lead to a continued increase rather than a decrease in puncta numbers with development.

      Protein tags such as tagRFP always have the caveat of impacting protein function. This is in partly why we complemented our live imaging with analyses in fixed tissue without transgenes (kif1aa mutants and nocodazole/taxol treatments).

      In our revision, we did perform an immunolabel on myo6b:riba-tagRFP transgenic fish and found that Riba-tagRFP expression did not impact ribbon synapse numbers or ribbon size. This analysis argues that the transgene is expressed at a level that does not impact ribbon synapses. This data is summarized in Figure 1-S1.

      Added to the results:

      “Although this latter transgene expresses Riba-TagRFP under a non-endogenous promoter, neither the tag nor the promoter ultimately impacts cell numbers, synapse counts, or ribbon size (Figure 1-S1A-E).”

      Added to methods:

      Tg(myo6b:ctbp2a-TagRFP)<sup>idc11Tg</sup> reliably labels mature ribbons, similar to a pan-CTBP immunolabel at 5 dpf (Figure 1-S1B). This transgenic line does not alter the number of hair cells or complete synapses per hair cell (Figure 1-S1A-D). In addition, myo6b:ctbp2a-TagRFP does not alter the size of ribbons (Figure 1-S1E).”

      (2) The examples of punctae colocalizing with microtubules look clear (Figures 1 F-G), but the presentation is anecdotal. It would be better and more informative, if quantified.

      We did attempt a co-localization analysis between microtubules and ribbons but did not move forward with it due to several issues:

      (1) Hair cells have an extremely crowded environment, especially since the nucleus occupies the majority of the cell. All proteins are pushed together in the small space surrounding the nucleus and ultimately, we found that co-localization analyses were not meaningful because the distances were too small.

      (2) We also attempted to segment microtubules in these images and quantify how many ribbons were associated with microtubules, but 3D microtubule segmentation was not accurate in hair cells due to highly varying filament intensities, filament dynamics and the presence of diffuse cytoplasmic tubulin signal.

      Because of these challenges we concluded the best evidence of ribbon-microtubule association is through visualization of ribbons and their association with microtubules over time (in our timelapses). We see that ribbons localize to microtubules in all our timelapses, including the examples shown (Movies S2-S10). The only instance of ribbon dissociation it when ribbons switch from one filament to another. We did not observe free-floating ribbons in our study.

      (3) It appears that any directed transport may be rare. Simply having an alpha >1 is not sufficient to declare movement to be directed (motor-driven transport typically has an alpha approaching 2). Due to the randomness of a random walk and errors in fits in imperfect data will yield some spread in movement driven by Brownian motion. Many of the tracks in Figure 3H look as though they might be reasonably fit by a straight line (i.e. alpha = 1).

      (4) The "directed motion" shown here does not really resemble motor-driven transport observed in other systems (axonal transport, for example) even in the subset that has been picked out as examples here. While the role of microtubules and kif1aa in synapse maturation is strong, it seems likely that this role may be something non-canonical (which would be interesting).

      Yes, it is true, that directed transport of ribbon precursors is relatively rare. Only a small subset of the ribbon precursors moves directionally (α > 1, 20 %) or have a displacement distance > 1 µm (36 %) during the time windows we are imaging. The majority of the ribbons are stationary. To emphasize this result we have added bar graphs to Figure 3I,K to illustrate this result and state the numbers behind this result more clearly.

      “Upon quantification, 20.2 % of ribbon tracks show α > 1, indicative of directional motion, but the majority of ribbon tracks (79.8 %) show α < 1, indicating confinement on microtubules (Figure 3I, n = 10 neuromasts, 40 hair cells, and 203 tracks).

      To provide a more comprehensive analysis of precursor movement, we also examined displacement distance (Figure 3J). Here, as an additional measure of directed motion, we calculated the percent of tracks with a cumulative displacement > 1 µm. We found 35.6 % of tracks had a displacement > 1 µm (Figure 3K; n = 10 neuromasts, 40 hair cells, and 203 tracks).”

      We cannot say for certain what is happening with the stationary ribbons, but our hypothesis is that these ribbons eventually exhibit directed motion sufficient to reach the active zone. This idea is supported by the fact that we see ribbons that are stationary begin movement, and ribbons that are moving come to a stop during the acquisition of our timelapses (Movies S4 and S5). It is possible that ribbons that are stationary may not have enough motors attached, or there may be a ‘seeding’ phase where Ribeye aggregates are condensing on the ribbon.

      We also reexamined our MSD a values as the a values we observed in hair cells were lower than those seen canonical motor-driven transport (where a approaches 2). One reason for this difference may arise from the dynamic microtubule network in developing hair cells, which could affect directional ribbon movement. In our revision we plotted the distribution of a values which confirmed that in control hair cells, the majority of the a values we see are typically less than 2 (Figure 7-S1A). Interestingly we also compared the distribution a values between control and taxol-treated hair cells, where the microtubule network is more stable, and found that the distribution shifted towards higher a values (Figure 7-S1A). We also plotted only ‘directional’ tracks (with a > 1) and observed significantly higher a values in taxol-treated hair cells (Figure 7-S1B). This is an interesting result which indicates that although the proportion of directional tracks (with a > 1) is not significantly different between control and taxol-treated hair cells (which could be limited by the number of motor/adapter proteins), the ribbons that move directionally do so with greater velocities when the microtubules are more stable. This supports our idea that the stability of the microtubule network could be why ribbon movement does not resemble canonical motor transport. This analysis is presented as a new figure (Figure 7-S1A-B) and is referred to in the text in the results and the discussion.

      Results:

      “Interestingly, when we examined the distribution of α values, we observed that taxol treatment shifted the overall distribution towards higher α a values (Figure 7-S1A). In addition, when we plotted only tracks with directional motion (α > 1), we found significantly higher α values in hair cells treated with taxol compared to controls (Figure 7-S1B). This indicates that in taxol-treated hair cells, where the microtubule network is stabilized, ribbons with directional motion have higher velocities.”

      Discussion:

      “Our findings indicate that ribbons and precursors show directed motion indicative of motor-mediated transport (Figure 3 and 7). While a subset of ribbons moves directionally with α values > 1, canonical motor-driven transport in other systems, such as axonal transport, can achieve even higher α values approaching 2 (Bellotti et al., 2021; Corradi et al., 2020). We suggest that relatively lower α values arise from the highly dynamic nature of microtubules in hair cells. In axons, microtubules form stable, linear tracks that allow kinesins to transport cargo with high velocity. In contrast, the microtubule network in hair cells is highly dynamic, particularly near the cell base. Within a single time frame (50-100 s), we observe continuous movement and branching of these networks. This dynamic behavior adds complexity to ribbon motion, leading to frequent stalling, filament switching, and reversals in direction. As a result, ribbon transport appears less directional than the movement of traditional motor cargoes along stable axonal filaments, resulting in lower α values compared to canonical motor-mediated transport. Notably, treatment with taxol, which stabilizes microtubules, increased α values to levels closer to those observed in canonical motor-driven transport (Figure 7-S1). This finding supports the idea that the relatively lower α values in hair cells are a consequence of a more dynamic microtubule network. Overall, this dynamic network gives rise to a slower, non-canonical mode of transport.”

      (5) The effect of acute treatment with nocodozole on microtubules in movie 7 and Figure 6 is not obvious to me and it is clear that whatever effect it has on microtubules is incomplete.

      When using nocodazole, we worked to optimize the concentration of the drug to minimize cytotoxicity, while still being effective. While the more stable filaments at the cell apex remain largely intact after nocodazole treatment, there are almost no filaments at the hair cell base, which is different from the wild-type hair cells. In addition, nocodazole-treated hair cells have more cytoplasmic YFP-tubulin signal compared to wild type. We have clarified this in our results. To better illustrate the effect of nocodazole and taxol we have also added additional side-view images of hair cells expressing YFP-tubulin (Figure 4-S1F-G), that highlight cytoplasmic YFP-tubulin and long, stabilized microtubules after 3-4 hr treatment with nocodazole and taxol respectively. In these images we also point out microtubules at the apical region of hair cells that are very stable and do not completely destabilize with nocodazole treatment at concentrations that are tolerable to hair cells.

      “We verified the effectiveness of our in vivo pharmacological treatments using either 500 nM nocodazole or 25 µM taxol by imaging microtubule dynamics in pLL hair cells (myo6b:YFP-tubulin). After a 30-min pharmacological treatment, we used Airyscan confocal microscopy to acquire timelapses of YFP-tubulin (3 µm z-stacks, every 50-100 s for 30-70 min, Movie S8). Compared to controls, 500 nM nocodazole destabilized microtubules (presence of depolymerized YFP-tubulin in the cytosol, see arrows in Figure 4-S1F-G) and 25 µM taxol dramatically stabilized microtubules (indicated by long, rigid microtubules, see arrowheads in Figure 4-S1F,H) in pLL hair cells. We did still observe a subset of apical microtubules after nocodazole treatment, indicating that this population is particularly stable (see asterisks in Figure 4-S1F-H).”

      To further address concerns about verifying the efficacy of nocodazole and taxol treatment on microtubules, we added a quantification of our immunostaining data comparing the mean acetylated-a-tubulin intensities between control, nocodazole and taxol-treated hair cells. Our results show that nocodazole treatment reduces the mean acetylated-a-tubulin intensity in hair cells. This is included as a new figure (Figure 4-S1D-E) and this result is referred to in the text. To better illustrate the effect of nocodazole and taxol we have also added additional side-view images of hair cells after overnight treatment with nocodazole and taxol (Figure 4-S1A-C).

      “After a 16-hr treatment with 250 nM nocodazole we observed a decrease in acetylated-a-tubulin label (qualitative examples: Figure 4A,C, Figure 4-S1A-B). Quantification revealed significantly less mean acetylated-a-tubulin label in hair cells after nocodazole treatment (Figure 4-S1D). Less acetylated-a-tubulin label indicates that our nocodazole treatment successfully destabilized microtubules.”

      “Qualitatively more acetylated-a-tubulin label was observed after treatment, indicating that our taxol treatment successfully stabilized microtubules (qualitative examples: Figure 4-S1A,C). Quantification revealed an overall increase in mean acetylated-a-tubulin label in hair cells after taxol treatment, but this increase did not reach significance (Figure 4-S1E).”

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) The manuscript is fairly dense. For instance, some information is repeated (page 3 ribbon synapses form along a condensed timeline in zebrafish hair cells: 12-18 hrs, and on .page 5. These hair cells form 3-4 ribbon synapses in just 12-18 hrs). Perhaps, the authors could condense some of the ideas? The introduction could be shortened.

      We have eliminated this repeated text in our revision. We have shortened the introduction 1275 to 1038 words (with references)

      (2) The mechanosensory structure on page 5 is not defined for readers outside the field.

      Great point, we have added addition information to define this structure in the results:

      “We staged hair cells based on the development of the apical, mechanosensory hair bundle. The hair bundle is composed of actin-based stereocilia and a tubulin-based kinocilium. We used the height of the kinocilium (see schematic in Figure 1B), the tallest part of the hair bundle, to estimate the developmental stage of hair cells as described previously…”

      (3) Figure 1E is quite interesting but I'd rather show Figure S1 B/C as they provide statistics. In addition, the authors define 4 stages : early, intermediate, late, and mature for counting but provide only 3 panels for representative examples by mixing late/mature.

      We were torn about which ribbon quantification graph to show. Ultimately, we decided to keep the summary data in Figure 1E. This is primarily because the supplementary Figure will be adjacent to the main Figure in the Elife format, and the statistics will be easy to find and view.

      Figure 1 now provides a representative image for both late and mature hair cells.

      (4.) The ribbon that jumps from one microtubule to another one is eye-catching. Can the authors provide any statistics on this (e.g. percentage)?

      Good point. In our revision, we have added quantification for these events. We observe 2.8 switching events per neuromast during our fast timelapses. This information is now in the text and is also shown in a graph in Figure 3-S1D.

      “Third, we often observed that precursors switched association between neighboring microtubules (2.8 switching events per neuromast, n= 10 neuromasts; Figure 3-S1C-D, Movie S7).”

      (5) With regard to acetyl-a-tub immunocytochemistry, I would suggest obtaining a profile of the fluorescence intensity on a horizontal plane (at the apical part and at the base).

      (6) Same issue with microtubule destruction by nocodazole. Can the authors provide fluorescence intensity measurements to convince readers of microtubule disruption for long and short-term application.

      Regarding quantification of microtubule disruption using nocodazole and taxol. We did attempt to create profiles of the acetylated tubulin or YFP-tubulin label along horizontal planes at the apex and base, but the amount variability among cells and the angle of the cell in the images made this type of display and quantification challenging. In our revision we as stated above in our response to Reviewer #1’s public comment, we have added representative side-view images to show the disruptions to microtubules more clearly after short and long-term drug experiments (Figure 4-S1A-C, F-H). In addition, we quantified the reduction in acetylated tubulin label after overnight treatment with nocodazole and found the signal was significantly reduced (Figure 3-S1D-E). Unfortunately, we were unable to do a similar quantification due to the variability in YFP-tubulin intensity due to variations in mounting. The following text has been added to the results:

      “Quantification revealed significantly less mean acetylated-a-tubulin label in hair cells after nocodazole treatment (Figure 4-S1D).”

      “Quantification revealed an overall increase in mean acetylated-a-tubulin label in hair cells after taxol treatment, but this increase did not reach significance (Figure 4-S1A,C,E).”

      (7) It is a bit difficult to understand that the long-term (overnight) microtubule destabilization leads to a reduction in the number of synapses (Figure 4F) whereas short-term (30 min) microtubule destabilization leads to the opposite phenotype with an increased number of ribbons (Figure 6G). Are these ribbons still synaptic in short-term experiments? What is the size of the ribbons in the short-term experiments? Alternatively, could the reduction in synapse number upon long-term application of nocodazole be a side-effect of the toxicity within the hair cell?

      Agreed-this is a bit confusing. In our revision, we have changed our analyses, so the comparisons are more similar between the short- and long-term experiments–we examined the number of ribbons and precursor per cells (apical and basal) in both experiments (Changed the panel in Figure 4G, Figure 4-S2G and Figure 5G). In our live experiments we cannot be sure that ribbons are synaptic as we do not have a postsynaptic co-label. Also, we are unable to reliably quantify ribbon and precursor size in our live images due to variability in mounting. We have changed the text to clarify as follows:

      Results:

      “In each developing cell, we quantified the total number of Riba-TagRFP puncta (apical and basal) before and after each treatment. In our control samples we observed on average no change in the number of Riba-TagRFP puncta per cell (Figure 6G). Interestingly, we observed that nocodazole treatment led to a significant increase in the total number of Riba-TagRFP puncta after 3-4 hrs (Figure 6G). This result is similar to our overnight nocodazole experiments in fixed samples, where we also observed an increase in the number of ribbons and precursors per hair cell. In contrast to our 3-4 hr nocodazole treatment, similar to controls, taxol treatment did not alter the total number of Riba-TagRFP puncta over 3-4 hrs (Figure 6G). Overall, our overnight and 3-4 hr pharmacology experiments demonstrate that microtubule destabilization has a more significant impact on ribbon numbers compared to microtubule stabilization.”

      Discussion:

      “Ribbons and microtubules may interact during development to promote fusion, to form larger ribbons. Disrupting microtubules could interfere with this process, preventing ribbon maturation. Consistent with this, short-term (3-4 hr) and long-term (overnight) nocodazole increased ribbon and precursor numbers (Figure 6AG; Figure 4G), suggesting reduced fusion. Long-term treatment (overnight) resulted in a shift toward smaller ribbons (Figure 4H-I), and ultimately fewer complete synapses (Figure 4F).”

      Nocodazole toxicity: in response to Reviewer # 2’s public comment we have added the following text in our discussion:

      Discussion:

      “Another important consideration is the potential off-target effects of nocodazole. Even at non-cytotoxic doses, nocodazole toxicity may impact ribbons and synapses independently of its effects on microtubules. While this is less of a concern in the short- and medium-term experiments (30 min to 4 hr), long-term treatments (16 hrs) could introduce confounding effects. Additionally, nocodazole treatment is not hair cell-specific and could disrupt microtubule organization within afferent terminals as well. Thus, the reduction in ribbon-synapse formation following prolonged nocodazole treatment may result from microtubule disruption in hair cells, afferent terminals, or a combination of the two.”

      (8) Does ribbon motion depend on size or location?

      It is challenging to reliability quantify the actual area of precursors in our live samples, as there is variability in mounting and precursors are quite small. But we did examine the location of ribbon precursors (using tracks > 1 µm as these tracks can easily be linked to cell location in Imaris) with motion in the cell. We found evidence of ribbons with tracks > 1 µm throughout the cell, both above and below the nucleus. This is now plotted in Figure 3M. We have also added the following test to the results:

      “In addition, we examined the location of precursors within the cell that exhibited displacements > 1 µm. We found that 38.9 % of these tracks were located above the nucleus, while 61.1 % were located below the nucleus (Figure 3M).”

      Although this is not an area or size measurement, this result suggests that both smaller precursors that are more apical, and larger precursors/ribbons that are more basal all show motion.

      (9) The fusion event needs to be analyzed in further detail: when one ribbon precursor fuses with another one, is there an increase in size or intensity (this should follow the law of mass conservation)? This is important to support the abstract sentence "ribbon precursors can fuse together on microtubules to form larger ribbons".

      As mentioned above it is challenging accurately estimate the absolute size or intensity of ribbon precursors in our live preparation. But we did examine whether there is a relative increase in area after ribbon fuse. We have plotted the change in area (within the same samples) for the two fusion events in shown in Figure 8-S1A-B. In these examples, the area of the puncta after fusion is larger than either of the two precursors that fuse. Although the areas are not additive, these plots do provide some evidence that fusion does act to form larger ribbons. To accompany these plots, we have added the following text to the results:

      “Although we could not accurately measure the areas of precursors before and after fusion, we observed that the relative area resulting from the fusion of two smaller precursors was greater than that of either precursor alone. This increase in area suggests that precursor fusion may serve as a mechanism for generating larger ribbons (see examples: Figure 8-S1A-B).”

      Because we were unable to provide more accurate evidence of precursor fusion resulting in larger ribbons, we have removed this statement from our abstract and lessened our claims elsewhere in the manuscript.

      (10) The title in Figure 8 is a bit confusing. If fusion events reflect ribbon precursors fusion, it is obvious it depends on ribbon precursors. I'd like to replace this title with something like "microtubules and kif1aa are required for fusion events"

      We have changed the figure title as suggested, good idea.

      Reviewer #2 (Recommendations For The Authors):

      (1) Figure 1C. The purple/magenta colors are hard to distinguish.

      We have made the magenta color much lighter in the Figure 1C to make it easier to distinguish purple and magenta.

      (2) There are places where some words are unnecessarily hyphenated. Examples: live-imaging and hair-cell in the abstract, time-course in the results.

      In our revision, we have done our best to remove unnecessary hyphens, including the ones pointed out here.

      (3) Figure 4H and elsewhere - what is "area of Ribeye puncta?" Related, I think, in the Discussion the authors refer to "ribbon volume" on line 484. But they never measured ribbon volume so this needs to be clarified.

      We have done best to clarify what is meant by area of Ribeye puncta in the results and the methods:

      Results:

      “We also observed that the average of individual Ribeyeb puncta (from 2D max-projected images) was significantly reduced compared to controls (Figure 4H). Further, the relative frequency of individual Ribeyeb puncta with smaller areas was higher in nocodazole treated hair cells compared to controls (Figure 4I).”

      Methods:

      “To quantify the area of each ribbon and precursor, images were processed in a FIJI ‘IJMacro_AIRYSCAN_simple3dSeg_ribbons only.ijm’ as previously described (Wong et al., 2019). Here each Airyscan z-stack was max-projected. A threshold was applied to each image, followed by segmentation to delineate individual Ribeyeb/CTBP puncta. The watershed function was used to separate adjacent puncta. A list of 2D objects of individual ROIs (minimum size filter of 0.002 μm2) was created to measure the 2D areas of each Ribeyeb/CTBP puncta.”

      We did refer to ribbon volume once in the discussion, but volume is not reflected in our analyses, so we have removed this mention of volume.

      (4) More validation data showing gene/protein removal for the crispants would be helpful.

      Great suggestion. As this is a relatively new method, we have created a figure that outlines how we genotype each individual crispant animal analyzed in our study Figure 6-S1. In the methods we have also added the following information:

      “fPCR fragments were run on a genetic analyzer (Applied Biosystems, 3500XL) using LIZ500 (Applied Biosystems, 4322682) as a dye standard. Analysis of this fPCR revealed an average peak height of 4740 a.u. in wild type, and an average peak height of 126 a.u. in kif1aa F0 crispants (Figure 6-S1). Any kif1aa F0 crispant without robust genomic cutting or a peak height > 500 a.u. was not included in our analyses.”

      Reviewer #3 (Recommendations For The Authors):

      Lines 208-209--should refer to the movie in the text.

      Movie S1 is now referenced here.

      It would be helpful if the authors could analyze and quantify the effect of nocodozole and taxol on microtubules (movie 7).

      See responses above to Reviewer #1’s similar request.

      Figure 7 caption says "500 mM" nocodozole.

      Thank you, we have changed the caption to 500 nM.

      One problem with the MSD analysis is that it is dependent upon fits of individual tracks that lead to inaccuracies in assigning diffusive, restricted, and directed motion. The authors might be able to get around these problems by looking at the ensemble averages of all the tracks and seeing how they change with the various treatments. Even if the effect is on a subset of ribeye spots, it would be reassuring to see significant effects that did not rely upon fitting.

      We are hesitant to average the MSD tracks as not all tracks have the same number of time steps (ribbon moving in and out of the z-stack during the timelapse). This makes it challenging for us to look at the ensembles of all averages accurately, especially for the duration of the timelapse. This is the main reason why added another analysis, displacements > 1µm as another readout of directional motion, a measure that does not rely upon fitting.

      The abstract states that directed movement is toward the synapse. The only real evidence for this is a statement in the results: "Of the tracks that showed directional motion, while the majority move to the cell base, we found that 21.2 % of ribbon tracks moved apically." A clearer demonstration of this would be to do the analysis of Figure 2G for the ribeye aggregates.

      If was not possible to do the same analysis to ribbon tracks that we did for the EB3-GFP analysis in Figure 2. In Figure 2 we did a 2D tracking analysis and measured the relative angles in 2D. In contrast, the ribbon tracking was done in 3D in Imaris not possible to get angles in the same way. Further the MSD analysis was outside of Imaris, making it extremely difficult to link ribbon trajectories to the 3D cellular landscape in Imaris. Instead, we examined the direction of the 3D vectors in Imaris with tracks > 1µm and determined the direction of the motion (apical, basal or undetermined). For clarity, this data is now included as a bar graph in Figure 3L. In our results, we have clarified the results of this analysis:

      “To provide a more comprehensive analysis of precursor movement, we also examined displacement distance (Figure 3J). Here, as an additional measure of directed motion, we calculated the percent of tracks with a cumulative displacement > 1 µm. We found 35.6 % of tracks had a displacement > 1 µm (Figure 3K; n = 10 neuromasts, 40 hair cells and 203 tracks). Of the tracks with displacement > 1 µm, the majority of ribbon tracks (45.8 %) moved to the cell base, but we also found a subset of ribbon tracks (20.8 %) that moved apically (33.4 % moved in an undetermined direction) (Figure 3L).”

      Some more detail about the F0 crispants should be provided. In particular, what degree of cutting was observed and what was the criteria for robust cutting?

      See our response to Reviewer 2 and the newly created Figure 6-S1.

    1. Author Response

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public Review):

      Several concerns are raised from the current study.

      1) Previous studies showed that iTregs generated in vitro from culturing naïve T cells with TGF-b are intrinsically unstable and prone to losing Foxp3 expression due to lack of DNA demethylation in the enhancer region of the Foxp3 locus (Polansky JK et al, Eur J Immunol., 2008, PMID: 18493985). It is known that removing TGF-b from the culture media leads to rapid loss of Foxp3 expression. In the current study, TGF-b was not added to the media during iTreg restimulation, therefore, the primary cause for iTreg instability should be the lack of the positive signal provided by TGF-b. NFAT signal is secondary at best in this culturing condition.

      In restimulation, void of TGFb is necessary to cause iTreg instability. Otherwise, the setup is similar to the iTreg-inducing environment (Author response image 1). On the other hand, the ultimate goal of this study is to provide a scenario that bears some resemblance of clinical treatment, where TGFb may not be available. The reviewer is correct in stating that TGFb is essential for iTreg stability, we are studying the role played by NFAT in iTreg instability in vitro, and possibly in potential clinical use of iTreg .

      Author response image 1.

      Restimulation with TGFb will persist iTreg inducing environment, resulting in less pronounced instability. Sorted Foxp3-GFP+ iTregs were rested for 1d, and then rested or restimulated in the presence of TGF-β for 2 d. Percentages of Foxp3+ cells were analyzed by intracellular staining of Foxp3 after 2 d.

      2) It is not clear whether the NFAT pathway is unique in accelerating the loss of Foxp3 expression upon iTreg restimulation. It is also possible that enhancing T cell activation in general could promote iTreg instability. The authors could explore blocking T cell activation by inhibiting other critical pathways, such as NF-kb and c-Jun/c-Fos, to see if a similar effect could be achieved compared to CsA treatment.

      We thank the reviewer for this suggestion. We performed this experiment according to see extent of the role that NFAT plays, or whether other major pathways are involved. As Author response image 2 shows, solely inhibiting NFAT effectively rescued the instability of iTreg. The inhibition of NFkB (BAY 11-7082), c-Jun (SP600125), or a c-Jun/c-Fos complex (T5224) had no discernable effect, or in one case, possibly further reduction in stability. These results may indicate that NFAT plays a crucial and special role in TCR activation, which leads to iTreg instability. Other pathways, as far as how this experiment is designed, do not appear to be significantly involved.

      Author response image 2.

      Comparing effects of NFAT, NF-kB and c-Jun/c-Fos inhibitors on iTreg instability. Sorted Foxp3-GFP+ iTregs were rested for 1d, then restimulated by anti-CD3 and CD28 in the presence of listed inhibitors. Percentages of Foxp3+ cells were analyzed by intracellular staining after 2d restimulation.

      3) The authors linked chromatin accessibility and increased expression of T helper cell genes to the loss of Foxp3 expression and iTreg instability. However, it is not clear how the former can lead to the latter. It is also not clear whether NFAT binds directly to the Foxp3 locus in the restimulated iTregs and inhibits Foxp3 expression.

      T helper gene activation is likely to cause instability in iTregs by secreting more inflammatory cytokines, as shown in Figure Q9, for example, IL-21 secretion. Further investigation is needed to understand how these genes contribute to Foxp3 gene instability exactly. With our limited insight, there may be two possibilities. 1. IL-21 directly affects Foxp3 through its impact on certain inflammation-related transcription factors (TFs). 2. There could be an indirect relationship where NFAT has a greater tendency to bind to those inflammatory TFs when iTreg instability appears, promoting the upregulation of these Th genes like in activated T cells, while being less likely to bind to SMAD and Foxp3, representing a competitive behavior. We at the moment cannot comprehend the intricacies that lead to the differential effects on T helper genes and Treg related genes.

      With that said, we have previously attempted to explore the direct effect of NFAT on Foxp3 gene locus. Foxp3 transcription in iTregs primarily relies on histone modifications such as H3K4me3 (Tone et al., 2008; Lu et al., 2011) rather than DNA demethylation (Ohkura et al., 2012; Hilbrands et al., 2016). Previous studies have reported that NFAT and SMAD3 can together promote the histone acetylation of Foxp3 genes (Tone et al., 2008). In our previous set of experiments, we simultaneously obtained information of NFAT binding sites and H3K4me3. In Foxp3 locus, we observed a decreasing trend in NFAT binding to the CNS3 region of Foxp3 in restimulated iTregs compared to resting iTregs (Author response image 3). Additionally, the H3K4me3 modification in the CNS3 region of Foxp3 decreased upon iTreg restimulation, but inhibiting NFAT nuclear translocation with CsA could maintain this modification at its original level (Author response image 3).

      Author response image 3.

      The NFAT binding and histone modification on Foxp3 gene locus. Genome track visualization of NFAT binding profiles and H3K4me3 profiles in Foxp3 CNS3 locus in two batches of dataset.

      Based on these preliminary explorations, it is concluded that NFAT can directly bind to the Foxp3 locus, and it appears that NFAT decreases upon restimulation, resulting in a decrease in H3K4me3, ultimately leading to the close association of NFAT and Foxp3 instability. However, due to limited sample replicates, these data need to be verified for more solid conclusions. We speculate that during the induction of iTregs, NFAT may recruit histone-modifying enzymes to open the Foxp3 CNS3 region, and this effect is synergistic with SMAD. When instability occurs upon restimulation, NFAT binding to Foxp3 weakens due to the absence of SMAD's assistance, subsequently reducing the recruitment of histone modifications enzyme and ultimately inhibiting Foxp3 transcription.

      Reviewer #2 (Public Review):

      (1) Some concerns about data processing and statistic analysis.

      The authors did not provide sufficient information on statistical data analysis; e.g. lack of detailed descriptions about

      -the precise numbers of technical/biological replicates of each experiment

      -the method of how the authors analyze data of multiple comparisons... Student t-test alone is generally insufficient to compare multiple groups; e.g. figure 1.

      These inappropriate data handlings are ruining the evidence level of the precious findings.

      We thank the reviewer for pointing out this important aspect. In the figure legend, numbers of independently-performed experiment repeats are shown as N, biological replicates of each experiment as n. Student’s t test was used for comparing statistical significance between two groups. In this manuscript, all calculations of significant differences were based on comparisons between two groups. There were no multiple conditions compared simultaneously within a single group, and thus, no other calculation methods were used.

      (2) Untransparent data production; e.g. the method of Motif enrichment analysis was not provided. Thus, we should wait for the author's correction to fully evaluate the significance and reliability of the present study.

      Per this reviewer’s request, we have provided detailed descriptions of the data analysis for Fig 5, including both the method section and the Figure legend, as presented below:

      “The peaks annotations were performed with the “annotatePeak” function in the R package ChIPseeker (Yu et al, 2015).

      The plot of Cut&Tag signals over a set of genomic regions were calculated by using “computeMatrix” function in deepTools and plotted by using “plotHeatmap” and “plotProfile” functions in deepTools. The motif enrichment analysis was performed by using the "findMotifsGenome.pl" command in HOMER with default parameters.

      The motif occurrences in each peak were identified by using FIMO (MEME suite v5.0.4) with the following settings: a first-order Markov background model, a P value cutoff of 10-4, and PWMs from the mouse HOCOMOCO motif database (v11).”

      Additionally, we have also supplemented the method section with further details on the analysis of RNA-seq and ATAC-seq data.

      (3) Lack of evidence in human cells. I wonder whether human PBMC-derived iTreg cells are similarly regulated.

      This is a rather complicated issue, human T cells express FoxP3 upon TCR stimulation (PNAS, 103(17): 6659–6664), whose function is likely to protect T cells from activation induced cell death, and does not offer Treg like properties. In contrast in mice, FoxP3 can be used as an indicator of Treg. Currently, this is not a definitive marker for Treg in human, our FoxP3 based readouts do not apply. Nevertheless, we have now investigated whether inhibiting calcium signaling or NFAT could enhance the stability of human iTreg. As shown in Author response image 4, we found that the proportion of Foxp3-expressing cells did not show significant changes across the different conditions, while the MFI analysis revealed that CsA-treated iTreg exhibited higher Foxp3 expression levels compared to both restimulated iTreg and rest iTreg. However, CM4620 had no significant effect on Foxp3 stability, consistent with the observation of its limited efficacy in suppressing human iTreg long term activation. In summary, our results suggest that inhibiting NFAT signaling through CsA treatment can help maintain higher levels of Foxp3 expression in human iTreg.

      Author response image 4.

      Effect of inhibiting NFAT and calcium on human iTreg stability. Human naïve CD4 cells from PBMC were subjected to a two-week induction process to generate human iTreg. Subsequently, human iTreg were restimulated for 2 days with dynabeads followed by 2 days of rest in the prescence of CsA and CM-4620. Four days later, percentages of Foxp3+ cells and Foxp3 mean fluorescence intensity (MFI) were analyzed by intracellular staining.

      (4) NFAT regulation did not explain all of the differences between iTregs and nTregs, as the authors mentioned as a limitation. Also, it is still an open question whether NFAT can directly modulate the chromatin configuration on the effector-type gene loci, or whether NFAT exploits pre-existing open chromatin due to the incomplete conversion of Treg-type chromatin landscape in iTreg cells. The authors did not fully demonstrate that the distinct pattern of chromatin regional accessibility found in iTreg cells is the direct cause of an effector-type gene expression.

      To our surprise, the inhibition of NFkB (BAY 11-7082), c-Jun (SP600125), and the c-Jun/c-Fos complex (T5224) resulted in minimal alterations, as shown in Fig Q1. This seems to argue that NFAT may play a more special role in events leading iTreg instability.

      We hypothesize that NFAT takes advantage of pre-existing open chromatin state due to the incomplete conversion of chromatin landscape in iTreg cells. Because iTreg cells, after induction, already exhibit inherent chromatin instability, with highly-open inflammatory genes. Furthermore, when iTreg cells were restimulated, the subsequent change in chromatin accessibility was relatively limited and not rescued by NFAT inhibitor treatment (Author response image 5). Therefore, in the case of iTreg cells, we propose that NFAT exploits the easy access of those inflammatory genes, leading to rapid destabilization of iTreg cells in the short term.

      In contrast, tTreg cells possess a relatively stable chromatin structure in the beginning, it would be interesting to investigate whether NFAT or calcium signaling could disrupt chromatin accessibility during the activation or expansion of tTreg cells. It is possible that NFAT might cause the loss of the originally established demethylation map and open up inflammatory loci, thereby inducing a shift in gene transcriptional profiles, equally leading to instability.

      Author response image 5.

      Chromatin accessibility of Rest, Retimulated, CsA/ORAIinh treated restimulated iTreg. PCA visualization of chromatin accessibility profiles of different cell types. Color indicates cell type.

      To establish a direct relationship between gene locus accessibility and its overexpression, a controlled experimental approach can be employed. One such method involves precise manipulation of the accessibility of a specific genomic locus using CRISPR-mediated epigenetic modifications at targeted loci. Subsequently, the impact of this manipulation on the expression level of the target gene can be precisely examined. By conducting these experiments, it will be possible to determine whether the augmented gene accessibility directly causes the observed gene overexpression.

      Reviewer #1 (Recommendations For The Authors):

      1) It might be helpful to add TGF-b to the iTreg restimulation culture to remove the influence of the lack of TGF-b from the equation, and measure the influence of SOCE/NFAT on iTreg instability.

      Please refer to Author response image 1.

      2) Alternatively, authors can also culture iTreg cells with TGF-b for 2 weeks when they undergo epigenetic changes and become more stabilized (Polansky JK et al, Eur J Immunol., 2008, PMID: 18493985). At this point, the stabilized iTregs can be used to measure the influence of SOCE/NFAT on iTreg instability.

      In the study conducted by Polansky, it was observed in Figure 1 that prolonged exposure to TGF-β fails to induce stable Foxp3 expression and demethylation of the Treg-specific demethylated region (TSDR). Based on this finding, we could consider exploring alternative approaches to obtain a more stabilized iTreg population. One such approach could be isolating Foxp3+helios-Nrp1- iTreg cells directly from the peripheral in vivo, which are also known as pTregs. Generally, pTreg cells generated in vivo tend to be more stable compared to iTreg cells induced in vitro, and they already exhibit partial demethylation of the Treg signature, as shown in Fig 6C (Polansky JK et al, Eur J Immunol., 2008, PMID: 18493985). Investigating the role of NFAT and calcium signaling in pTreg cells would provide further insights into the additional roles of NFAT in Treg phenotypical transitions, particularly its role in chromatin accessibility.

      3) In Figure 3, NFAT binding to the inflammatory genes in iTreg cells was even stronger than in activated T conventional cells. This is possibly due to Tconv cells being stimulated only once while iTregs were restimulated. A fair comparison should be conducted with restimulated activated conventional T cells.

      Figure 3 demonstrates the accessibility of inflammatory gene loci, rather than NFAT binding. Comparing restimulated Tconvs with restimulated iTreg cells is indeed a valuable suggestion, as their activation state and polarization in iTreg directions could lead to distinct chromatin accessibility. Although one is activated long term regularly and the other is activated long term under iTreg polarization, it is highly likely that the chromatin state of both activated Tconvs and iTreg cells is highly open, especially in terms of the accessibility of inflammatory genes. This may provide us with a new perspective to understand iTreg cells, but will unlikely affect our central conclusion.

      4) In the in vivo experiment in Figure 6, a control condition without OVA immunization should be included as a baseline.

      We have performed this experiment in the absence of OVA, as depicted in Author response image 6. In the absence of OVA immunization, both WT-ORAI and DN-ORAI iTreg exhibited substantial stability, although DN-ORAI demonstrated a slightly less stable trend. Upon activation with 40ug and 100ug of OVA, DN-ORAI iTreg demonstrated enhanced stability than WT-ORAI iTreg, maintaining a higher proportion of Foxp3 expression.

      Author response image 6.

      Stability of DN-ORAI iTreg in vivo with or without OVA immunization. WT-ORAI/DN-ORAI-GFP+-transfected CD45.2+ Foxp3-RFP+ OT-II iTregs were transferred i.v. into CD45.1 mice. Recipients were left or immunized with OVA323-339 in Alum adjuvant. On day 5, mLN were harvested and analyzed for Foxp3 expression by intracellular staining.

      Reviewer #2 (Recommendations For The Authors):

      Major

      Some concerns about the data processing and statistic analysis, as mentioned in the public review. In the figure legend, what does it mean e.g. n=3, N=3? Technical triplicate experiments? Three mice? Independently-performed three experiments? The authors should define it at least in the "Statistical analysis" in the method section otherwise the readers cannot determine the reason why they mainly use SEM for the data description.

      Moreover, in some cases, the number of experiments was not sure; e.g., Fig.1B, Fig. 5.

      How did the authors analyze data including multiple comparisons? Student t-test alone is generally insufficient to compare multiple groups; e.g. figure 1.

      We thank the reviewer for pointing out this omission. Now, in the figure legend, numbers of independently-performed experiment repeats are shown as N, biological replicates of each experiment as n. For Fig. 1B, N=2, and for Fig 5, we have acquired NFAT Cut&Tag data for 2 times, N=2. Student’s t test was used for comparing statistical significance between two groups. In this manuscript, all calculations of significant differences were based on comparisons between two groups. There were no multiple conditions compared simultaneously within a single group, and thus, no other calculation methods were involved apart from the Student's t-test.

      In Figure 1A, the difference in suppressiveness seemed subtle. Data collection of multiple doses of Tconv:Treg ratio will enhance the reliability of such kind of analysis.

      We have now attempted the suppression assay with varying Treg:Tconv ratios and observed that the suppressive effect of iTreg was more obvious than that of tTreg when co-cultured at a 1:1 ratio with Tconv cells. However, as the cell number of tTreg and iTreg decreased, the inhibitory effects converged.

      Author response image 7.

      Compare multiple dose of Tconv:Treg ratio in suppression function CFSE-labelled OT-II T cells were stimulated with OVA-pulsed DC, then different number of Foxp3-GFP+ iTregs and tTregs were added to the culture to suppress the OT-II proliferation. After 4 days, CFSE dilution were analyzed. Left, Representative histograms of CFSE in divided Tconvs. Right, graph for the percentage of divided Tconvs.

      In Figure 3F, to which group did the shaded peaks belong? In this context, the authors should focus on "Activation Region" peaks (open chromatin signature in both TcAct & iTreg defined in Fig. 4D) but I did not find the peak in the focusing DNA regions in TcAct (e.g. the shaded regions in IL-4 loci). The clear attribution of the peaks to the heatmap will enhance the visibility and understanding of readers.

      We have selected some typical peaks that belong to Fig 3D. These genes encompass some T-cell activation-associated transcription factors, such as Irf4, Atf3, as well as multiple members of the Tnf family including Lta, Tnfsf4, Tnfsf8, and Tnfsf14. Additionally, genes related to inflammation such as Il12rb2, Il9, and Gzmc are included. These genes show elevated accessibility upon T-cell activation, partially open in activated nTreg cells, referred to as the "Activation Region." They collectively exhibit high accessibility in iTreg cells, which may contribute to their instability.

      Author response image 8.

      Chromatin accessibility of some “Activation Region”. Genomic track showing chromatin accessibility of Irf4, Atf3, Lta, Tnfsf8, Tnfsf4, Tnsfsf14, Il12rb2, Il9, Gzmc in activated Tconv and iTreg.

      In Figure 4A/S4A, the information on cell death will help the understanding of readers because the sustained SOCE is associated with cell survival as shown in Fig. S2. The authors can discuss the relationships between cell death and Foxp3 retention, which potentially leads to a further interesting question; e.g. the selective/resistance to activation-induced cell death as the identity of Treg cells.

      As shown in Author response image 9, activated iTreg cells indeed exhibit a certain degree of cell death compared to resting iTreg cells. The inhibition of NFAT by CsA enhances the survival rate of iTreg cells, but the inhibition of ORAI by CM-4620 leads to more severe cell death. The cell death induced by CsA and CM-4620 is not consistent, indicating that there may not be a direct proportional relationship between cell death and the expression of Foxp3 and Treg identity.

      Author response image 9.

      Relationship of cell death and Foxp3 stability in restimulated iTregs. Sorted Foxp3-GFP+ iTregs were rested for 1d, then restimulated by anti-CD3 and CD28 in the presence of CsA or CM-4620. After 2d restimulation, live cell percentage were analyzed by staining of Live/Dead fixable Aqua, and percentages of Foxp3+ cells were analyzed by intracellular staining of Foxp3. Upper, live cell percentage of iTregs. Lower, percentages of Foxp3 in iTregs.

      In Figure 5, the information for the data interpretation was insufficient.

      We have provided detailed descriptions of the data analysis for Fig 5, including both the method section and the Figure legend, as presented below:

      “The peaks annotations were performed with the “annotatePeak” function in the R package ChIPseeker (Yu et al, 2015). The plot of Cut&Tag signals over a set of genomic regions were calculated by using “computeMatrix” function in deepTools and plotted by using “plotHeatmap” and “plotProfile” functions in deepTools. The motif enrichment analysis was performed by using the "findMotifsGenome.pl" command in HOMER with default parameters. The motif occurrences in each peak were identified by using FIMO (MEME suite v5.0.4) with the following settings: a first-order Markov background model, a P value cutoff of 10-4, and PWMs from the mouse HOCOMOCO motif database (v11).”

      Additionally, we have also supplemented the method section with further details on the analysis of RNA-seq and ATAC-seq data.

      The correlation between the open chromatin status of the gene loci described in Fig.5E and the expression at mRNA level? e.g.; Do iTreg-Act cells produce a higher level of IL-21 than nTreg-act? The analysis in Fig.5F-G should be performed in parallel with nTreg cells to emphasize the distinct NFAT-chromatin regulation in iTreg cells.

      We have now compared the secretion levels of IL-21 in tTreg and iTreg upon activation and treated with CsA by ELISA. As shown in Author response image 10, tTreg did not secrete IL-21 regardless of activation status (undetectable), while iTreg did not secrete IL-21 at resting state but exhibited IL-21 secretion after 48 h of activation. Moreover, the secretion of IL-21 was inhibited by CsA and CM-4620 treatment. This observation aligns with our earlier findings where we observed nuclear binding of NFAT to gene loci of these cytokines, enhancing their expression and pushing iTreg unstable under inflammatory conditions. These findings further underscore the likelihood that the inhibition of calcium and NFAT signaling might contribute to the stabilization of iTreg by suppressing the secretion of inflammatory cytokines.

      Author response image 10.

      IL-21 secretion in tTreg and iTreg upon activation. iTregs and tTregs were sorted and restimulated with anti-CD3 and anti-CD28 antibodies, in the presence of CsA and CM-4620. Cell culture supernatant were harvested after 2 d restimulation and IL-21 secretion was analyzed by ELISA.

      Performing a parallel comparison of NFAT activity between tTreg and iTreg cells was initially part of our experimental plan. However, it proved challenging in practice, as we encountered difficulties in efficiently infecting tTreg cells with NFAT-flag. Consequently, we could not obtain a sufficient number of tTreg cells for conducting Cut&Tag experiments.

      Based on our observations, we speculate that there might be substantial differences in the accessibility of genes in tTreg cells, leading to considerable variations in the repertoire of genes available for NFAT to regulate. As a result, we expect significant differences in the nuclear localization and activity of NFAT between iTreg and tTreg cells.

      In Figure 6C, what does the FCM plot between Foxp3-CFSE look like?

      The authors can discuss the mechanism of ORAI-DN-mediated through such analysis; e.g. the possibility that selective proliferation defect by ORAI-DN in Foxp3- cells led to an increased percentage of Foxp3, not only just unstable transcription of Foxp3.

      This is an in vitro experiment to assess the suppressive effect of iTreg on Tconv proliferation. Therefore, CFSE is used to stain Tconv cells, but not iTreg cells, so we did not detect proliferation feature of iTreg.

      Minor

      Confusing terminology of "tTreg" at line 47, etc. "natural Treg" contains both thymic-derived Treg and periphery-derived Treg cells. (A Abbas et al. Nat Immunol. 2013)

      We have now changed the designation to tTreg at line 47. tTreg refers to thymus-derived regulatory T cells, while nTreg includes both tTreg and pTreg. However, it is important to note that the Treg cells used in our study were isolated from the spleen of 2-4-month-old Foxp3-GFP or Foxp3-RFP mice. The CD4+ T cells were first enriched using the CD4 Isolation kit, and the FACSAriaII was utilized to collect CD4+ Foxp3-GFP/RFP+ Treg cells. Subsequently, Helios and Nrp-1 staining revealed that the majority of these cells were nTreg, with only approximately 6% being pTreg. Overall, we consider the cells we used as tTreg.

      In all FCM analyses, the authors should clarify how to detect Foxp3 expression; Foxp3-GFP/Foxp3-RFP/Intracellular staining like Figure S5A (but not specified in the other FCM plots)

      All Foxp3 expressions in the article were assessed using intracellular staining, as described in the methods section, and we have added specific descriptions to each figure legend. The reason for employing intracellular staining is that we used Foxp3-IRES-GFP mice, where GFP and Foxp3 are not fused into a single protein, existing as separate proteins after expression. Therefore, during induction, the appearance of GFP protein might potentially represent the presence of Foxp3. However, in cases of Foxp3 instability, the degradation of GFP protein may not be entirely synchronized with that of Foxp3 protein, making GFP an unreliable indicator of Foxp3 expression levels. As a result, for the purification of pure iTreg cells, we used Foxp3-GFP/RFP fluorescence, while for observing instability, we employed intranuclear staining of Foxp3.

      In Figure 6B, the captions were lacking in the two graphs on the right side

      The two restimulation conditions, 0.125+0.25 and 0.25+0.5, have been added into Fig 6B right side.

      In Figure S2, the annotation of the x-y axis was missing.

      Added.

      Lack of reference at line 292.

      Reference 42-46 were added.

      In the method section, the authors should note the further product information of antibodies and reagents to enhance reproducibility and transparency. Making a list that clarifies the suppliers, Ab clone, product IDs, etc. is encouraged. The authors did not specify the supplier of recombinant proteins and which type of TGF-beta (TGF-beta 1, 2, or 3?).

      A detailed description of the mice, antibodies, Peptide recombinant protein, commercial kit, and software has been provided and incorporated into the methods section.

      In the method section, the authors should clarify which Foxp3-reporter strain. There are many strains of Foxp3-reporter mice in the world. In line 373, is the "FoxP3-IRES-GFP transgenic mice" true? Knock-in strain or BAC-transgene?

      This mouse is a gift from Hai Qi Lab in Tsinghua University. They acquired this mouse strain from Jackson Laboratory, and the strain name is B6.Cg-Foxp3tm2Tch/J, Strain #:006772. An IRES-EGFP-SV40 poly A sequence was inserted immediately downstream of the endogenous Foxp3 translational stop codon, but upstream of the endogenous polyA signal, generating a bicistronic locus encoding both Foxp3 and EGFP.

      The age of mice used in the experiments should be specified, and confusing words such as "young" should not be used in any method descriptions; e.g. line 405.

      The detailed mouse age has been added in the methods section. “To prepare Tconv, tTreg and iTreg for experiments, spleen was isolated from 2-4-month-old Foxp3-GFP mice for Tconv and tTreg sorting, and 6-week-old mice for iTreg induction.”

      The method of how the original ATAC-seq/Cut & Tag data were generated was not described in the method section.

      Added in method section.

      The reference section was incomplete, and the style was not unified. e.g.; ref 7, 24, 25, 26 ... I gave up checking all.

      The style of ref 7, 22, 24, 26, 28, 31, 33, 35 were modified.

      Changes in manuscript:

      Author Name: “Huiyun Lv” to “Huiyun Lyu”.

      Fig 1A was updated according to Reviwer 2’s suggestion.

      Fig S3E and associated description was added according to Reviwer 2’s suggestion.

      Fig S4C and associated description was added according to Reviwer 1’s suggestion.

      Fig 5H and associated description was added according to Reviwer 2’s suggestion.

      Fig 6D were updated according to Reviwer 1’s suggestion.

      Fig 2D was corrected, the labels for gapdh and actin in the iTreg panel were inadvertently switched. The mistake has been rectified, and the original gel image will be provided.

      Fig 2A and Fig 4A was updated.

      The style of Fig 6B and Fig S2A was modified.

      Method:

      Mice: FoxP3-IRES-GFP with more description.

      Flow Cytometry sorting and FACS: the detailed mouse age has been added. RNA-seq analysis, ATAC-sequencing, ATAC-seq analysis, Cut&Tag assay, Cut&Tag data analysis: more description was added.

      Statistical analysis: “Numbers of independently-performed experiment repeats are shown as N, biological replicates of each experiment as n.” were added.

      Reference: Ref 42-46 and 49-52 were added. The style of ref 7, 22, 24, 26, 28, 31, 33, 35 were corrected.

      A detailed description of the mice, antibodies, Peptide recombinant protein, commercial kit, and software has been provided.

    1. Author Response

      Reviewer #1 (Public Review):

      [...] Genes expressed in the same direction in lowland individuals facing hypoxia (the plastic state) as what is found in the colonised state are defined as adaptative, while genes with the opposite expression pattern were labelled as maladaptive, using the assumption that the colonised state must represent the result of natural selection. Furthermore, genes could be classified as representing reversion plasticity when the expression pattern differed between the plasticity and colonised states and as reinforcement when they were in the same direction (for example more expressed in the plastic state and the colonised state than in the ancestral state). They found that more genes had a plastic expression pattern that was labelled as maladaptive than adaptive. Therefore, some of the genes have an expression pattern in accordance with what would be predicted based on the plasticity-first hypothesis, while others do not.

      Thank you for a precise summary of our work. We appreciate the very encouraging comments recognizing the value of our work. We have addressed concerns from the reviewer in greater detail below.

      Q1. As pointed out by the authors themselves, the fact that temperature was not included as a variable, which would make the experimental design much more complex, misses the opportunity to more accurately reflect the environmental conditions that the colonizer individuals face at high altitude. Also pointed out by the authors, the acclimation experiment in hypoxia lasted 4 weeks. It is possible that longer term effects would be identifiable in gene expression in the lowland individuals facing hypoxia on a longer time scale. Furthermore, a sample size of 3 or 4 individuals per group depending on the tissue for wild individuals may miss some of the natural variation present in these populations. Stating that they have a n=7 for the plastic stage and n= 14 for the ancestral and colonized stages refers to the total number of tissue samples and not the number of individuals, according to supplementary table 1.

      We shared the same concerns as the reviewer. This is partly because it is quite challenging to bring wild birds into captivity to conduct the hypoxia acclimation experiments. We had to work hard to perform acclimation experiments by taking lowland sparrows in a hypoxic condition for a month. We indeed have recognized the similar set of limitations as the review pointed out and have discussed the limitations in the study, i.e., considering hypoxic condition alone, short time acclimation period, etc. Regarding sample sizes, we have collected cardiac muscle from nine individuals (three individuals for each stage) and flight muscle from 12 individuals (four individuals for each stage). We have clarified this in Supplementary Table 1.

      Q2. Finally, I could not find a statement indicating that the lowland individuals placed in hypoxia (plastic stage) were from the same population as the lowland individuals for which transcriptomic data was already available, used as the "ancestral state" group (which themselves seem to come from 3 populations Qinghuangdao, Beijing, and Tianjin, according to supplementary table 2) nor if they were sampled in the same time of year (pre reproduction, during breeding, after, or if they were juveniles, proportion of males or females, etc). These two aspects could affect both gene expression (through neutral or adaptive genetic variation among lowland populations that can affect gene expression, or environmental effects other than hypoxia that differ in these populations' environments or because of their sexes or age). This could potentially also affect the FST analysis done by the authors, which they use to claim that strong selective pressure acted on the expression level of some of the genes in the colonised group.

      The reviewer asked how individual tree sparrows used in the transcriptomic analyses were collected. The individuals used for the hypoxia acclimation experiment and represented the ancestral lowland population were collected from the same locality (Beijing) and at the same season (i.e., pre-breeding) of the year. They are all adults and weight approximately 18g. We have clarified this in the Supplementary Table S1 and Methods. We did not distinguish males from females (both sexes look similar) under the assumption that both sexes respond similarly to hypoxia acclimation in their cardiac and flight muscle gene expression.

      The Supplementary Table 2 lists the individuals that were used for sequence analyses. These individuals were only used for sequence comparisons but not for the transcriptomic analyses. The population genetic structure analyzed in a previously published study showed that there is no clear genetic divergence within the lowland population (i.e., individuals collected from Beijing, Tianjing and Qinhuangdao) or the highland population (i.e., Gangcha and Qinghai Lake). In addition, there was no clear genetic divergence between the highland and lowland populations (Qu et al. 2020).

      Author response image 1.

      Population genetic structure of the Eurasian Tree Sparrow (Passer montanus). The genetic structure generated using FRAPPE. The colors in each column represent the contribution from each subcluster (Qu et al. 2020). Yellow, highland population; blue, lowland population.

      Q4. Impact of the work There has been work showing that populations adapted to high altitude environments show changes in their hypoxia response that differs from the short-term acclimation response of lowland population of the same species. For example, in humans, see Erzurum et al. 2007 and Peng et al. 2017, where they show that the hypoxia response cascade, which starts with the gene HIF (Hypoxia-Inducible Factor) and includes the EPO gene, which codes for erythropoietin, which in turns activates the production of red blood cell, is LESS activated in high altitude individuals compared to the activation level in lowland individuals (which gives it its name). The present work adds to this body of knowledge showing that the short-term response to hypoxia and the long term one can affect different pathways and that acclimation/plasticity does not always predict what physiological traits will evolve in populations that colonize these environments over many generations and additional selection pressure (UV exposure, temperature, nutrient availability). Altogether, this work provides new information on the evolution of reaction norms of genes associated with the physiological response to one of the main environmental variables that affects almost all animals, oxygen availability. It also provides an interesting model system to study this type of question further in a natural population of homeotherms.

      Erzurum, S. C., S. Ghosh, A. J. Janocha, W. Xu, S. Bauer, N. S. Bryan, J. Tejero et al. "Higher blood flow and circulating NO products offset high-altitude hypoxia among Tibetans." Proceedings of the National Academy of Sciences 104, no. 45 (2007): 17593-17598. Peng, Y., C. Cui, Y. He, Ouzhuluobu, H. Zhang, D. Yang, Q. Zhang, Bianbazhuoma, L. Yang, Y. He, et al. 2017. Down-regulation of EPAS1 transcription and genetic adaptation of Tibetans to high-altitude hypoxia. Molecular biology and evolution 34:818-830.

      Thank you for highlighting the potential novelty of our work in light of the big field. We found it very interesting to discuss our results (from a bird species) together with similar findings from humans. In the revised version of manuscript, we have discussed short-term acclimation response and long-term adaptive evolution to a high-elevation environment, as well as how our work provides understanding of the relative roles of short-term plasticity and long-term adaptation. We appreciate the two important work pointed out by the reviewer and we have also cited them in the revised version of manuscript.

      Reviewer #2 (Public Review):

      This is a well-written paper using gene expression in tree sparrow as model traits to distinguish between genetic effects that either reinforce or reverse initial plastic response to environmental changes. Tree sparrow tissues (cardiac and flight muscle) collected in lowland populations subject to hypoxia treatment were profiled for gene expression and compared with previously collected data in 1) highland birds; 2) lowland birds under normal condition to test for differences in directions of changes between initial plastic response and subsequent colonized response. The question is an important and interesting one but I have several major concerns on experimental design and interpretations.

      Thank you for a precise summary of our work and constructive comments to improve this study. We have addressed your concerns in greater detail below.

      Q1. The datasets consist of two sources of data. The hypoxia treated birds collected from the current study and highland and lowland birds in their respective native environment from a previous study. This creates a complete confounding between the hypoxia treatment and experimental batches that it is impossible to draw any conclusions. The sample size is relatively small. Basically correlation among tens of thousands of genes was computed based on merely 12 or 9 samples.

      We appreciate the critical comments from the reviewer. The reviewer raised the concerns about the batch effect from birds collected from the previous study and this study. There is an important detail we didn’t describe in the previous version. All tissues from hypoxia acclimated birds and highland and lowland birds have been collected at the same time (i.e., Qu et al. 2020). RNA library construction and sequencing of these samples were also conducted at the same time, although only the transcriptomic data of lowland and highland tree sparrows were included in Qu et al. (2020). The data from acclimated birds have not been published before.

      In the revised version of manuscript, we also compared log-transformed transcript per million (TPM) across all genes and determined the most conserved genes (i.e., coefficient of variance ≤  0.3 and average TPM ≥ 1 for each sample) for the flight and cardiac muscles, respectively (Hao et al. 2023). We compared the median expression levels of these conserved genes and found no difference among the lowland, hypoxia-exposed lowland, and highland tree sparrows (Wilcoxon signed-rank test, P<0.05). As these results suggested little batch effect on the transcriptomic data, we used TPM values to calculate gene expression level and intensity. This methodological detail has been further clarified in the Methods and we also provided a new supplementary Figure (Figure S5) to show the comparative results.

      Author response image 2.

      The median expression levels of the conserved genes (i.e., coefficient of variance ≤ 0.3 and average TPM ≥ 1 for each sample) did not differ among the lowland, hypoxia-exposed lowland, and highland tree sparrows (Wilcoxon signed-rank test, P<0.05).

      The reviewer also raised the issue of sample size. We certainly would have liked to have more individuals in the study, but this was not possible due to the logistical problem of keeping wild bird in a common garden experiment for a long time. We have acknowledged this in the manuscript. In order to mitigate this we have tested the hypothesis of plasticity following by genetic change using two different tissues (cardiac and flight muscles) and two different datasets (co-expressed gene-set and muscle-associated gene-set). As all these analyses show similar results, they indicate that the main conclusion drawn from this study is robust.

      Q2. Genes are classified into two classes (reversion and reinforcement) based on arbitrarily chosen thresholds. More "reversion" genes are found and this was taken as evidence reversal is more prominent. However, a trivial explanation is that genes must be expressed within a certain range and those plastic changes simply have more space to reverse direction rather than having any biological reason to do so.

      Thank you for the critical comments. There are two questions raised we should like to address them separately. The first concern centered on the issue of arbitrarily chosen thresholds. In our manuscript, we used a range of thresholds, i.e., 50%, 100%, 150% and 200% of change in the gene expression levels of the ancestral lowland tree sparrow to detect genes with reinforcement and reversion plasticity. By this design we wanted to explore the magnitudes of gene expression plasticity (i.e., Ho & Zhang 2018), and whether strength of selection (i.e., genetic variation) changes with the magnitude of gene expression plasticity (i.e., Campbell-Staton et al. 2021).

      As the reviewer pointed out, we have now realized that this threshold selection is arbitrarily. We have thus implemented two other categorization schemes to test the robustness of the observation of unequal proportions of genes with reinforcement and reversion plasticity. Specifically, we used a parametric bootstrap procedure as described in Ho & Zhang (2019), which aimed to identify genes resulting from genuine differences rather than random sampling errors. Bootstrap results suggested that genes exhibiting reversing plasticity significantly outnumber those exhibiting reinforcing plasticity, suggesting that our inference of an excess of genes with reversion plasticity is robust to random sampling errors. We have added these analyses to the revised version of manuscript, and provided results in the Figure 2d and Figure 3d.

      Author response image 3.

      Figure 2a (left) and Figure 2b (right). Frequencies of genes with reinforcement and reversion plasticity (>50%) and their subsets that acquire strong support in the parametric bootstrap analyses (≥ 950/1000).

      In addition, we adapted a bin scheme (i.e., 20%, 40% and 60% bin settings along the spectrum of the reinforcement/reversion plasticity). These analyses based on different categorization schemes revealed similar results, and suggested that our inference of an excess of genes with reversion plasticity is robust. We have provided these results in the Supplementary Figure S2 and S4.

      Author response image 4.

      (A) and Figure S4 (B). Frequencies of genes with reinforcement and reversion plasticity in the flight and cardiac muscle. (A) For genes identified by WGCNA, all comparisons show that there are more genes showing reversion plasticity than those showing reinforcement plasticity for both the flight and cardiac msucles. (B) For genes that associated with muscle phentoypes, all comparisons show that there are more genes showing reversion plasticity than those showing reinforcement plasticity for the flight muscle, while more than 50% of comparisons support an excess of genes with reversion plasticity for the cardiac muscle. Two-tailed binomial test, NS, non-significant; , P < 0.05; , P < 0.01; **, P < 0.001.

      The second issue that the reviewer raised is that the plastic changes simply have more space to reverse direction rather than having any biological reason to do so. While a causal reason why there are more genes with expression levels being reversed than those with expression levels being reinforced at the late stages is still contentious, increasingly many studies show that genes expression plasticity at the early stage may be functionally maladapted to novel environment that the species have recently colonized (i.e., lizard, Campbell-Staton et al. 2021; Escherichia coli, yeast, guppies, chickens and babblers, Ho and Zhang 2018; Ho et al. 2020; Kuo et al. 2023). Our comparisons based on the two genesets that are associated with muscle phenotypes corroborated with these previous studies and showed that initial gene expression plasticity may be nonadaptive to the novel environments (i.e., Ghalambor et al. 2015; Ho & Zhang 2018; Ho et al. 2020; Kuo et al. 2023; Campbell-Staton et al. 2021).

      Q3. The correlation between plastic change and evolved divergence is an artifact due to the definitions of adaptive versus maladaptive changes. For example, the definition of adaptive changes requires that plastic change and evolved divergence are in the same direction (Figure 3a), so the positive correlation was a result of this selection (Figure 3d).

      The reviewer raised an issue that the correlation between plastic change and evolved divergence is an artifact because of the definition of adaptive versus maladaptive changes, for example, Figure 3d. We agree with the reviewer that the correlation analysis is circular because the definition of adaptive and maladaptive plasticity depends on the direction of plastic change matched or opposed that of the colonized tree sparrows. We have thus removed previous Figure 3d-e and related texts from the revised version of manuscript. Meanwhile, we have changed Figure 3a to further clarify the schematic framework.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      In this study, Kim et al. investigated the mechanism by which uremic toxin indoxyl sulfate (IS) induces trained immunity, resulting in augmented pro-inflammatory cytokine production such as TNF and IL6. The authors claim that IS treatment induced epigenetic and metabolic reprogramming, and the aryl hydrocarbon receptor (AhR)-mediated arachidonic acid pathway is required for establishing trained immunity in human monocytes. They also demonstrated that uremic sera from end-stage renal disease (ESRD) patients can generate trained immunity in healthy control-derived monocytes.

      These are interesting results that introduce the important new concept of trained immunity and its importance in showing endogenous inflammatory stimuli-induced innate immune memory. Additional evidence proposing that IS plays a critical role in the initiation of inflammatory immune responses in patients with CKD is also interesting and a potential advance of the field. This study is in large part well done, but some components of the study are still incomplete and additional efforts are required to nail down the main conclusions.

      Thank you very much for your positive feedback.

      Specific comments:

      (1) Of greatest concern, there are concerns about the rigor of these experiments, whether the interpretation and conclusions are fully supported by the data. (1) Although many experiments have been sporadically conducted in many fields such as epigenetic, metabolic regulation, and AhR signaling, the causal relationship between each mechanism is not clear. (2) Throughout the manuscript, no distinction was made between the group treated with IS for 6 days and the group treated with the second LPS (addressed below). (3) Besides experiments using non-specific inhibitors, genetic experiments including siRNA or KO mice should be examined to strengthen and justify central suggestions.

      We are grateful for the invaluable constructive feedback provided. 

      (1) In response to the reviewer's feedback, we conducted additional experiments employing appropriate inhibitors to investigate the causal relationship among the AhR pathway, epigenetic modifications, and metabolic rewiring in IS-induced trained immunity. Notably, metabolic rewiring, particularly the upregulation of aerobic glycolysis via the mTORC1 signaling pathway, stands as a pivotal mechanism underlying the induction of trained immunity through the modulation of epigenetic modifications (Riksen NP et al. Figure 1). Initially, we assessed the enrichment of H3K4me3 at 6-day on promoters of TNFA and IL6 loci after treatment of zileuton, an inhibitor of ALOX5, and 2-DG, a glycolysis inhibitor. Additionally, we evaluated the alteration in the activity of S6K, a downstream molecule of mTORC1, following zileuton treatment. Our findings indicate that AhR-dependent arachidonic acid (AA) signaling induces epigenetic modifications, albeit without inducing metabolic rewiring, in IS-induced trained immunity (Author response image 1). However, IS stimulation promotes mTORC1-mediated glycolysis in an AhR-independent manner. Notably, inhibition of glycolysis with 2-DG impacts epigenetic modifications. We have updated Figure 7 of the revised manuscript to incorporate these additional experimental findings, elucidating the correlation between the diverse mechanisms implicated in IS-induced innate immune memory (Fig. 7 in the revised manuscript). These data have been integrated into the revised manuscript as Figure 3D and 5I, and supplementary Figure 5I.

      (2) We apologize for any confusion arising from the unclear description regarding the distinction between the group treated with IS for 6 days and the group subjected to secondary lipopolysaccharide (LPS) stimulation. It is imperative to clarify that induction of trained immunity necessitates 1 day of IS stimulation followed by 5 days of rest, rendering the 6th day sample representative of a trained state. Subsequent to this, a 24-hour LPS stimulation is applied, designating the 7th day sample as a secondary LPS-stimulated cell. This clarification is now explicitly indicated throughout the entirety of Figure 1A and Figure 3A in the revised manuscript.

      (3) In accordance with your feedback, we performed siRNA knockdown of AhR and ALOX5 in primary human monocytes. AhR knockdown markedly attenuated the mRNA expression of TNF-α and IL-6, which are augmented in IS-trained macrophages. Similarly, knockdown of ALOX5 using ALOX5 siRNA abrogated the increase in TNF-α and IL-6 levels upon LPS stimulation in IS-trained macrophages (Author response image 2). Our experiments utilizing AhR siRNA corroborate the involvement of AhR in the expression of AA pathway-related molecules, such as ALOX5, ALOX5AP, and LTB4R1, in IS-induced trained immunity. These data have been incorporated into the revised manuscript as Figure 4E and 5G, and supplementary Figure 5H.  

      Author response image 1.

      Epigenetic modification is regulated by arachidonic acid (AA) pathway and metabolic rewiring, but metabolic rewiring is not affected by the AA pathway. A-B. Monocytes were pre-treated with zileuton (ZLT), an inhibitor of ALOX5, or 2DG, a glycolysis inhibitor, followed by stimulation with IS for 24 hours. After a resting period of 5 days, the enrichment of H3K4me3 on the promoters of TNFA and IL6 loci was assessed. Normalization was performed using 2% input. C. Monocytes were pre-treated with zileuton (ZLT) and stimulated with IS for 24 hr. Cell lysates were immunoblotted for phosphorylated S6 Kinase, with β-actin serving as a normalization control. Band intensities in the immunoblots were quantified using densitometry. D, A schematic representation of the mechanistic framework underlying IS-trained immunity. Bar graphs show the mean ± SEM. * = p < 0.05, **= p < 0.01, and *** = p < 0.001 by two-tailed paired t-test.

      Author response image 2.

      Inhibition of IS-trained immunity by knockdown of AhR or ALOX5 in human monocytes. A-C. Human monocytes were transfected with siRNA targeting AhR (siAhR), ALOX5 (siALOX5), or negative control (siNC) for 1 day, followed by stimulation with IS for 24 hours. After a resting period of 5 days, cells were re-stimulated with LPS for 24 hours. mRNA expression levels of AhR and ALOX5 at 1 day after transfection, and TNF-α and IL-6 at 1 day after LPS treatment, were assessed using RT-qPCR. D. Human monocytes were transfected with AhR siRNA or negative control (NC) siRNA for 1 day, followed by stimulation with IS for 24 hours. After resting for 5 days, mRNA expression levels of ALOX5, ALOX5AP, and LTB4R1 were analyzed using RT-qPCR. Bar graphs show the mean ± SEM. * = p < 0.05, ** = p < 0.01, and *** = p < 0.001 by two-tailed paired t-test.  

      (2) The authors showed that IS-trained monocytes showed no change in TNF or IL-6, but increased the expression levels of TNF and IL-6 in response to the second LPS (Fig. 1B). This suggests that the different LPS responsiveness in IS-trained monocytes caused altered gene expression of TNF and IL6. However, the authors also showed that IS-trained monocytes without LPS stimulation showed increased levels of H3K4me3 at the TNF and IL-6 loci, as well as highly elevated ECAR and OCR, leading to no changes in TNF and IL-6. Therefore, it is unclear why or how the epigenetic and metabolic states of IS-trained monocytes induce different LPS responses. For example, increased H3K4me3 in HK2 and PFKP is important for metabolic rewiring, but why increased H3K4me3 in TNF and IL6 does not affect gene expression needs to be explained.

      We acknowledge the constructive critiques provided by the reviewer. While epigenetic modifications in the promoters of TNF-α, IL-6, HK2, and PFKP (Figure 3B and Supplementary Figure 3C in the revised manuscript), and metabolic rewiring (Figure 2A-D in the revised manuscript) were observed in IS-trained macrophages at 6 days prior to LPS stimulation, these macrophages do not exhibit an increase in TNF-α and IL-6 mRNA and protein levels before LPS stimulation. This lack of response is attributed to a 5-day resting period, allowing the macrophages to revert to a non-activated state, as depicted in Author response image 3 and 4. This phenomenon aligns with the concept of typical trained immunity.

      Trained immunity is characterized by the long-term functional reprogramming of innate immune cells, which is evoked by various primary insults and which leads to an altered response towards a second challenge after the return to a non-activated state. Metabolic and epigenetic reprogramming events during the primary immune response persist partially even after the initial stimulus is removed. Upon a secondary challenge, trained innate immune cells exhibit a more robust and more prompt response than the initial response (Netea MG et al. Defining trained immunity and its role in health and disease. Nat Rev Immunol. 2020 Jun;20(6):375-388).

      Numerous studies have demonstrated the observation of epigenetic modifications in the promoters of TNF-α and IL-6, and metabolic rewiring prior to LPS stimulation as a secondary challenge. However, cytokine production is contingent on LPS stimulation (Arts RJ et al. Glutaminolysis and Fumarate Accumulation Integrate Immunometabolic and Epigenetic Programs in Trained Immunity. Cell Metab. 2016 Dec 13;24(6):807-819; Arts RJW et al. Immunometabolic Pathways in BCG-Induced Trained Immunity. Cell Rep. 2016 Dec 6;17(10):2562-2571; Ochando J et al. Trained immunity - basic concepts and contributions to immunopathology. Nat Rev Nephrol. 2023 Jan;19(1):23-37). The prolonged presence of higher levels of H3K4me3 on immune gene promoters, even after returning to baseline, is associated with open chromatin and results in a more rapid and stronger response, such as cytokine production, upon a secondary insult (Netea MG et al. Defining trained immunity and its role in health and disease. Nat Rev Immunol. 2020 Jun;20(6):375-388).

      The results in Figure 1B may be interpreted as indicating different LPS responsiveness in IStrained monocytes caused altered gene expression of TNF and IL-6. However, it is plausible that trained immune cells respond more robustly even to low concentrations of LPS. In fact, the aim of this experiment was to determine the appropriate LPS concentration.

      Author response image 3.

      The changes in mRNA and protein level of TNF-α and IL-6 during induction of IS-trained immunity. Human monocytes were treated with or without IS (1 mM) for 24 hrs, succeeded by 5-day resting period to induce trained immunity. Cells were stimulated with LPS for 24 hrs. Protein and mRNA levels were assessed by ELISA and RT-qPCR, respectively. Bar graphs show the mean ± SEM. * = p < 0.05 and **= p < 0.01, by two-tailed paired t-test.

      Author response image 4.

      The changes in mRNA of HK2 and PFKP induced by IS during induction of IS-trained immunity. Human monocytes were treated with or without IS (1 mM) for 24 hrs, succeeded by 5-day resting period to induce trained immunity. mRNA levels were assessed by RT-qPCR. Bar graphs show the mean ± SEM. * = p < 0.05 by two-tailed paired ttest.

      (3) The authors used human monocytes cultured in human serum without growth factors such as MCSF for 5-6 days. When we consider the short lifespan of monocytes (1-3 days), the authors need to explain the validity of the experimental model.

      We appreciate the reviewer’s constructive critiques. As pointed out by the reviewer, human circulating CD14+ monocytes exhibit a relatively short lifespan (1-3 days) when cultured in the absence of growth factors (Patel AA et al. The fate and lifespan of human monocyte subsets in steady state and systemic inflammation. J Exp Med. 2017 Jul 3;214(7):1913-1923). In this study, purified CD14+ monocytes were subjected to adherent culture for a duration of 7 days in RPMI1640 media supplemented with 10% human AB serum, a standard in vitro culture protocol widely employed in studies focusing on trained immunity (Domínguez-Andrés J et al. In vitro induction of trained immunity in adherent human monocytes. STAR Protoc. 2021 Feb 24;2(1):100365). In response to the reviewer's suggestions, we assessed cell viability on days 0, 1, 4, and 6, utilizing the WST assay. Despite a marginal reduction in cell viability observed at day 1, attributed to detachment from the culture plate, the cultured monocytes exhibited a notable enhancement in cell viability on days 4 and 6 when compared to days 0 or 1 (Author response image 5).

      It has been demonstrated that the adhesion of human monocytes to a cell culture dish leads to their activation and induces the synthesis of substantial amounts of IL-1β mRNA as observed in monocytes adherent to extracellular matrix components such as fibronectin and collagen.

      Morphologically, human adherent monocytes cultured with 10% human serum appear to undergo partial differentiation into macrophages by day 6, potentially explaining the observed lack of decrease in monocyte viability. Notably, Safi et al. have reported that adherent monocytes cultured with 10% human serum exhibit no significant difference in cell viability over a 7-day period when compared to cultures supplemented with growth factors such as M-CSF and IL-3 (Safi W et al. Differentiation of human CD14+ monocytes: an experimental investigation of the optimal culture medium and evidence of a lack of differentiation along the endothelial line. Exp Mol Med. 2016 Apr 15;48(4):e227).

      Author response image 5.

      Viability of human monocytes during the induction of trained immunity. Purified human monocytes were seeded on plates with RPIM1640 media supplemented with 10% human AB serum. Cell viability was assessed on days 0, 1, 4, and 6 utilizing the WST assay (Left panel). Cell morphology was examined under a light-inverted microscope at the indicated times (Right panel).

      (4) The authors' ELISA results clearly showed increased levels of TNF and IL-6 proteins, but it is well established that LPS-induced gene expression of TNF and IL-6 in monocytes peaked within 1-4 hours and returned to baseline by 24 hours. Therefore, authors need to investigate gene expression at appropriate time points.

      We appreciate the valuable constructive feedback provided by the reviewer. As indicated by the reviewer, the LPS-induced gene expression of TNF-α and IL-6 in IS-trained monocytes exhibited a peak within the initial 1 to 4 hours, followed by a decrease by the 24-hour time point, as illustrated in Author response image 6. Nevertheless, the mRNA expression levels of TNFα and IL-6 were still elevated at the 24-hour mark. Furthermore, the protein levels of both TNFα and IL-6 apparently increased 24 hours after LPS stimulation. Due to technical constraints, sample collection had to be conducted at a single time point, and the 24-hour post-stimulation interval was deemed optimal for this purpose.

      Author response image 6.

      Kinetics of protein and mRNA expression of TNF-α and IL-6 after treatment of LPS as secondary insult in IS-trained monocytes. IS-trained cells were re-stimulated by LPS (10 ng/ml) for the indicated time. The supernatant and lysates were collected for ELISA assay and RT-qPCR analysis, respectively. Bar graphs show the mean ± SEM. * = p <0.05 and **= p < 0.01, by two-tailed paired t-test.

      (5) It is a highly interesting finding that IS induces trained immunity via the AhR pathway. The authors also showed that the pretreatment of FICZ, an AhR agonist, was good enough to induce trained immunity in terms of the expression of TNF and IL-6. However, from this point of view, the authors need to discuss why trained immunity was not affected by kynurenic acid (KA), which is a well-known AhR ligand accumulated in CKD and has been reported to be involved in innate immune memory mechanisms (Fig. S1A).

      We appreciate the constructive criticism provided by the reviewer, and we comprehend the raised points. In our initial experiments, we hypothesized that kynurenic acid (KA), an aryl hydrocarbon receptor (AhR) ligand, might instigate trained immunity in monocytes, despite KA not being our primary target uremic toxin. However, our findings, as depicted in Fig. S1A, demonstrated that KA did not induce trained immunity. Notably, KA-treated monocytes exhibited induction of CYP1B1, an AhR-responsive gene, and elevated levels of TNF-α and IL-6 mRNA at 24 hours post-treatment, comparable to FICZ-treated monocytes. This observation underscores KA's role as an AhR ligand in human monocytes, as emphasized by the reviewer. 

      Of particular interest, proteins associated with the arachidonic acid pathway, such as ALOX5 and ALOX5AP - integral to the mechanisms underlying IS-induced trained immunity - did not exhibit an increase at day 6 following KA treatment, in contrast to the significant elevation observed with IS and FICZ treatments (Author response image 7). The rationale behind this disparity remains unknown, necessitating further investigation to elucidate the underlying factors. These data have been incorporated into the revised manuscript as Supplementary Figure 5C.

      Author response image 7.

      Divergent impact of AhR agonists, especially IS, FICZ, and KA on the AhR-ALOX5 pathway. Purified ytes underwent treatment with IS (1 mM), FICZ (100 nM), or KA (0.5 mM) for 1 day, followed by 5-day resting period to trained immunity. Activation of AhR through ligand binding was assessed by examining the induction of CYP1B1, an AhR ene, and cytokines one day post-treatment. The expression of genes related to the arachidonic acid pathway, such as ALOX5, 5AP, and LTB4R1, was analyzed via RT-qPCR six days after inducing trained immunity. Bar graphs show the mean ± SEM. * .05, **= p < 0.01, and ***= p < 0.001 by two-tailed paired t-test.

      Indeed, it has been demonstrated that FICZ and TCDD, two high-affinity AhR ligands, exert opposite effects on T-cell differentiation, with TCDD inducing regulatory T cells and FICZ inducing Th17 cells. This dichotomy has been attributed to ligand-intrinsic differences in AhR activation (Ho PP et al. The aryl hydrocarbon receptor: a regulator of Th17 and Treg cell development in disease. Cell Res. 2008 Jun;18(6):605-8; Ehrlich AK et al. TCDD, FICZ, and Other High Affinity AhR Ligands Dose-Dependently Determine the Fate of CD4+ T Cell Differentiation. Toxicol Sci. 2018 Feb 1;161(2):310-320). These outcomes imply the involvement of an intricate interplay involving metabolic rewiring, epigenetic reprogramming, and the AhR-ALOX5 pathway in IS-induced trained immunity within monocytes.

      (6) The authors need to clarify the role of IL-10 in IS-trained monocytes. IL-10, an anti-inflammatory cytokine that can be modulated by AhR, whose expression (Fig. 1E, Fig. 4D) may explain the inflammatory cytokine expression of IS-trained monocytes.

      We appreciate the reviewer’s valuable comment, recognizing its significant importance. IL-10, characterized by potent anti-inflammatory attributes, assumes a pivotal role in constraining the host immune response against pathogens. This function serves to mitigate potential harm to the host and uphold normal tissue homeostasis. In the context of atherosclerosis (Mallat Z et al. Protective role of interleukin-10 in atherosclerosis. Circ Res. 1999 Oct 15;85(8):e17-24.) and kidney disease (Wei W et al. The role of IL-10 in kidney disease. Int Immunopharmacol. 2022 Jul;108:108917), IL-10 exerts potent deactivating effects on macrophages and T cells, influencing various cellular processes that could impact the development and stability of atherosclerotic plaques. Additionally, it is noteworthy that IL-10-deficient macrophages exhibit an augmentation in the proinflammatory cytokine TNF-α (Smallie T et al. IL-10 inhibits transcription elongation of the human TNF gene in primary macrophages. J Exp Med. 2010 Sep 27;207(10):2081-8; Couper KN et al. IL-10: the master regulator of immunity to infection. J Immunol. 2008 May 1;180(9):5771-7). As emphasized by the reviewer, the reduced gene expression of IL-10 by IS-trained monocytes may contribute to the heightened expression of proinflammatory cytokines. We have thoroughly addressed and discussed this specific point in response to the reviewer's comment (Line 394-399 of page 18 in the revised manuscript).

      (7) The authors need to show H3K4me3 levels in TNF and IL6 genes in all conditions in one figure. (Fig. 2B). Comparing Fig. 2B and Fig. S2B, H3K4me3 does not appear to be increased at all by LPS in the IL6 region. 

      We are grateful for the constructive criticism provided by the reviewer. In response to the reviewer's comment, we endeavored to conduct an experiment demonstrating H3K4me3 enrichment on the promoters of TNF-α and IL-6 across all experimental conditions. However, due to limitations in the availability of purified human monocytes, we conducted an additional three independent experiments for ChIP-qPCR across all conditions. Despite encountering a notable variability among individuals, even within the healthy donor cohort, our results demonstrated an increase in H3K4me3 enrichment on the TNF-α and IL-6 promoters in IS-trained groups, irrespective of subsequent LPS treatment (Author response image 8).

      Author response image 8.

      Analysis of H3K4me3 enrichment on the promoters of TNFA and IL6 Loci in IS-trained macrophages. ChIP-qPCR was employed to assess the enrichment of H3K4me3 on the promoters of TNFA and IL6 loci before (day 6) and after LPS stimulation (day 7) in IS-trained macrophages. The normalization control utilized 2% input. Bar graphs show the mean ± SEM. The data presented are derived from three independent experiments utilizing samples from different donors.

      (8) The authors need to address the changes of H3K4me3 in the presence of MTA.

      We appreciate the constructive criticism provided by the reviewer. In response to the reviewer's feedback, we conducted an analysis of the changes in H3K4me3 in the presence of MTA, a general methyltransferase inhibitor, using identical conditions as depicted in Figure 2C of the original manuscript. Our findings revealed that MTA exerted inhibitory effects on the levels of H3K4me3, as isolated through the acid histone extraction method, which were otherwise increased by IS-training, as illustrated in Author response image 9. 

      Author response image 9.

      The reduction of H3K4me3 by MTA treatment in IS-trained macrophages. IS-trained cells were restimulated by LPS (10 ng/ml) as a secondary challenge for 24 hrs, followed by isolation of histone and WB analysis for H3K4me3, Histone 3 (H3), and β-actin. The blot data from two independent experiments with different donors were shown.

      (9) Interpretation of ChIP-seq results is not entirely convincing due to doubts about the quality of sequencing results. First, authors need to provide information on the quality of ChIP-seq data in reliable criteria such as Encode Pipeline. It should also provide representative tracks of H3K4me3 in the TNF and IL-6 genes (Fig. 2F). And in Fig. 2F, the author showed the H3K4me3 track of replicates, but the results between replicates were very different, so there are concerns about reproducibility. Finally, the authors need to show the correlation between ChIP-seq (Fig. 2) and RNA-seq (Fig. 5).

      We appreciate the constructive criticism provided by the reviewer. 

      As indicated by the reviewer, for evaluation of sample read quality, analysis was performed using the histone ChIP-seq standard from the ENCODE project, focusing on metrics such as read depth, PCR bottleneck coefficient (PBC)1, PBC2, and non-redundant fraction (NRF). Five of the total samples were displayed moderate bottleneck levels (0.5 ≤ PBC1 < 0.8, 1 ≤ PBC2 < 3) with acceptable (0.5 ≤ NRF < 0.8) complexity. One sample showed mild bottlenecks (0.8 ≤ PBC1 < 0.9, 3 ≤ PBC2 < 10) with compliance (0.8 ≤ NRF < 0.9) complexity. This quality metrics indicated ChIP-seq data quality meets at least the standards required for downstream analysis according to ENCODE project criteria (Author response image 10A).

      To examine the differences in H3K4me3 enrichment patterns between two groups, we normalized the read counts around the TSS ±2 kb of human genes to CPM. Sequentially, we compared the average values of IS-treated macrophage compare to control and displayed in waterfall plots. In addition, we marked genes of interest in red including the phenotypes of IStrained macrophages (TNF and IL6), the activation of the innate immune responses (XRCC5, IFI16, PQBP1), and the regulation of ornithine decarboxylase (OAZ3, PSMA3, PSMA1) (Author response image 10B and C). Also, H3K4me3 peak tracks of TNF and IL6 loci and H3K4me3 enrichment pattern were added in supplementary Figure 3D and 3F in the revised manuscript.

      Next, to evaluate the consistency among replicates within a group, we analyzed enrichment values, expressed as Counts per Million (CPM) using edgeR R-package, by applying Spearman's correlation coefficients. we analyzed two sets included total 7,136 H3K4me3 peak sets, as described in Figure 3E in the revised manuscript and 2 kbp around transcription start sites (TSS) from hg19 human genomes. The resulting Spearman's correlation coefficients and associated P-values demonstrated a concordance between replicates, confirming reproducibility and consistent performance (Author response image 10D). 

      Finally, the correlation between gene expression and H3K4me3 enrichment around transcription start sites (TSS) has been reported in previous research (Reshetnikov VV et al. Data of correlation analysis between the density of H3K4me3 in promoters of genes and gene expression: Data from RNA-seq and ChIP-seq analyses of the murine prefrontal cortex. Data Brief. 2020 Oct 2;33:106365). To verify this association in our study, we applied Spearman's correlation for comparative analysis and conducted linear regression to determine if a consistent global trend in RNA expression existed. In our analysis, count values from regions extending 2 kbp around the TSSs in H3K4me3 ChIP-seq data were converted to Counts per Million (CPM) using edgeR R-package. These were then contrasted with the Transcripts Per Million (TPM) values of genes. Our results revealed a significant positive correlation, reinforcing the consistent relationship between H3K4me3 enrichment and gene expression (Author response image 10E and Supplementary Fig. 6D in revised manuscripts).

      Author response image 10.

      The information on quality of ChIP-seq data and correlation between ChIP-seq and RNA-seq. A, information on quality of ChIP-seq data. B, H3K4me3 peak of promoter region on TNFA and IL6. C, The differences in H3K4me3 enrichment patterns between control group and IS-training group. D, The consistency among replicates within a group. E, Correlation between ChIP-seq and RNA-seq in IS-induced trained immunity.

      (10) AhR changes in the cell nucleus should be provided (Fig. 4A).

      We appreciate the constructive feedback from the reviewer. In response to the reviewer's suggestions, we investigated the nuclear translocation of AhR on 6 days after the induction of ISmediated trained immunity, as illustrated in Author response image 11. For this purpose, the lysate from IS-trained monocytes was fractionated into the nucleus and cytosol, and AhR protein was subsequently immunoblotted. The results depicted in Figure X demonstrate that IS-trained monocytes exhibited a higher level of AhR protein in the nucleus compared to non-trained monocytes. Notably, the nuclear translocation of AhR was significantly attenuated in IS-trained monocytes treated with GNF351. These findings imply that the activation of AhR, facilitated by the binding of IS, persisted partially up to 6 days, indicating that IS-mediated degradation of AhR was not fully recovered even on day 6 after the induction of IS training. Consequently, we have replaced Figure 4A in the revised manuscript.

      Author response image 11.

      The activation of AhR, facilitated by IS binding, is persisted partially up to 6 days during induction of trained immunity. The lysate of IS-trained cells treated with or without GNF351, were separated into nuclear and cytosol fraction, followed by WB analysis for AhR protein (Left panel). Band intensity in immunoblots was quantified by densitometry (Right panel). β-actin was used as a normalization control. Bar graphs show the mean ± SEM. * = p < 0.05, by two-tailed paired t-test.

      (11) Do other protein-bound uremic toxins (PBUTs), such as PCS, HA, IAA, and KA, change the mRNA expression of ALOX5, ALOX5AP, and LTB4R1? In the absence of genetic studies, it is difficult to be certain of the ALOX5-related mechanism claimed by the authors.

      We are grateful for the constructive criticism provided by the reviewer. In response to the reviewer's comment, we investigated whether uremic toxins, specifically PBUTs such as PCS, HA, IAA, and KA, induce changes in the mRNA expression of ALOX5, ALOX5AP, and LTB4R1 in trained monocytes. Intriguingly, the examination revealed no discernible induction in the mRNA expression of these genes by PBUTs, with the exception of IS, as depicted in Author response image 12 of the letter. These findings once again underscore the implication of the AhR-ALOX5 pathway in the induction of trained immunity in monocytes by IS.

      Author response image 12.

      No obvious impact of PBUTs except IS on the expression of arachidonic acid pathway-related genes on 6 days after treatment with PBUTs. Purified monocytes were treated with several PBUTs including IS, PCS, HA, IAA, and KA for 24 hrs., following by 5-day resting period to induce trained immunity. The mRNA expression of ALOX5, ALOX5AP, and LTB4R1 were quantified using RT-qPCR. Bar graphs show the mean ± SEM. * = p < 0.05, by two-tailed paired t-test.

      (12) Fig.6 is based on the correlated expression of inflammatory genes or AA pathway genes. It does not clarify any mechanisms the authors claimed in the previous figures. 

      We express our sincere appreciation for the constructive criticism provided by the reviewer, and we have taken careful note of the points raised. In response to the reviewer's feedback, we adopted two distinct approaches utilizing samples obtained from ESRD patients and IS-trained mice. Initially, we investigated the correlation between ALOX5 protein expression in monocytes and IS concentration in the plasma of ESRD patients presented in Figure 6E of the original manuscript. Despite the limited number of samples, our analysis revealed a nonsignificant correlation between IS concentration and ALOX5 expression; however, it demonstrated a positive trend (Author response image 13A). Subsequently, we examined the potential inhibitory effects of zileuton, an ALOX5 inhibitor, on the production of TNF-α and IL-6 in LPSstimulated splenic myeloid cells derived from IS-trained mice. Our findings indicate that zileuton significantly inhibits the production of TNF-α and IL-6 induced by LPS in splenic myeloid cells from IS-trained mice (Author response image 13B). These data were added in Figure 6N of the revised manuscript (Line 350-354 of page 16 in the revised manuscript).

      Author response image 13.

      Assessment of the correlation between ALOX5 and the concentration of IS in ESRD patients, and investigation of ALOX5 effects in mouse splenic myeloid cells in IS-trained mice. A. Examination of the correlation between ALOX5 protein expression in monocytes and IS concentration in the plasma of ESRD patients. B. C57BL/6 mice were administered daily injections of 200 mg/kg IS for 5 days, followed by a resting period of another 5 days. Subsequently, IS-trained mice were sacrificed, and spleens were mechanically dissociated. Isolated splenic myeloid cells were subjected to ex vivo treatment with LPS (10 ng/ml), along with zileuton (100 µM). The levels of TNF-α and IL-6 in the supernatants were quantified using ELISA. The graphs show the mean ± SEM. * = p < 0.05, by two-tailed paired t-test between zileuton treatment group and no-treatment group.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      Minor corrections to the figures

      (1) No indicators for the control group in Fig. 1B.

      We thank you for the reviewer’s comment. According to the reviewer’s comment, the control group was indicated with (-).

      (2) The same paper is listed twice in the references section. (No. 19 and 28)

      We thank you for the reviewer’s comment. We deleted the reference No. 28.

      Reviewer #2 (Public Review):

      Manuscript entitled "Uremic toxin indoxyl sulfate (IS) induces trained immunity via the AhR-dependent arachidonic acid pathway in ESRD" presented some interesting findings. The manuscript strengths included use of H3K4me3-CHIP-Seq, AhR antagonist, IS treated cell RNA-Seq, ALOX5 inhibitor, MTA inhibitor to determine the roles of IS-AhR in trained immunity related to ESRD inflammation and trained immunity.

      Thank you very much for your positive feedback.

      Reviewer #2 (Recommendations For The Authors):

      However, the manuscript needs to be improved by fixing the following concerns.

      There are concerns:

      (1) The experiments in Figs. 1G, 1H and 1I need to have AhR siRNA, and siRNA control to demonstrate that the results in uremic toxins-containing serum-treated experiments were related to IS;

      We extend our gratitude to the reviewer for their invaluable comment, acknowledging its significant relevance to our study. In accordance with the reviewer's suggestion, we endeavored to conduct additional experiments utilizing AhR siRNA to elucidate the direct impact of IS present in the serum of end-stage renal disease (ESRD) patients on the induction of IS-mediated trained immunity. 

      Regrettably, owing to limitations in the availability of monocytes post-siRNA transfection, we were unable to establish a direct relationship between the observed outcomes in experiments utilizing uremic toxins-containing serum and IS in AhR siRNA knockdown monocytes. However, treatment with GNF351, an AhR antagonist, resulted in the inhibition of TNF-α production in trained monocytes exposed to uremic toxins-containing serum (Author response image 14).

      In our previous studies, we have already reported that uremic serum-induced TNF-α production in human monocytes is dependent on the AhR pathway, using GNF351 (Kim HY et al. Indoxyl sulfate (IS)-mediated immune dysfunction provokes endothelial damage in patients with end-stage renal disease (ESRD). Sci Rep. 2017 Jun 8;7(1):3057). Additionally, we have provided evidence demonstrating an augmentation in the activity of the AhR pathway within monocytes derived from ESRD patients, indicative of a significant reduction in AhR protein levels (Kim HY et al. Indoxyl sulfate-induced TNF-α is regulated by crosstalk between the aryl hydrocarbon receptor, NF-κB, and SOCS2 in human macrophages. FASEB J. 2019 Oct;33(10):10844-10858). It is noteworthy that other major protein-bound uremic toxins (PBUTs), such as PCS, HA, IAA, and KA, failed to induce trained immunity in human monocytes (Supplementary Figure 1A in the revised manuscript). Nevertheless, knockdown of AhR via siRNA effectively impeded the induction of IS-mediated trained immunity in human monocytes (Figure 4E in the revised manuscript). 

      Taken collectively, our findings suggest a critical role for IS present in the serum of ESRD patients in the induction of trained immunity in human monocytes. 

      Author response image 14.

      Inhibition of uremic serum (US)-induced trained immunity by AhR antagonist, GNF351. Monocytes were pre-treated with or without GNF351 (AhR antagonist; 10 µM) for 1 hour, followed by treatment with pooled normal serum (NS) or uremic serum (US) at a concentration of 30% (v/v) for 24 hours. After a resting period of 5 days, cells were stimulated with LPS for 24 hours. The production of TNF-α and IL-6 in the supernatants was quantified using ELISA. The data presented are derived from three independent experiments utilizing samples from different donors.

      (2) Fig. 3 needs to be moved as Fig. 2

      We express appreciation for the constructive suggestion provided by the reviewer. In response to the reviewer's comment, the sequence of Figure 3 and Figure 2 was adjusted in the revised manuscript.

      (3, 4) The connection between bioenergetic metabolism pathways and H3K4me3 was missing; The connection between bioenergetic metabolism pathways and ALOX5 was missing;

      We appreciate the reviewer’s constructive criticism and fully understood the reviewer's points. In response to the reviewer's feedback, we conducted additional experiments employing appropriate inhibitors to elucidate the interrelation between bioenergetic metabolism and H3K4me3 and between bioenergetic metabolism and ALOX5. Initially, we assessed the enrichment of H3K4me3 at 6-day on promoters of TNFA and IL6 loci after treatment of 2-DG, a glycolysis inhibitor. Additionally, we evaluated the alteration in the activity of S6K, a downstream molecule of mTORC1, following treatment with zileuton, an inhibitor of ALOX5. Our findings indicate that AhR-dependent arachidonic acid (AA) signaling induces epigenetic modifications, albeit without inducing metabolic rewiring, in IS-induced trained immunity (Author response image 15). However, IS stimulation promotes mTORC1-mediated glycolysis in an AhR-independent manner. Notably, inhibition of glycolysis with 2-DG impacts epigenetic modifications. We have updated Figure 7 of the revised manuscript to incorporate these additional experimental findings, elucidating the correlation between the diverse mechanisms implicated in IS-induced innate immune memory (Fig. 7 in the revised manuscript).

      Author response image 15.

      Epigenetic modification is regulated by arachidonic acid (AA) pathway and metabolic rewiring, but metabolic rewiring is not affected by the AA pathway. A-B. Monocytes were pre-treated with zileuton (ZLT), an inhibitor of ALOX5, or 2DG, a glycolysis inhibitor, followed by stimulation with IS for 24 hours. After a resting period of 5 days, the enrichment of H3K4me3 on the promoters of TNFA and IL6 loci was assessed. Normalization was performed using 2% input. C. Monocytes were pre-treated with ziluton (ZLT) and stimulated with IS for 24 hr. Cell lysates were immunoblotted for phosphorylated S6 Kinase, with β-actin serving as a normalization control. Band intensities in the immunoblots were quantified using densitometry. D, A schematic representation of the mechanistic framework underlying IS-trained immunity. Bar graphs show the mean ± SEM. * = p < 0.05, **= p < 0.01, and *** = p < 0.001 by two-tailed paired t-test.

      (5) It was unclear whether histone acetylations such as H3K27acetylation and H3K14 acetylation are involved in IS-induced epigenetic reprogramming or IS-induced trained immunity is highly histone methylation-specific.

      We appreciate the constructive comment provided by the reviewer. As highlighted by the reviewer, alterations in epigenetic histone markers, specifically H3K4me3 or H3K27ac, have been recognized as the underlying molecular mechanism in trained immunity. Due to limitations in the availability of trained cells, this study primarily focused on histone methylation. In response to the reviewer's inquiry, we briefly investigated the impact of histone acetylation using C646, a histone acetyltransferase inhibitor, on IS-induced trained immunity (Author response image 16). Our experiments revealed that C646 treatment effectively hinders the production of TNF-α and IL-6 by IS-trained monocytes in response to LPS stimulation, comparable to the effects observed with MTA (5’methylthioadenosine), a non-selective methyltransferase inhibitor. This suggests that histone acetylation also contributes to the epigenetic modifications associated with IS-induced trained immunity. We sincerely appreciate the valuable input from the reviewer.

      Author response image 16.

      The role of histone acetylation in epigenetic modifications in IS-induced trained immunity. Monocytes were pretreated with MTA (methylthioadenosine, methyltransferase inhibitor) or C646 (histone acetyltransferase p300 inhibitor), followed treatment with IS 1 mM for 24 hrs. After resting for 5 days, trained cells were re-stimulated by LPS 10 ng/ml as secondary insult. TNF-α and IL-6 in supernatants were quantified by ELISA. Bar graphs show the mean ± SEM. * = p < 0.05 and **= p < 0.01 by two-tailed paired t-test.

      Reviewer #3 (Public Review):

      The manuscript entitled, "Uremic toxin indoxyl sulfate induces trained immunity via the AhRdependent arachidonic acid pathway in ESRD" demonstrates that indoxyl sulfate (IS) induces trained immunity in monocytes via epigenetic and metabolic reprogramming, resulting in augmented cytokine production. The authors conducted well-designed experiments to show that the aryl hydrocarbon receptor (AhR) contributes to IS-trained immunity by enhancing the expression of arachidonic acid (AA) metabolism-related genes such as arachidonate 5-lipoxygenase (ALOX5) and ALOX5 activating protein (ALOX5AP). Overall, this is a very interesting study that highlights that IS mediated trained immunity may have deleterious outcomes in augmented immune responses to the secondary insult in ESRD. Key findings would help to understand accelerated inflammation in CKD or RSRD.

      We greatly appreciate your positive feedback.

      Reviewer #3 (Recommendations for The Authors):

      This reviewer, however, has the following concerns.

      Major comments:

      (1) Figure 1B: IS is known to induce the expression of TNF-a and IL-6. This reviewer wonders why these molecules were not detected in the IS (+) LPS (-) condition.

      We appreciate the constructive comment provided by the reviewer. In our prior investigation, it was observed that the expression of TNF-α and IL-6 was induced 24 hours after IS treatment in human monocytes and macrophages (Couper KN et al. IL-10: the master regulator of immunity to infection. J Immunol. 2008 May 1;180(9):5771-7). In adherence to the trained immunity protocol, the medium was replaced at the 24 hours post-IS treatment to eliminate IS, with a subsequent change after a 5-day resting period. Probably, TNF-α and IL-6 are accumulated and detected in the IS (+) LPS (-) culture supernatant if the media was not changed at these specific time points. Our primary objective, however, was to ascertain the role of IS in the induction of trained immunity, prompting an investigation into whether IS contributes to an increase in the production of TNF-α and IL-6 in response to LPS stimulation as a secondary insult. 

      (2) 1' stimulus is IS followed by 2' stimulus LPS/Pam3. It would be interesting to know what the immune profile is when other uremic toxin is used for secondary insult, this would be more relevant in clinical context of ESRD.

      The reviewer's insightful comment is greatly appreciated. To address their feedback, IStrained macrophages were subjected to additional stimulation using protein-bound uremic toxins (PBUTs) as a secondary challenge. As illustrated in Letter figure 17, the examined uremic toxins, namely p-cresyl sulfate (PCS), Hippuric acid (HA), Indole 3-acetic acid (IAA), and kynurenic acid (KA), failed to elicit the production of proinflammatory cytokines, specifically TNF-α and IL-6, by IS-trained monocytes.

      Author response image 17.

      No obvious effect of protein-bound uremic toxin (PBUTs) as secondary insults on the production of proinflammatory cytokines in IS-trained monocytes. IS-trained monocytes were re-stimulated with several PBUTs, such as IS (1 mM), PCS (1 mM), HA (2 mM), IAA. (0.5 mM), and KA (0.5 mM) as a secondary challenge for 24 hrs. TNF-α and IL-6 in supernatants were quantified by ELISA. The data from two independent experiments with different donors were shown. ND indicates ‘not detected’.

      (3) The authors need to explain a rationale why RNA and protein data used different markers.

      We appreciate the constructive input provided by the reviewer. Given that TNF-α and IL6 represent prototypical cytokines synthesized by trained monocytes in humans, we conducted a comprehensive analysis of their mRNA and protein levels. In human macrophages, the release of active IL-1β necessitates a second priming event, such as the presence of ATP. Consequently, we posited that assessing the mRNA levels of IL-1β would suffice to demonstrate the induction of trained immunity in our experimental protocol. Nevertheless, in response to the reviewer's comment, we proceeded to assess the protein levels of IL-1β, IL-10, and MCP-1 as illustrated in Author response image 189. These data have been incorporated into the revised manuscript as supplementary Figure 1E. 

      Author response image 18.

      Modulation of cytokine levels in IS-trained macrophages in response to secondary stimulation with LPS. Human monocytes were stimulated with the IS for 24 hr, followed by resting period for 5 days. On day 6, the cells were re-stimulated with LPS for 24 hr. The levels of each cytokine in the supernatants were quantified using ELISA. Bar graphs show the mean ± SEM. ** = p < 0.01 and ***= p < 0.001 by two-tailed paired t-test.

      (4) Epigenetic modification primarily involves histone modification and DNA methylation. The authors presented convincing data on histone modification (Figure 2), but did not provide any insights in the promoter DNA methylation status.

      We express our gratitude to the reviewer for providing valuable comments, which highlight a crucial aspect of our study. Despite the well-established primary role of DNA methylation in epigenetic modifications, recent suggestions propose that histone modifications, particularly H3K4me3 or H3K27ac, play a predominant role in the induction of trained immunity. In this context, our primary inquiry was focused on determining whether IS, as an endogenous insult, induces trained immunity in monocytes, and if so, whether IS-trained immunity is mediated through metabolic and epigenetic modifications - recognized as the major mechanisms underlying the generation of trained immunity. It is imperative to note that our study's primary objective did not encompass the identification of various epigenetic changes. In response to the reviewer's inquiry, we conducted a brief examination of the impact of DNA methylation using ZdCyd (5-aza-2’-deoxycytidine), a DNA methylation inhibitor, on IS-induced trained immunity. Our experimental findings indicate that ZdCyd treatment exerts no discernible effect on the production of TNF-α and IL-6 by IS-trained monocytes upon stimulation with LPS, as illustrated in Author response image 19. However, a recent study has shed light on the role of DNA methylation in BCG vaccine-induced trained immunity in human monocytes (Bannister S et al. Neonatal BCG vaccination is associated with a long-term DNA methylation signature in circulating monocytes. Sci Adv. 2022 Aug 5;8(31):eabn4002). Consequently, further investigations utilizing DNA methylation sequencing are warranted to elucidate whether DNA methylation is implicated in the induction of IS-trained immunity.

      Author response image 19.

      The effect of DNA methylation on IS-induced trained immunity. Monocytes were pretreated with ZdCyd (5-aza-2’-deoxycytidine, DNA methylation inhibitor), followed by treatment with IS 1 mM for 24 hrs. After resting for 5 days, cells were re-stimulated by LPS 10 ng/ml as secondary insult. TNF-α and IL-6 in supernatants were quantified by ELISA. Bar graphs show the mean ± SEM. * = p < 0.05 and **= p < 0.01 by two-tailed paired t-test.

                     

      (5) Metabolic rewiring in trained immunity cells undergo metabolic changes which involved intertwined pathways of glucose and cholesterol metabolism. The authors presented nice data on glucose pathway (Figure 3) but failed to show any changes related to cholesterol metabolism.

      We express our gratitude to the reviewer for providing valuable comments, which underscore a noteworthy observation. In the current investigation, our primary emphasis has been on glycolytic reprogramming, recognized as a principal mechanism for inducing trained immunity in monocytes. This focus stems from preliminary experiments wherein Fluvastatin, a cholesterol synthesis inhibitor, demonstrated no discernible impact on TNF-α production by IS-trained monocytes, as illustrated in Author response image 20. Intriguingly, Fluvastatin treatment exhibited a partial inhibitory effect on the production of IL-6 by IS-trained monocytes. Subsequent investigations are imperative to elucidate the role of cholesterol metabolism in the induction of IS-trained immunity.

      Author response image 20.

      The effect of cholesterol metabolism on IS-induced trained immunity. Monocytes were pretreated with Fluvastatin (cholesterol synthesis inhibitor, HMG-CoA reductase inhibitor), followed treatment with IS 1 mM for 24 hrs. After resting for 5 days, cells were re-stimulated by LPS 10 ng/ml as secondary insult. TNF-α and IL-6 in supernatants were quantified by ELISA. Bar graphs show the mean ± SEM. * = p < 0.05 and **= p < 0.01 by two-tailed paired t-test.

      (6) Trained immunity involves neutrophils in addition to monocyte/macrophages. It is evident from the RNAseq data that neutrophil degranulation (Figure 5B) is the top enriched pathway. This reviewer wonders why the authors did not perform any assays on neutrophils.

      We appreciate the reviewer for valuable comment. IS represents a major uremic toxin that accumulates in the serum of patients with chronic kidney disease (CKD), correlating with CKD progression and the onset of CKD-related complications, including cardiovascular diseases (CVD). Our prior investigations have demonstrated that IS promotes the production of TNF-α and IL-1β by human monocytes and macrophages. Additionally, macrophages pre-treated with IS exhibit a significant augmentation in TNF-α production when exposed to a low dose of lipopolysaccharide (LPS). Considering the pivotal role of proinflammatory macrophages and TNF-α, a principal cardiotoxic cytokine, in CVD pathogenesis, our focus in this study has primarily focused on elucidating the trained immunity of monocytes/macrophages. Consequently, all experiments were meticulously conducted using highly purified monocytes and monocytederived macrophages derived from both healthy controls and end-stage renal disease (ESRD) patients. The reviewer's observation regarding the potential involvement of neutrophils in trained immunity has been duly noted. Subsequent investigations will be imperative to explore the conceivable role of IS-trained neutrophils in the pathogenesis of CVD. Once again, we appreciate the reviewer for their valuable comment.

      (7) Figure 5C (GSEA plots): This reviewer is not sure if one can present the plots assigned with groups (eg. IS(T) vs Control). More details are required in the Methods related to this.

      We apologize for any ambiguity resulting from the previously unclear description of methods concerning Gene Set Enrichment Analysis (GSEA) plots. To provide clarification, additional details pertaining to this aspect have been explained upon in the revised manuscript's Methods section. 

      (8) In vivo data (Figure 6 I-M): Instead of serum profile and whole set of spleen myeloid cells, it would be interesting to see changes of markers on peritoneal macrophages or bone marrow-derived macrophages since the in vitro findings are on monocyte-derived macrophages.

      We appreciate comment and the insightful suggestion provided by the reviewer. In response to the reviewer's feedback, we conducted additional in vivo experiments to examine the production of TNF-α and IL-6 in bone marrow-derived macrophages (BMDMs) derived from IStrained mice. Upon LPS stimulation, we observed an increase in the production of TNF-α and IL-6 in spleen myeloid cells from IS-trained mice. However, no such increase in these cytokines was noted in BMDMs derived from the same mice (Author response image 22, A and B). In fact, we already observed that that the expression of ALOX5 was not elevated in BM cells derived from IS-trained mice presented in Figure 6L and M of the original manuscript (Author response image 22C). 

      Recent studies have indicated that trained immunity can be induced in circulating immune cells, such as monocytes or resident macrophages (peripheral trained immunity), as well as in hematopoietic stem and progenitor cells (HSPCs) within the bone marrow (central trained immunity) (Kaufmann E et al. BCG Educates Hematopoietic Stem Cells to Generate Protective Innate Immunity against Tuberculosis. Cell. 2018 Jan 11;172(1-2):176-190.e19; Riksen NP et al. Trained immunity in atherosclerotic cardiovascular disease. Nat Rev Cardiol. 2023 Dec;20(12):799-811). It is plausible that central trained immunity in BM progenitor cells may not be elicited in our mouse model, which is relatively acute in nature. Further investigations are warranted to explore the role of IS in inducing central trained immunity, utilizing appropriate chronic disease models.

      We have included this additional data as supplementary figures in the revised manuscript (Suppl. Fig. 7, D and E, and line 355-362 of page 16 in the revised manuscript).

      Author response image 21.

      Absence of trained immunity in bone marrow derived macrophages (BMDMs) derived from IStrained mice. A-B, IS was intraperitoneally injected daily for 5 days, followed by training for another 5 days. Isolated BM progenitor cells and spleen myeloid cells were differentiated or treated with LPS for 24 hr. The supernatants were collected for ELISA. C, The level of ALOX5 protein in BM cells isolated from IS-trained or control mice was analyzed by western blot. The graph illustrates the band intensity quantified by densitometry. Bar graphs show the mean ± SEM. * = p < 0.05 and **= p < 0.01, by unpaired t-test.

      (9) Figure 7: There are no data on signaling pathway(s) that links IS and epigenetic changes, the authors therefore may want to add "?" to the proposed mechanism.

      We extend our sincere appreciation to the reviewer for providing valuable feedback. In light of the constructive comments provided by three reviewers, we have undertaken a series of additional experiments. These efforts have enabled us to propose a more elucidating schematic representation of the proposed mechanism, free of any ambiguous elements (Figure 7 in the revised manuscript). We are grateful for your insightful input.

      (10) Demographic data (Table S2): ESRD patients have co-morbidities including diabetes (33% of subjects), CAD (28%). How did the authors factor out the co-morbidities in the overall context of their findings?

      We express gratitude to the reviewer for providing valuable comments, particularly on a noteworthy and significant aspect. The investigation employed an End-Stage Renal Disease (ESRD) Cohort involving approximately 60 subjects undergoing maintenance hemodialysis at Severance Hospital in Seoul, Korea. The subset of participants subjected to analysis consisted of stable individuals who provided informed consent and had not undergone hospitalization for reasons related to infection or acute events within the preceding three months.

      (11) There are no data on the purity of IS.

      According to the reviewer's suggestion, we have included information regarding the purity (99%) of IS in the Methods section.

      (12) Figure 6L: Immunoblot on b-actin were merged. This reviewer wonders how the authors analyzed these blots. 

      We express gratitude for the constructive criticism provided by the reviewer, and we acknowledge and comprehend the concerns raised. In response to the reviewer's comments, a reanalysis of the ALOX5 expression level in Figure 6M was conducted, employing immunoblot analysis on β-actin, as depicted in Figure 6L, with a short exposure time (Author response image 22).

      Author response image 22.

      ALOX5 protein exhibited an elevation in splenic myeloid cells obtained from IS-trained mice.

      (13) qPCR data throughout the manuscript have control group with no error bar. The authors may not set all controls arbitrarily equal to 1 (Example Figure 1H and I). Data should be normalized in a test standard way. The average of a single datapoint may be scaled to 1, but variation must remain within the control groups.

      We express gratitude to the reviewer for their valuable feedback, acknowledging a comprehensive understanding of their perspectives. Our qPCR assays predominantly investigated the impact of various treatments on the expression of specific target genes (e.g., TNF-α, IL-6, Alox5) within monocytes/macrophages obtained from the same donors.

      Subsequently, normalization of gene expression levels occurred relative to ACTINB expression, followed by relative fold-increase determination using the comparative CT method (ΔΔCT).

      Statistical significance was assessed through a two-tailed paired analysis in these instances. Additionally, a substantial portion of the qPCR data was validated at the protein level through ELISA and immunoblotting techniques.

      Minor Comments:

      (1) Molecular weight markers are missing in immunoblots throughout the manuscript.

      According to the reviewer's comment, molecular weight markers are added into immunoblots

      (2)  ESRD should be spelled out in the title.

      According to the reviewer's comment, we spelled out ESRD in the title.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      In their manuscript, Yu et al. describe the chemotactic gradient formation for CCL5 bound to - i.e. released from - glycosaminoglycans. The authors provide evidence for phase separation as the driving mechanism behind chemotactic gradient formation. A conclusion towards a general principle behind the finding cannot be drawn since the work focuses on one chemokine only, which is particularly prone to glycan-induced oligomerisation.

      Strengths:

      The principle of phase separation as a driving force behind and thus as an analytical tool for investigating protein interactions with strongly charged biomolecules was originally introduced for protein-nucleic acid interactions. Yu et al. have applied this in their work for the first time for chemokine-heparan sulfate interactions. This opens a novel way to investigate chemokine-glycosaminoglycan interactions in general.

      Response: Thanks for the encouragement of the reviewer.

      Weaknesses:

      As mentioned above, one of the weaknesses of the current work is the exemplification of the phase separation principle by applying it only to CCL5-heparan sulfate interactions. CCL5 is known to form higher oligomers/aggregates in the presence of glycosaminoglycans, much more than other chemokines. It would therefore have been very interesting to see, if similar results in vitro, in situ, and in vivo could have been obtained by other chemokines of the same class (e.g. CCL2) or another class (like CXCL8).

      Response: We share the reviewer’s opinion that to investigate more molecules/cytokines that interact with heparan sulfate in the system should be of interesting. We expect that researchers in the field will adapt the concept to continue the studies on additional molecules. Nevertheless, our earlier study has demonstrated that bFGF was enriched to its receptor and triggered signaling transduction through phase separation with heparan sulfate (PMID: 35236856; doi: 10.1038/s41467-022-28765-z), which supports the concept that phase separation with heparan sulfate on the cell surface may be a common mechanism for heparan sulfate binding proteins. The comment of the reviewer that phase separation is related to oligomerization is demonstrated in (Figure 1—figure supplement 2C and D), showing that the more easily aggregated mutant, A22K-CCL5, does not undergo phase separation.

      In addition, the authors have used variously labelled CCL5 (like with the organic dye Cy3 or with EGFP) for various reasons (detection and immobilisation). In the view of this reviewer, it would have been necessary to show that all the labelled chemokines yield identical/similar molecular characteristics as the unlabelled wildtype chemokine (such as heparan sulfate binding and chemotaxis). It is well known that labelling proteins either by chemical tags or by fusion to GFPs can lead to manifestly different molecular and functional characteristics.

      Response: We agree with the reviewer that labeling may lead to altered property of a protein, thus, we have compared chemotactic activity of CCL5 and CCL5-EGFP (Figure 2—figure supplement 1). To further verify this, we performed additional experiment to compare chemotactic activity between CCL5 and Cy3-CCL5 (see Author response image 1). For the convenience of readers, we have combined the original Figure 2—figure supplement 1 with the new data (Figure R1), which replaced original Figure 2—figure supplement 1.

      Author response image 1.

      Chemotactic function of CCL5-EGFP and CCL5-Cy3. Cy3-Labeled CCL5 has similar activity as CCL5, 50 nM CCL5 or CCL5-Cy3 were added to the lower chamber of the Transwell. THP-1 cells were added to upper chambers. Data are mean ± s.d. n=3. P values were determined by unpaired two-tailed t-tests. NS, Not Significant.

      Reviewer #2 (Public Review):

      Although the study by Xiaolin Yu et al is largely limited to in vitro data, the results of this study convincingly improve our current understanding of leukocyte migration.

      (1) The conclusions of the paper are mostly supported by the data although some clarification is warranted concerning the exact CCL5 forms (without or with a fluorescent label or His-tag) and amounts/concentrations that were used in the individual experiments. This is important since it is known that modification of CCL5 at the N-terminus affects the interactions of CCL5 with the GPCRs CCR1, CCR3, and CCR5 and random labeling using monosuccinimidyl esters (as done by the authors with Cy-3) is targeting lysines. Since lysines are important for the GAG-binding properties of CCL5, knowledge of the number and location of the Cy-3 labels on CCL5 is important information for the interpretation of the experimental results with the fluorescently labeled CCL5. Was the His-tag attached to the N- or C-terminus of CCL5? Indicate this for each individual experiment and consider/discuss also potential effects of the modifications on CCL5 in the results and discussion sections.

      Response: We agree with the reviewer that labeling may lead to altered property of a protein, thus, we have compared chemotactic activity of CCL5 and CCL5-EGFP (Figure 2—figure supplement 1). To further verify this, we performed additional experiment to compare chemotactic activity between CCL5 and Cy3-CCL5 (see Author response image 1). For the convenience of readers, we have combined the original Figure 2—figure supplement 1 with the new data (Author response image 1), which replaced original Figure 2—figure supplement 1.

      The His-tag is attached to the C-terminus of CCL5, in consideration of the potential impact on the N-terminus.

      (2) In general, the authors appear to use high concentrations of CCL5 in their experiments. The reason for this is not clear. Is it because of the effects of the labels on the activity of the protein? In most biological tests (e.g. chemotaxis assays), unmodified CCL5 is active already at low nM concentrations.

      Response: We agree with the reviewer that the CCL5 concentrations used in our experiments were higher than reported chemotaxis assays and also higher than physiological levels in normal human plasma. In fact, we have performed experiments with lower concentration of CCL5, where the effect of LLPS was not seen though the chemotactic activity of the cytokine was detected. Thus, LLPS-associated chemotactic activity may represent a scenario of acute inflammatory condition when the inflammatory cytokines can increase significantly.

      (3) For the statistical analyses of the results, the authors use t-tests. Was it confirmed that data follow a normal distribution prior to using the t-test? If not a non-parametric test should be used and it may affect the conclusions of some experiments.

      Response: We thank the reviewer for pointing out this issue. As shown in Author response table 1, The Shapiro-Wilk normality test showed that only two control groups (CCL5 and 44AANA47-CCL5+CHO K1) in Figure 3 did not conform to the normal distribution. The error was caused by using microculture to count and calculate when there were very few cells in the microculture. For these two groups, we re-counted 100 μL culture medium to calculate the number of cells. The results were consistent with the positive distribution and significantly different from the experimental group (Author response image 3). The original data for the number of cells chemoattractant by 500 nM CCL5 was revised from 0, 247, 247 to 247, 123, 370 and 500 nM 44AANA47 +CHO-K1 was revised from 1111, 1111, 98 to 740, 494, 617. The revised data does not affect the conclusion.

      Author response table 1.

      Table R1 Shapiro-Wilk test results of statistical data in the manuscript

      Author response image 3.

      Quantification of THP-1collected from the lower chamber. Data are mean ± s.d. n=3. P values were determined by unpaired two-tailed t-tests.

      Recommendations for the authors:

      Reviewer #1:

      See the weaknesses section of the Public Review. In addition, the authors should discuss the X-ray structure of CCL5 in complex with a heparin disaccharide in comparison with their docked structure of CCL5 and a heparin tetrasaccharide.

      Response: Our study, in fact, is strongly influenced by the report (Shaw, Johnson et al., 2004) that heparin disaccharide interaction with CCL5, which is highlighted in the text (page5, line100-102).

      Reviewer #2:

      (1) Clearly indicate in the results section and figure legends (also for the supplementary figures) which form and concentration of CCL5 is used.

      Response: The relevant missing information is indicated across the manuscript.

      (2) Clearly indicate which GAG was used. Was it heparin or heparan sulfate and what was the length (e.g. average molecular mass if known) or source (company?)?

      Response: Relevant information is added in the section “Materials and Methods.

      (3) Line 181: What do you mean exactly with "tiny amounts"?

      Response: “tiny amounts” means 400 transfected cells. This is described in the section of Materials and Methods. It is now also indicated in the text and legend to the figure.

      (4) Lines 216-217: This is a very general statement without a link to the presented data. No combination of chemokines is used, in vivo testing is limited (and I agree very difficult). You may consider deleting this sentence (certainly as an opening sentence for the Discussion).

      Response: We appreciate very much for the thoughtful suggestion of the reviewer. This sentence is deleted in the revised manuscript.

      (5) Why was 5h used for the in vitro chemotaxis assay? This is extremely long for an assay with THP-1 cells.

      Response: We apologize for the unclear description. The 5 hr includes 1 hr pre- incubation of CCL5 with the cells enable to form phase separation. After transferring the cells into the upper chamber, the actual chemotactic assay was 4 hr. This is clarified in the Materials and Methods section and the legend to each figure.

      (6) Define "Sec" in Sec-CCL5-EGFP and "Dil" in the legend of Figure 4.

      Response: The Sec-CCL5-EGFP should be “CCL5-EGFP’’, which has now been corrected. Dil is a cell membrane red fluorescent probe, which is now defined.

      (7) Why are different cell concentrations used in the experiment described in Figure 5?

      Response: The samples were from three volunteers who exhibited substantially different concentrations of cells in the blood. The experiment was designed using same amount of blood, so we did not normalize the number of the cell used for the experiment. Regardless of the difference in cell numbers, all three samples showed the same trend.

      (8) Check the text for some typos: examples are on line 83 "ratio of CCL5"; line 142 "established cell lines"; line 196 "peripheral blood mononuclear cells"; line 224 "to mediate"; line 226 "bind"; line 247 "to form a gradient"; line 248 "of the glycocalyx"; line 343 and 346 "tetrasaccharide"; line 409-410 "wild-type"; line 543 "on the surface of CHO-K1 and CHO-677"; line 568 "white".

      Response: Thanks for the careful reading. The typo errors are corrected and Manuscript was carefully read by colleagues.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1 (Public Review):

      Weaknesses:

      (1) Figure 1: Histomorphological analysis using immunostaining for type I, IIA, IIX, and IIB should be performed and quantified across different muscle groups and also in the soleus. Fiber type switch measured based on qPCR and Westerns does not sufficiently indicate the extent of fiber type switch. Better images for Fig. 1c should be provided.

      Thanks for your suggestion. In fact, we attempted immunofluorescent staining for Slow MyHC and Fast MyHC in GAS muscle. However, for the majority of our results, we only observed positive expression of Slow MyHC in a small portion of the muscle sections (as shown in the figure below), so we did not present this result.

      In addition, due to the size limitations on uploading image files to Biorxiv, we had to compress the images, resulting in lower resolution pictures. We have attempted to submit clearer images in Fig. 1C

      Author response image 1.

      Green: Slow MyHC; Red: Fast MyHC

      (2) Figure 2: Histomorphological analysis for SDH and NADH-TR should be performed and quantified in different muscle groups. Seahorse or oroborous respirometry experiments should be performed to determine the actually increase in mitochondrial respiratory capacity either in isolated mitochondria or single fibers from vehicle and Eugenol-treated mice. Em for mitochondrial should be added to determine the extent of mitochondrial remodeling. The current data is insufficient to indicate the extent of mitochondrial or oxidative remodeling.

      That's a good suggestion. However, we regret to inform you that we are unable to present these results due to a lack of relevant experimental equipment and samples.

      (3) Figure 2: Gene expression analysis is limited to a few transcriptional factors. A thorough analysis of gene expression through RNA-seq should be performed to get an unbiased effect of Eugenol on muscle transcriptome. This is especially important because eugenol is proposed to work through CaN/NFAT signaling, major transcriptional regulators of muscle phenotype.

      Thanks for your suggestion. Indeed, we believe that in terms of reliability and accuracy, RNA-seq is not as good as RT-qPCR. The advantage of RNA-seq lies in its high throughput, making it suitable for screening unknown transcription factor regulatory mechanisms. In this study, the signaling pathways regulating myokines and muscle fiber type transformation are known and limited, with only the CaN/NFATc1 and the AMPK pathway. Since eugenol mainly acts through the Ca2+ pathway, we primarily focus on the CaN/NFATc1 signaling pathway.

      (4) I suggest the inclusion of additional exercise or performance testing including treadmill running, wheel running, and tensiometry. Quantification with a swimming test and measurement of the exact intensity of exercise, etc. is limited.

      That's a good suggestion. We apologize for being unable to detect this indicator due to a lack of relevant experimental equipment.

      (5) In addition to muscle performance, whole-body metabolic/energy homeostatic effects should also be measured to determine a potential increase in aerobic metabolism over anaerobic metabolism.

      That's a good suggestion. We apologize for being unable to detect this indicator due to a lack of relevant experimental equipment.

      (6) For the swimming test and other measurements, only 4 weeks of vehicle vs. Eugenol treatment was used. For this type of pharmacological study, a time course should be performed to determine the saturation point of the effect. Does exercise tolerance progressively increase with time?

      Thanks for your suggestion. Due to the potential damage that exhaustive swimming tests inflict on mice, the tested mice are subsequently eliminated to avoid potential interference with the experiment. Therefore, this experiment is only suitable for conducting tests at individual time points.

      (7) The authors should also consider measuring adaptation to exercise training with or without Eugenol.

      Thanks for your suggestion. The purpose of this study is to investigate whether eugenol mimics exercise under standard dietary conditions. In our future research, we will consider exploring the effects of eugenol under HFD and exercise conditions.

      (8) Histomorphological analysis of Wat is also lacking. EchoMRI would give a better picture of lean and fat mass.

      That's a good suggestion. However, we did not collect the slices of WAT tissue, so we are unable to supplement this result, we feel sorry for it. In addition, we apologize for being unable to detect lean and fat mass due to a lack of EchoMRI equipment.

      (9) The experiments performed to demonstrate that Eugenol functions through trpv1 are mostly correlational. Some experiments are needed with trpv1 KO or KD instead of inhibitor. Similarly, KD for other trpv channels should be tested (at least 1-4 that seem to be expressed in the muscle). Triple KO or trpv null cells should be considered to demonstrate that eugenol does not have another biological target.

      Thanks for your professional suggestion. AMG-517 is a specific inhibitor of TRPV1, with a much greater inhibitory effect on TRPV1 compared to other TRP channels. AMG-517 inhibits capsaicin (500 nM), acid (pH 5.0), or heat (45°C) induced Ca2+ influx in cells expressing human TRPV1, with IC50 values of 0.76 nM, 0.62 nM, and 1.3 nM, respectively. However, the IC50 values of AMG-517 for recombinant TRPV2, TRPV3, TRPV4, TRPA1, and TRPM8 cells are >20 μM (Gavva, 2008). Therefore, we believe that using AMG-517 instead of TRPV1 KO cells is sufficient to demonstrate the involvement of TRPV1 in the function of eugenol.

      While this study did not exclude the possibility of other TRP channels' involvement, it was based on the fact that eugenol does not promote mRNA expression of other TRP channels, as shown in Fig4A-C. Indeed, as far as we know, besides TRPV1, the effects of other TRP channels on myofiber type transformation remain unknown. This is an aspect that we plan to investigate in the future.

      Reference

      Gavva NR, Treanor JJ, Garami A, et al. Pharmacological blockade of the vanilloid receptor TRPV1 elicits marked hyperthermia in humans. Pain. 2008;136(1-2):202-210.

      (10) Eugenol + trpv1 inhibition studies are performed in c2c12 cells and only looks at myofiber genes expression. This is incomplete. Some studies in mitochondrial and oxsphos genes should be done.

      Thanks for your suggestion. In the inhibition experiment, we additionally examined the expression of mitochondrial complex proteins as shown in Figure 5C. And the relevant description has been added in lines 178-183 and 764-765.

      (11) The experiments linking Eugenol to ca handling, and calcineurin/nfat activation are all performed in c2c12 cells. There seems to be a link between Eugenol activation and CaN/NFAT activation and fiber type regulation in cells, however, this needs to be tested in mouse studies at the functional level using some of the parameters measured in aims 1 and 2.

      Thank you for your professional suggestion. We will attempt to continue these experiments in future studies.

      (12) The myokine studies are incomplete. The authors show a link between Eugenol treatment and myokines/IL-15 induction. However, this is purely co-relational, without any experiments performed to show whether IL-15 mediates any of the effects of eugenol in mice.

      Indeed, previous studies have adequately demonstrated the regulation of skeletal muscle oxidative metabolism by IL-15. The initial aim of this experiment was to investigate the mechanism by which eugenol promotes IL-15 expression. Through inhibition assays, EMSA, and dual luciferase reporter gene experiments, we have thoroughly demonstrated that eugenol promotes IL-15 expression via the CaN/NFATc1 signaling pathway, thus establishing a novel link between CaN/NFATc1 signaling and the myokine IL-15 expression. In the subsequent experiments, we plan to knock out IL-15 in eugenol-treated C2C12 cells to explore whether IL-15 mediates the effects of eugenol. This will be another aspect of our investigation.

      (13) An additional major concern is that it cannot be ruled out that Engenol is uniquely mediating its effects through trpv1. Ideally, muscle-specific trpv1 mice should be used to perform some experiments with Eugenol to confirm that this ion channel is involved in the physiological effects of eugenol.

      As you suggested, we agree that muscle-specific TRPV1 mice should be used to conduct some experiments with eugenol. In our mice experiments, due to the lack of validation of skeletal muscle-specific TRPV1 knockout, we indeed cannot rule out that eugenol is uniquely mediating its effects through TRPV1. We acknowledge this as a limitation of our study. However, due to limitations in research funding and time, we are currently unable to supplement these experiments. Nevertheless, we believe that our results from in vitro experiments using a TRPV1 inhibitor (which selectively inhibits TRPV1) provide evidence of eugenol's action through TRPV1.

      Reviewer #2 (Public Review):

      Weaknesses:

      (1) Apart from Fig.2A and 2B, they mostly utilised protein expression changes as an index of tissue functional changes. Most of the data supporting the conclusions are thus rather indirect. More direct functional evidence would be more compelling. For example, a lipolysis assay could be used to measure the metabolic function of adipocytes after eugenol treatment in Fig.3. Functional activation of NFAT can be demonstrated by examining the nuclear translocation of NFAT.

      Thank you for your professional suggestion. Indeed, as shown in Figure 4G-I, we detected the expression of NFATc1 in the nucleus to illustrate its nuclear translocation.

      (2) To further demonstrate the role of TRPV1 channels in the effects of eugenol, TRPV1-deficient mice and tissues could also be used. Will the improved swimming test in Fig. 2B and increased CaN, NFAT, and IL-15 triggered by eugenol be all prevented in TRPV1-lacking mice and tissues?

      Thank you for your professional suggestion. We agree that muscle-specific TRPV1 mice should be used to conduct some experiments with eugenol. However, due to limitations in research funding and time, we are currently unable to supplement these experiments.

      (3) Direct evidence of eugenol activation of TRPV1 channels in skeletal muscles is also lacking. The flow cytometry assay was used to measure Ca2+ changes in the C2C12 cell line in Fig. 5A. But this assay is rather indirect. It would be more convincing to monitor real-time activation of TRPV1 channels in skeletal muscles not in cell lines using Ca2+ imaging or electrophysiology.

      Thank you for your professional suggestion. As you suggested, we initially planned to use patch-clamp technique to detect membrane potential changes in skeletal muscle cells under eugenol treatment. However, due to experimental technical limitations, this experiment was not successfully conducted. Therefore, we were compelled to rely solely on flow cytometry to detect Ca2+ levels.

      Reviewer #2 (Recommendations For The Authors):

      (1) Most of the mRNA and protein data are consistent with each other. However, some of them are not obvious. For example, PGC1a mRNA was increased by eugenol in Fig. 2C but not seen in protein in Fig. 2D. Similarly, Complex I and V mRNA was increased in Fig. 2C but not obvious at protein levels in Fig. 2D, even though they claimed that Complex I and V were both upregulated by eugenol (see: line 123). Another example: IL-15 mRNA was increased by EUG100 but not by EUG50 in the GAS muscle in Fig. 8A. However, EUG50 increased IL-15 protein expression in Fig. 8B. Similar conflict was also seen in IL-15 expression in the TA muscle in Fig. 8A and 8C.

      Thanks for your question. As shown in the table below, by standardizing with β-Actin, our statistical data indeed indicate that eugenol promotes the expression of Complex I and V proteins (although the upregulation is minimal). Additionally, protein and mRNA expression do not always correlate, which may be due to potential post-transcriptional and post-translational regulation.

      Author response table 1.

      (2) Line 115: Figure 2A should be Figure 2B; Line 119: Figure 2B should be Figure 2A. Alternatively, swap Fig2A with Fig. 2B.

      Thanks for your correction, we have revised the relevant content in lines 111-113 and 724-725.

      (3) Abbreviations of ADF and ADG in Fig. 3A should be defined.

      Thank you for your suggestion. We have defined these abbreviations in lines 123-125.

      (4) Line 154: TRPV1 mRNA expression was promoted by 25 and 50uM eugenol, not by 12.5uM.

      Thank you for your correction. We have revised it in line 150.

      (5) Line 173: Increased expression of NFAT suggests that NFAT is activated. This is a rather weak statement. It is more convincing to show the nuclear translocation of NFAT by eugenol treatment.

      Thank you for your correction. We have revised the describtion in line 166.

      (6) Line 185: The data showing EUG increased slow MyHC fluorescence intensity in Fig. 5D are not clear at all. Quantification is required.

      Thank you for your suggestion. We have attempted to submit clearer images in Figure 5E, and the quantification have been provided.

      (7) Line 235: IL-15 expression is positively correlated with MyHC IIa, suggesting IL-15 is a slow muscle myokine (See line 2398). However, MyHC IIa is a marker of fast muscle fibres (see line 50).

      Thank you for your correction. As you pointed, MyHC IIa is fast-twitch oxidative muscle fiber. We have replaced ‘slow’ with ‘oxidative’ in line 235.

      (8) Fig.9C and 9D show that inhibition of TRPV1 and CaN attenuated the upregulation of IL-15 mRNA and protein by eugenol in C2C12 cell line. This result is important in demonstrating the link of TRPV1 and CaN to IL-15. It will be more interesting and physiologically relevant to perform this experiment in primary skeletal muscle cells isolated from mice.

      Thank you for your suggestion. This is indeed an interesting idea. We will attempt to continue our experiments in mice and primary porcine muscle cells in future studies.

      (9) It is concerning that 4-week-old male mice were used for the study. The 4-week-old mice are immature. Adult mice over 8 weeks should be used. It is thus unknown whether the findings are broadly applicable to adult age.

      Thanks for your professional question. Age indeed has an impact on the muscle fiber type in mammals. Based on previously observed patterns of muscle fiber changes with age in various mammals (Katsumata et al., 2021; Pandorf et al., 2012; Hill et al., 2020), we believe that changes in muscle fiber types occur more frequently in juvenile mammals, mainly manifesting as a sharp increase in fast muscle fibers. Therefore, interventions during the juvenile stage might be more effective in promoting the transformation of fast to slow muscle fibers. As a result, in most of our group's research using nutritional interventions to regulate muscle fiber types, we tend to start interventions from the age of 4 weeks in mice. If we began intervention at 8 weeks, we speculate that the effectiveness would not be as potent as starting at 4 weeks. Below are the patterns of muscle fiber changes with age in various mammalian models, provided for reference:

      (1) Changes in muscle fiber types with age in pigs:

      As shown in the following figure, there is a dramatic change in the muscle fiber types 12 days post birth in pigs, especially with a sharp increase in fast muscle fibers, which continues until day 45. After 45 days of age, the changes in muscle fiber types become relatively gradual.

      Author response table 2.

      Developmental change Of proportions Of muscle fiber types in Longissimus dorsi muscle determined by histochemical analysis for myosin adenosine triphosphatase activity (%)

      Least squares means and pooled standard errors (n = 3). MHC, myosin heavy chain; ND, not detected. *P<0.10, **P<0.01 Least square means followed by different letters on the same row are significantly different (P < 0.05).

      Reference:

      Katsumata, M., Yamaguchi, T., Ishida, A., & Ashihara, A. (2017). Changes in muscle fiber type and expression of mRNA of myosin heavy chain isoforms in porcine muscle during pre- and postnatal development. Animal science journal, 88(2), 364–371.

      (2) Changes in muscle fiber types with age in rats:

      As illustrated in the subsequent figure, the muscle fiber types in rats undergo significant changes before 20 days of age (3-week-old), notably with a pronounced increase in type IIb fast-twitch fibers. After reaching 20 days of age, the changes in type IIb muscle fibers tend to stabilize and become more gradual.

      Author response image 2.

      Reference:

      Pandorf, C. E., Jiang, W., Qin, A. X., Bodell, P. W., Baldwin, K. M., & Haddad, F. (2012). Regulation of an antisense RNA with the transition of neonatal to IIb myosin heavy chain during postnatal development and hypothyroidism in rat skeletal muscle. American journal of physiology. 302(7), R854–R867.

      (3) Changes in muscle fiber types with age in mice:

      As depicted in the following figure, when comparing 10-week-old mice to 78-week-old aged mice, there are no significant changes in muscle fiber types.

      Author response image 3.

      Reference:

      Hill, C., James, R. S., Cox, V. M., Seebacher, F., & Tallis, J. (2020). Age-related changes in isolated mouse skeletal muscle function are dependent on sex, muscle, and contractility mode. American journal of physiology. Regulatory, integrative and comparative physiology, 319(3), R296–R314.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1:

      Specificity of MYL3 Selection:

      My previous question focused on why MYL3 was prioritized over other myosin family members. While the response broadly implicates myosins in viral entry, it does not justify why MYL3 was specifically chosen. For clarity, the "Introduction sections" should explicitly state the unique features of MYL3 (e.g., domain structure, binding affinity, or prior evidence linking it to NNV) that distinguish it from other myosins.

      Thank you for your valuable comment regarding the specificity of MYL3 selection. In response, we have revised the "Introduction" section to explicitly clarify the rationale for prioritizing MYL3 over other myosin family members. Specifically, we have now included prior evidence linking MYL3 to NNV infection, citing our studies that identified MYL3 as a potential host factor interacting with NNV CP protein. In our previous study, sixteen CP-interacting proteins were identified by Co-IP assays followed by MS, including HSP90ab1, Centrosomal protein 170B, MYL3 and so on. In addition to our findings, previous study by other researchers has also reported that Epinephelus coioides MYL3 can bind to NNV (page 3, lines 79–81). These revisions provide a clearer justification for the selection of MYL3 and distinguish it from other myosin proteins. The added content can be found in the revised manuscript on page 3, lines 81–84.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Response to the reviewer #2 (Public review):

      We greatly appreciate the reviewer’s high evaluation of our paper and helpful comments and suggestions.

      Regarding in vivo Treg homing assay, we did not exclude doublets and dead cells from the analysis of Kaede-expressing Tregs migrated to the aorta, which may affect the results. We described this issue as the limitation of this study in the revised manuscript. Nonetheless, we believe the reliability of our findings because we repeated this experiment three times and obtained similar results.

      There is no evidence to support the clinical relevance of our findings. Future clinical research on this topic is highly desired.

      Response to the reviewer #3 (Public review):

      We greatly appreciate the reviewer’s high evaluation of our paper and helpful comments and suggestions.

      Despite the controversial role of Th17 cells in atherosclerosis, we understand the possible involvement of Th17 cells and the Th1 cell/Th17 cell balance in lymphoid tissues and aortic lesions in accelerated inflammation and atherosclerosis in Ccr4<sup>-/-</sup>Apoe<sup>-/-</sup> mice. Although we could not completely evaluate the changes in these immune responses in detail, future study may elucidate interesting mechanisms mediated by Th17 cell responses.

      As the reviewer suggested, we understand that it is necessary to provide in vivo evidence for the Treg suppressive effects on DC activation. Based on the results of in vitro experiments, we described the discussion on the in vivo evidence in the revised manuscript.

      We understand methodological limitations for flow cytometric analysis of immune cells in the aorta and in vivo Treg homing assay. We described this issue as the limitation of this study in the revised manuscript. Regarding in vivo Treg homing assay, we statistically re-analyzed the combined data from multiple experiments and observed a tendency toward reduction in the proportion of CCR4-deficient Kaede-expressing Tregs in the aorta of recipient Apoe<sup>-/-</sup> mice, though there was no statistically significant difference in the migratory capacity of CCR4-intact or CCR4-deficient Kaede-expressing Tregs. Accordingly, we toned down our claim that CCR4 expression on Tregs plays a critical role in mediating Treg migration to the atherosclerotic aorta under hypercholesterolemia.

      The reviewer requested us to evaluate aortic inflammation in Ccr4<sup>-/-</sup>Apoe<sup>-/-</sup> mice injected with CCR4-intact or CCR4-deficient Tregs. However, we think that this experiment will provide marginal information because Treg transfer experiments in Apoe<sup>-/-</sup> mice have already shown the protective role of CCR4 in Tregs against aortic inflammation and early atherosclerosis.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) #1 and #2: CD103 and CD86 expression should be discussed on the text and not only in the response to reviewer.

      In accordance with the reviewer’s suggestion, we added a discussion on the downregulated CD103 expression in peripheral LN Tregs and upregulated CD86 expression on DCs in Ccr4<sup>-/-</sup>Apoe<sup>-/-</sup> mice in the discussion section in the revised manuscript.

      (2) #5: Authors response is not satisfactory. No gate percentage is shown. As it currently is, the difference in the number of cells shown in the figure could be due to differences in events recorded. Furthermore, the gate strategy is not thorough. Considering the very low frequency of Kaede + cells detected, it is crucial to properly exclude doublets and dead cells.

      Authors reported a dramatic difference in Kaede + Tregs cells in the aorta across experiments. This could be addressed by normalization followed by appropriate statistical analysis (One sample t-test).

      The data shown is not strong enough to conclude that there is a reduced migration to the aorta.

      We understand the importance of reviewer’s suggestion. We described the percentage of Kaede+ Tregs in the aorta of Apoe<sup>-/-</sup> mice receiving transfer of Kaede-expressing CCR4-intact or CCR4-deficient Tregs in Figure 5I.

      As the reviewer pointed out, we understand that it would be important to properly exclude doublets and dead cells in in vivo Treg homing assay. However, it is difficult for us to resolve this issue because we need to perform the same experiments again which will require a great number of additional mice and substantial amount of time. We deeply regret that these important experimental procedures were not performed. We described this issue as the limitation of this study.

      In accordance with the reviewer’s suggestion, we re-analyzed the combined data from multiple experiments using one-sample t-test. We observed a tendency toward reduction in the proportion of CCR4-deficient Kaede-expressing Tregs in the aorta of recipient Apoe<sup>-/-</sup> mice, though there was no statistically significant difference in the migratory capacity of CCR4-intact or CCR4-deficient Kaede-expressing Tregs. By modifying the corresponding descriptions in the manuscript, we toned down our claim that CCR4 expression on Tregs plays a critical role in mediating Treg migration to the atherosclerotic aorta under hypercholesterolemia.

      (3) #8: There are still several not shown data

      In accordance with the reviewer’s suggestion, we showed the data on the responses of Tregs and effector memory T cells in 8-week-old wild-type or Ccr4<sup>-/-</sup> mice and Ccr4 mRNA expression in Tregs and non-Tregs from Apoe<sup>-/-</sup> or Ccr4<sup>-/-</sup>Apoe<sup>-/-</sup> mice in Supplementary Figures 4 and 7.

      Reviewer #3 (Recommendations for the authors):

      (1) Issue 1. For future studies, I recommend not omitting viability controls during cell staining. Removal of dead cells and doublets should always be included during the gating strategy to avoid undesirable artefacts, especially when analysing less-represented cell populations. According to your previous report (ref #40), I agree that isotype controls were unnecessary using the same staining protocol. FMO controls should always be included in flow cytometry analysis (not mentioned in the methodology description and ref#40).

      As the reviewer suggested, we understand that it would be important to properly exclude dead cells and doublets and to prepare FMO controls in flow cytometric analysis. We deeply regret that these important experimental procedures were not performed. We described this issue as the limitation of this study.

      (2) Issue 3. Although Th17's role in atherosclerosis remains controversial, the data obtained in this work could provide valuable insights if discussed appropriately. As noted in my public review, I found it noteworthy that ROR γ t+ cells represented around 13% of effector TCD45+CD3+CD4+ lymphocytes in the aorta of Apoe<sup>-/-</sup> mice while Th1 less than 5% (Fig 4H and F, respectively). I recognise that differences in cell staining sensibility and robustness for different transcription factors may influence these percentages. However, analysing how CCR4 deficiency influences the Th1/TI h17 balance would yield interesting data, similar to what was done for the Th1/Treg ratio.

      Considering the higher proportion of Th17 cells than Th1 or Th2 cells in atherosclerotic aorta, we understand the importance of reviewer’s suggestion. However, we could not evaluate the effect of CCR4 deficiency on the Th1/Th17 balance in aorta because we did not perform flow cytometric analysis of aortic Th1 and Th17 cells in the same mice. Meanwhile, we could examine the Th1/Th17 balance in peripheral lymphoid tissues by flow cytometry. We found a significant increase in the Th1/Th17 ratio in the peripheral LNs of Ccr4<sup>-/-</sup>Apoe<sup>-/-</sup> mice, while there were no changes in its ratio in the spleen or para-aortic LNs of these mice, which limits the contribution of the Th1/Th17 balance to exacerbated atherosclerosis. We showed these data below.

      Author response image 1.

      (3) Issue 4. I appreciate the authors for sharing data on the flow cytometry analysis of Tregs in para-aortic LNs of Apoe<sup>-/-</sup> and Ccr4<sup>-/-</sup> Apoe<sup>-/-</sup> mice, which would have been included as a Supplementary figure. These results reinforce the notion that Treg dysfunction in CCR4-deficient mice may not be due to the downregulation of regulatory cell surface receptors.

      We showed the data on the expression of CTLA-4, CD103, and PD1 in Tregs in the para-aortic LNs of Apoe<sup>-/-</sup> and Ccr4<sup>-/-</sup>Apoe<sup>-/-</sup> mice in Supplementary Figure 8.

      (4) Issue 5. I agree that CD4+ T cell responses are substantially regulated by DCs. While CD80 and CD86 on DC primarily serve as costimulatory signals for T-cell activation, cytokines secreted by DCs are primordial signals for determining the differentiation phenotype of effector Th cells. Since the analysis of DC phenotype in lymphoid tissues of Apoe<sup>-/-</sup> and Ccr4<sup>-/-</sup> Apoe<sup>-/-</sup> mice could not be addressed in this study, it is not possible to differentiate which processes may be mainly affected by CCR4-deficiency during CD4+ T cell activation. In this scenario, and considering in vitro studies, the results suggest a possible role of CCR4 in controlling the extent of activation of CD4+T cells rather than shifting the CD4+T cell differentiation profile in peripheral lymphoid tissues, where a predominant Th1 profile was already established in Apoe<sup>-/-</sup> mice. Therefore, I advise caution when concluding about shifts in CD4+ T cell responses.

      We thank the reviewer for providing us thoughtful comments. As the reviewer pointed out, we understand that we should carefully interpret the mechanisms for the shift of CD4+ T cell responses by CCR4 deficiency.

      (5) Regarding migration studies in the revised manuscript. I fully understand that Treg transference assays are challenging. The results do not suggest that CCR4 was critical for Treg migration to lymphoid tissues in the conditions assayed. Concerning migration to the aorta, I found the results inconclusive since the authors mention that: i) there was a dramatic difference in the absolute numbers of Kaede-expressing Tregs that migrated to the aorta impairing statistical analysis; ii) the number of Kaede-expressing Tregs that migrated to the aorta was extremely low; iii) dead cells and doublets were not removed in the flow cytometry analysis. In this context, I do not agree with the following statements and recommend revising them:

      - "CCR4 deficiency in Tregs impaired their migration to the atherosclerotic aorta" (lines 36-7),

      - "…we found a significant reduction in the proportion of CCR4 deficient Kaede-expressing Tregs in the aorta of recipient Apoe<sup>-/-</sup> mice" (lines 356-7),

      - "CCR4 expression on Tregs regulates the development of early atherosclerosis by....... mediating Treg migration to the atherosclerotic aorta" (lines 409-411),

      - "…we found that CCR4 expression on Tregs is critical for regulating atherosclerosis by mediating their migration to the atherosclerotic aorta" (lines 437-438),

      - "CCR4 protects against early atherosclerosis by mediating Treg migration to the aorta.... (lines 464-465),

      - "We showed that CCR4 expression on Tregs is critical for ...... mediating Treg migration to the atherosclerotic aorta" (503-505).

      We understand the importance of the reviewer’s suggestion. We described this issue as the limitation of this study. In accordance with the reviewer’s suggestion, we modified the above descriptions and toned down our claim that CCR4 expression on Tregs plays a critical role in mediating Treg migration to the atherosclerotic aorta under hypercholesterolemia.

      (6) Line 206: Mention the increased expression of CD86 by DCs

      We mentioned this result in the revised manuscript. We also added a discussion on the upregulated CD86 expression on DCs in Ccr4<sup>-/-</sup>Apoe<sup>-/-</sup> mice in the discussion section in the revised manuscript.

      (7) Lines 304-305. According to Fig 4F-H, a selective accumulation of Th1 cells seems to have occurred only in the aorta, coinciding with a higher Th1/Treg ratio. No selective accumulation of Th1 cells was observed in para-aortic lymph nodes. These results could be clarified.

      We modified the above description in the revised manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1:

      (1) I miss some treatment of the lack of behavioural correlate. What does it mean that metamine benefits EEG classification accuracy without improving performance? One possibility here is that there is an improvement in response latency, rather than perceptual sensitivity. Is there any hint of that in the RT results? In some sort of combined measure of RT and accuracy? 

      First, we would like to thank the reviewer for their positive assessment of our work and for their extremely helpful and constructive comments that helped to significantly improve the quality of our manuscript.  

      The reviewer rightly points out that, to our surprise, we did not obtain a correlate of the effect of memantine in our behavioral data, neither in the reported accuracy data nor in the RT data. We do not report RT results as participants were instructed to respond as accurately as possible, without speed pressure. We added a paragraph in the discussion section to point to possible reasons for this surprising finding:

      “There are several possible reasons for this lack of behavioral correlate.  For example, EEG decoding may be a more sensitive measure of the neural effects of memantine, in particular given that perceptual sensitivity may have been at floor (masked condition, experiment 1) or ceiling (unmasked condition, experiment 1, and experiment 2). It is also possible that the present decoding results are merely epiphenomenal, not mapping onto functional improvements (e.g., Williams et al., 2007). However, given that we found a tight link between these EEG decoding markers and behavioral performance in our previous work (Fahrenfort et al., 2017; Noorman et al., 2023), it is possible that the effect of memantine was just too subtle to show up in changes in overt behavior.”

      (2) An explanation is missing, about why memantine impacts the decoding of illusion but not collinearity. At a systems level, how would this work? How would NMDAR antagonism selectively impact long-range connectivity, but not lateral connectivity? Is this supported by our understanding of laminar connectivity and neurochemistry in the visual cortex?

      We have no straightforward or mechanistic explanation for this finding. In the revised discussion, we are highlighting this finding more clearly, and included some speculative explanations:

      “The present effect of memantine was largely specific to illusion decoding, our marker of feedback processing, while collinearity decoding, our marker of lateral processing, was not (experiment 1) or only weakly (experiment 2) affected by memantine. We have no straightforward explanation for why NMDA receptor blockade would impact inter-areal feedback connections more strongly than intra-areal lateral connections, considering their strong functional interdependency and interaction in grouping and segmentation processes (Liang et al., 2017). One possibility is that this finding reflects properties of our EEG decoding markers for feedback vs. lateral processing: for example, decoding of the Kanizsa illusion may have been more sensitive to the relatively subtle effect of our pharmacological manipulation, either because overall decoding was better than for collinearity or because NMDA receptor dependent recurrent processes more strongly contribute to illusion decoding than to collinearity decoding.”

      (3) The motivating idea for the paper is that the NMDAR antagonist might disrupt the modulation of the AMPA-mediated glu signal. This is in line with the motivating logic for Self et al., 2012, where NMDAR and AMPAR efficacy in macacque V1 was manipulated via microinfusion. But this logic seems to conflict with a broader understanding of NMDA antagonism. NMDA antagonism appears to generally have the net effect of increasing glu (and ACh) in the cortex through a selective effect on inhibitory GABAergic cells (eg. Olney, Newcomer, & Farber, 1999). Memantine, in particular, has a specific impact on extrasynaptic NMDARs (that is in contrast to ketamine; Milnerwood et al, 2010, Neuron), and this type of receptor is prominent in GABA cells (eg. Yao et al., 2022, JoN). The effect of NMDA antagonists on GABAergic cells generally appears to be much stronger than the effect on glutamergic cells (at least in the hippocampus; eg. Grunze et al., 1996).

      This all means that it's reasonable to expect that memantine might have a benefit to visually evoked activity. This idea is raised in the GD of the paper, based on a separate literature from that I mentioned above. But all of this could be better spelled out earlier in the paper, so that the result observed in the paper can be interpreted by the reader in this broader context.

      To my mind, the challenging task is for the authors to explain why memantine causes an increase in EEG decoding, where microinfusion of an NMDA antagonist into V1 reduced the neural signal Self et al., 2012. This might be as simple as the change in drug... memantine's specific efficacy on extrasynaptic NMDA receptors might not be shared with whatever NMDA antagonist was used in Self et al. 2012. Ketamine and memantine are already known to differ in this way. 

      We addressed the reviewer’s comments in the following way. First, we bring up our (to us, surprising) result already at the end of the Introduction, pointing the reader to the explanation mentioned by the reviewer:

      “We hypothesized that disrupting the reentrant glutamate signal via blocking NMDA receptors by memantine would impair illusion and possibly collinearity decoding, as putative markers of feedback and lateral processing, but would spare the decoding of local contrast differences, our marker of feedforward processing. To foreshadow our results, memantine indeed specifically affected illusion decoding, but enhancing rather than impairing it. In the Discussion, we offer explanations for this surprising finding, including the effect of memantine on extrasynaptic NMDA receptors in GABAergic cells, which may have resulted in boosted visual activity.”

      Second, as outlined in the response to the first point by Reviewer #2, we are now clear throughout the title, abstract, and paper that memantine “improved” rather than “modulated” illusion decoding.

      Third, and most importantly, we restructured and expanded the Discussion section to include the reviewer’s proposed mechanisms and explanations for the effect. We would like to thank the reviewer for pointing us to this literature. We also discuss the results of Self et al. (2012), specifically the distinct effects of the two NMDAR antagonists used in this study, more extensively, and speculate that their effects may have been similar to ketamine and thus possibly opposite of memantine (for the feedback signal):

      “Although both drugs are known to inhibit NMDA receptors by occupying the receptor’s ion channel and are thereby blocking current flow (Glasgow et al., 2017; Molina et al., 2020), the drugs have different actions at receptors other than NMDA, with ketamine acting on dopamine D2 and serotonin 5-HT2 receptors, and memantine inhibiting several subtypes of the acetylcholine (ACh) receptor as well as serotonin 5HT3 receptors. Memantine and ketamine are also known to target different NMDA receptor subpopulations, with their inhibitory action displaying different time courses and intensity (Glasgow et al., 2017; Johnson et al., 2015). Blockade of different NMDA receptor subpopulations can result in markedly different and even opposite results. For example, Self and colleagues (2012) found overall reduced or elevated visual activity after microinfusion of two different selective NMDA receptor antagonists (2-amino-5phosphonovalerate and ifendprodil) in macaque primary visual cortex. Although both drugs impaired the feedback-related response to figure vs. ground, similar to the effects of ketamine (Meuwese et al., 2013; van Loon et al., 2016) such opposite effects on overall activity demonstrate that the effects of NMDA antagonism strongly depend on the targeted receptor subpopulation, each with distinct functional properties.”

      Finally, we link these differences to the potential mechanism via GABAergic neurons:

      “As mentioned in the Introduction, this may be related to memantine modulating processing at other pre- or post-synaptic receptors present at NMDA-rich synapses, specifically affecting extrasynaptic NMDA receptors in GABAergic cells (Milnerwood et al, 2010; Yao et al., 2022). Memantine’s strong effect on extrasynaptic NMDA receptors in GABAergic cells leads to increases in ACh levels, which have been shown to increase firing rates and reduce firing rate variability in macaques (Herrero et al., 2013, 2008). This may represent a mechanism through which memantine (but not ketamine or the NMDA receptor antagonists used by Self and colleagues) could boost visually evoked activity.”

      (4) The paper's proposal is that the effect of memantine is mediated by an impact on the efficacy of reentrant signaling in visual cortex. But perhaps the best-known impact of NMDAR manipulation is on LTP, in the hippocampus particularly but also broadly.

      Perception and identification of the kanisza illusion may be sensitive to learning (eg. Maertens & Pollmann, 2005; Gellatly, 1982; Rubin, Nakayama, Shapley, 1997); what argues against an account of the results from an effect on perceptual learning? Generally, the paper proposes a very specific mechanism through which the drug influences perception. This is motivated by results from Self et al 2012 where an NMDA antagonist was infused into V1. But oral memantine will, of course, have a whole-brain effect, and some of these effects are well characterized and - on the surface - appear as potential sources of change in illusion perception. The paper needs some treatment of the known ancillary effects of diffuse NMDAR antagonism to convince the reader that the account provided is better than the other possibilities. 

      We cannot fully exclude an effect based on perceptual learning but consider this possibility highly unlikely for several reasons. First, subjects have performed more than a thousand trials in a localizer session before starting the main task (in experiment 2 even more than two thousand) containing the drug manipulation. Therefore, a large part of putative perceptual learning would have already occurred before starting the main experiment. Second, the main experiment was counterbalanced across drug sessions, so half of the participants first performed the memantine session and then the placebo session, and the other half of the subjects the other way around. If memantine would have improved perceptual learning in our experiments, one may actually expect to observe improved decoding in the placebo session and not in the memantine session. If memantine would have facilitated perceptual learning during the memantine session, the effect of that facilitated perceptual learning would have been most visible in the placebo session following the memantine session. Because we observed improved decoding in the memantine session itself, perceptual learning is likely not the main explanation for these findings. Third, perceptual learning is known to occur for several stimulus dimensions (e.g., orientation, spatial frequency or contrast). If these findings would have been driven by perceptual learning one would have expected to see perceptual learning for all three features, whereas the memantine effects were specific to illusion decoding. Especially in experiment 2, all features were equally often task relevant and in such a situation one would’ve expected to observe perceptual learning effects on those other features as well.  

      To further investigate any potential role of perceptual learning, we analyzed participants’ performance in detecting the Kanizsa illusion over the course of the experiments. To investigate this, we divided the experiments’ trials into four time bins, from the beginning until the end of the experiment. For the first experiment’s first target (T1), there was no interaction between the factors bin and drug (memantine/placebo; F<sub>3,84</sub>=0.89, P\=0.437; Figure S6A). For the second target (T2), we performed a repeatedmeasures ANOVA with the factors bin, drug, T1-T2 lag (short/long), and masks (present/absent). There was only a trend towards a bin by drug interaction (F<sub>3,84</sub>=2.57, P\=0.064; Figure S6B), reflecting worse performance under memantine in the first three bins and slightly better performance in the fourth bin. The other interactions that include the factors bin and drug factors were not significant (all P>0.117). For the second experiment, we performed a repeated-measures ANOVA with the factors bin, drug, masks, and task-relevant feature (local contrast/collinearity/illusion). None of the interactions that included the bin and drug factors were significant (all P>0.219; Figure S6C). Taken together, memantine does not appear to affect Kanizsa illusion detection performance through perceptual learning. Finally, there was no interaction between the factors bin and task-relevant feature (F<sub>6,150</sub>=0.76, P\=0.547; Figure S6D), implying there is no perceptual learning effect specific to Kanizsa illusion detection. We included these analyses in our revised Supplement as Fig. S6.

      (5) The cross-decoding approach to data analysis concerns me a little. The approach adopted here is to train models on a localizer task, in this case, a task where participants matched a kanisza figure to a target template (E1) or discriminated one of the three relevant stimuli features (E2). The resulting model was subsequently employed to classify the stimuli seen during separate tasks - an AB task in E1, and a feature discrimination task in E2. This scheme makes the localizer task very important. If models built from this task have any bias, this will taint classifier accuracy in the analysis of experimental data. My concern is that the emergence of the kanisza illusion in the localizer task was probably quite salient, respective to changes in stimuli rotation or collinearity. If the model was better at detecting the illusion to begin with, the data pattern - where drug manipulation impacts classification in this condition but not other conditions - may simply reflect model insensitivity to non-illusion features.

      I am also vaguely worried by manipulations implemented in the main task that do not emerge in the localizer - the use of RSVP in E1 and manipulation of the base rate and staircasing in E2. This all starts to introduce the possibility that localizer and experimental data just don't correspond, that this generates low classification accuracy in the experimental results and ineffective classification in some conditions (ie. when stimuli are masked; would collinearity decoding in the unmasked condition potentially differ if classification accuracy were not at a floor? See Figure 3c upper, Figure 5c lower).

      What is the motivation for the use of localizer validation at all? The same hypotheses can be tested using within-experiment cross-validation, rather than validation from a model built on localizer data. The argument may be that this kind of modelling will necessarily employ a smaller dataset, but, while true, this effect can be minimized at the expense of computational cost - many-fold cross-validation will mean that the vast majority of data contributes to model building in each instance. 

      It would be compelling if results were to reproduce when classification was validated in this kind of way. This kind of analysis would fit very well into the supplementary material.

      We thank the reviewer for this excellent question. We used separate localizers for several reasons, exactly to circumvent the kind of biases in decoding that the reviewer alludes to. Below we have detailed our rationale, first focusing on our general rationale and then focusing on the decisions we made in designing the specific experiments.  

      Using a localizer task in the design of decoding analysis offers several key advantages over relying solely on k-fold cross-validation within the main task:

      (1) Feature selection independence and better generalization: A separate localizer task allows for independent feature selection, ensuring that the features used for decoding are chosen without bias from the main task data. Specifically, the use of a localizer task allows us to determine the time-windows of interest independently based on the peaks of the decoding in the localizer. This allows for a better direct comparison between the memantine and placebo conditions because we can isolate the relevant time windows outside a drug manipulation. Further, training a classifier on a localizer task and testing it on a separate experimental task assesses whether neural representations generalize across contexts, rather than simply distinguishing conditions within a single dataset. This supports claims about the robustness of the decoded information.

      (2) Increased sensitivity and interpretability: The localizer task can be designed specifically to elicit strong, reliable responses in the relevant neural patterns. This can improve signal-to-noise ratio and make it easier to interpret the features being used for decoding in the test set. We facilitate this by having many more trials in the localizer tasks (1280 in E1 and 5184 in E2) than in the separate conditions of the main task, in which we would have to do k-folding (e.g., 2, mask, x 2 (lag) design in E1 leaves fewer than 256 trials, due to preprocessing, for specific comparisons) on very low trial numbers. The same holds for experiment 2 which has a 2x3 design, but also included the base-rate manipulation. Finally, we further facilitate sensitivity of the model by having the stimuli presented at full contrast without any manipulations of attention or masking during the localizer, which allows us to extract the feature specific EEG signals in the most optimal way.

      (3) Decoupling task-specific confounds: If decoding is performed within the main task using k-folding, there is a risk that task-related confounds (e.g., motor responses, attention shifts, drug) influence decoding performance. A localizer task allows us to separate the neural representation of interest from these taskrelated confounds.

      Experiment 1 

      In experiment 1, the Kanizsa was always task relevant in the main experiment in which we employed the pharmacological manipulation. To make sure that the classifiers were not biased towards Kanizsa figures from the start (which would be the case if we would have done k-folding in the main task), we used a training set in which all features were equally relevant for task performance. As can be seen in figure 1E, which plots the decoding accuracies of the localizer task, illusion decoding as well as rotation decoding were equally strong, whereas collinearity decoding was weaker. It may be that the Kanizsa illusion was quite salient in the localizer task, which we can’t know at present, but it was at least less salient and relevant than in the main task (where it was the only task-relevant feature). Based on the localizer decoding results one could argue that the rotation dimension and illusion dimension were most salient, because the decoding was highest for these dimensions. Clearly the model was not insensitive to nonillusory features. The localizer task of experiment 2 reveals that collinearity decoding tends to be generally lower, even when that feature is task relevant.  

      Experiment 2 

      In experiment 2, the localizer task and main task were also similar, with three exceptions: during the localizer task no drug was active, and no masking and no base rate manipulation were employed. To make sure that the classifier was not biased towards a certain stimulus category (due to the bias manipulation), e.g. the stimulus that is presented most often, we used a localizer task without this manipulation. As can be seen in figure 4D decoding of all the features was highly robust, also for example for the collinearity condition. Therefore the low decoding that we observe in the main experiment cannot be due to poor classifier training or feature extraction in the localizer. We believe this is actually an advantage instead of a disadvantage of the current decoding protocol.

      Based on the rationale presented above we are uncomfortable performing the suggested analyses using a k-folding approach in the main task, because according to our standards the trial numbers are too low and the risk that these results are somehow influenced by task specific confounds cannot be ruled out.  

      Line 301 - 'Interestingly, in both experiments the effect of memantine... was specific to... stimuli presented without a backward mask.' This rubs a bit, given that the mask broadly disrupted classification. The absence of memantine results in masked results may simply be a product of the floor ... some care is needed in the interpretation of this pattern. 

      In the results section of experiment 1, we added:

      “While the interaction between masking and memantine only approached significance (P\=0.068), the absence of an effect of memantine in the masked condition could reflect a floor effect, given that illusion decoding in the masked condition was not significantly better than chance.”

      While floor is less likely to account for the absence of an effect in the masked condition in experiment 2, where illusion decoding in the masked condition was significantly above chance, it is still possible that to obtain an effect of memantine, decoding accuracy needed to be higher. We therefore also added here:

      “For our time window-based analyses of illusion decoding, the specificity of the memantine effect to the unmasked condition was supported by a significant interaction between drug and masking (note, however, given overall much lower decoding accuracy in the masked condition, the lack of a memantine effect could reflect a floor effect).”

      In the discussion, we changed the sentence to read “…the effect of memantine on illusion decoding tended to be specific to attended, task-relevant stimuli presented without a backward mask.”

      Line 441 - What were the contraindications/exclusion parameters for the administration of memantine? 

      Thanks for spotting this. We have added the relevant exclusion criteria in the revised version of the supplement. See also below.

      – Allergy for memantine or one of the inactive ingredients of these products;

      – (History of) psychiatric treatment;

      – First-degree relative with (history of) schizophrenia or major depression;

      – (History of) clinically significant hepatic, cardiac, obstructive respiratory, renal, cerebrovascular, metabolic or pulmonary disease, including, but not limited to fibrotic disorders;

      – Claustrophobia;

      –  Regular usage of medicines (antihistamines or occasional use of paracetamol);

      – (History of) neurological disease;

      –  (History of) epilepsy;

      –  Abnormal hearing or (uncorrected) vision;

      –  Average use of more than 15 alcoholic beverages weekly;

      – Smoking

      – History of drug (opiate, LSD, (meth)amphetamine, cocaine, solvents, cannabis, or barbiturate) or alcohol dependence;

      – Any known other serious health problem or mental/physical stress;

      – Used psychotropic medication, or recreational drugs over a period of 72 hours prior to each test session,  

      – Used alcohol within the last 24 hours prior to each test session;

      – (History of) pheochromocytoma.

      – Narrow-angle glaucoma;

      – (History of) ulcer disease;

      – Galactose intolerance, Lapp lactase deficiency or glucose­galactose malabsorption.

      – (History of) convulsion;

      Line 587 - The localizer task used to train the classifier in E2 was collected in different sessions. Was the number of trials from separate sessions ultimately equal? The issue here is that the localizer might pick up on subtle differences in electrode placement. If the test session happens to have electrode placement that is similar to the electrode placement that existed for a majority of one condition of the localizer... this will create bias. This is likely to be minor, but machine classifiers really love this kind of minor confound.

      Indeed, the trial counts in the separate sessions for the localizer in E2 were equal. We have added that information to the methods section.  

      Experiment 1: 1280 trials collected during the intake session.

      In experiment 2: 1728 trials were collected per session (intake, and 2 drug sessions), so there were 5184 trials across three sessions.

      Reviewer #2:

      To start off, I think the reader is being a bit tricked when reading the paper. Perhaps my priors are too strong, but I assumed, just like the authors, that NMDA-receptors would disrupt recurrent processing, in line with previous work. However, due to the continuous use of the ambiguous word 'affected' rather than the more clear increased or perturbed recurrent processing, the reader is left guessing what is actually found. That's until they read the results and discussion finding that decoding is actually improved. This seems like a really big deal, and I strongly urge the authors to reword their title, abstract, and introduction to make clear they hypothesized a disruption in decoding in the illusion condition, but found the opposite, namely an increase in decoding. I want to encourage the authors that this is still a fascinating finding.

      We thank the reviewer for the positive assessment of our manuscript, and for many helpful comments and suggestions.  

      We changed the title, abstract, and introduction in accordance with the reviewer’s comment, highlighting that “memantine […] improves decoding” and “enhances recurrent processing” in all three sections. We also changed the heading of the corresponding results section to “Memantine selectively improves decoding of the Kanizsa illusion”.

      Apologies if I have missed it, but it is not clear to me whether participants were given the drug or placebo during the localiser task. If they are given the drug this makes me question the logic of their analysis approach. How can one study the presence of a process, if their very means of detecting that process (the localiser) was disrupted in the first place? If participants were not given a drug during the localiser task, please make that clear. I'll proceed with the rest of my comments assuming the latter is the case. But if the former, please note that I am not sure how to interpret their findings in this paper.

      Thanks for asking this, this was indeed unclear. In experiment 1 the localizer was performed in the intake session in which no drugs were administered. In the second experiment the localizer was performed in all three sessions with equal trial numbers. In the intake session no drugs were administrated. In the other two sessions the localizer was performed directly after pill intake and therefore the memantine was not (or barely) active yet. We started the main task four hours after pill intake because that is the approximate peak time of memantine. Note that all three localizer tasks were averaged before using them as training set. We have clarified this in the revised manuscript.

      The main purpose of the paper is to study recurrent processing. The extent to which this study achieves this aim is completely dependent to what extent we can interpret decoding of illusory contours as uniquely capturing recurrent processing. While I am sure illusory contours rely on recurrent processing, it does not follow that decoding of illusory contours capture recurrent processing alone. Indeed, if the drug selectively manipulates recurrent processing, it's not obvious to me why the authors find the interaction with masking in experiment 2. Recurrent processing seems to still be happening in the masked condition, but is not affected by the NMDA-receptor here, so where does that leave us in interpreting the role of NMDA-receptors in recurrent processing? If the authors can not strengthen the claim that the effects are completely driven by affecting recurrent processing, I suggest that the paper will shift its focus to making claims about the encoding of illusory contours, rather than making primary claims about recurrent processing.

      We indeed used illusion decoding as a marker of recurrent processing. Clearly, such a marker based on a non-invasive and indirect method to record neural activity is not perfect. To directly and selectively manipulate recurrent processing, invasive methods and direct neural recordings would be required. However, as explained in the revised Introduction,

      “In recent work we have validated that the decoding profiles of these features of different complexities at different points in time, in combination with the associated topography, can indeed serve as EEG markers of feedforward, lateral and recurrent processes (Fahrenfort et al., 2017; Noorman et al., 2023).”  

      The timing and topography of the decoding results of the present study were consistent with our previous EEG decoding studies (Fahrenfort et al., 2017; Noorman et al., 2023). This validates the use of these EEG decoding signatures as (imperfect) markers of distinct neural processes, and we continue to use them as such. However, we expanded the discussion section to alert the reader to the indirect and imperfect nature of these EEG decoding signatures as markers of distinct neural processes: “Our approach relied on using EEG decoding of different stimulus features at different points in time, together with their topography, as markers of distinct neural processes. Although such non-invasive, indirect measures of neural activity cannot provide direct evidence for feedforward vs. recurrent processes, the timing, topography, and susceptibility to masking of the decoding signatures obtained in the present study are consistent with neurophysiology (e.g., Bosking et al., 1997; Kandel et al., 2000; Lamme & Roelfsema, 2000; Lee & Nguyen, 2001; Liang et al., 2017; Pak et al., 2020), as well as with our previous work (Fahrenfort et al., 2017; Noorman et al., 2023).” 

      The reviewer is also concerned about the lack of effect of memantine on illusion decoding in the masked condition in experiment 2. In our view, the strong effect of masking on illusion decoding (both in absolute terms, as well as when compared to its effect on local contrast decoding), provides strong support for our assumption that illusion decoding represents a marker of recurrent processing. Nevertheless, as the reviewer points out, weak but statistically significant illusion decoding was still possible in the masked condition, at least when the illusion was task-relevant. As the reviewer notes, this may reflect residual recurrent processing during masking, a conclusion consistent with the relatively high behavioral performance despite masking (d’ > 1). However, rather than invalidating the use of our EEG markers or challenging the role of NMDA-receptors in recurrent processing, this may simply reflect a floor effect. As outlined in our response to reviewer #1 (who was concerned about floor effects), in the results section of experiment 1, we added:

      “While the interaction between masking and memantine only approached significance (P\=0.068), the absence of an effect of memantine in the masked condition could reflect a floor effect, given that illusion decoding in the masked condition was not significantly better than chance.”

      And for experiment 1:

      “For our time window-based analyses of illusion decoding, the specificity of the memantine effect to the unmasked condition was supported by a significant interaction between drug and masking (note, however, given overall much lower decoding accuracy in the masked condition, the lack of a memantine effect could reflect a floor effect).”

      An additional claim is being made with regards to the effects of the drug manipulation. The authors state that this effect is only present when the stimulus is 1) consciously accessed, and 2) attended. The evidence for claim 1 is not supported by experiment 1, as the masking manipulation did not interact in the cluster-analyses, and the analyses focussing on the peak of the timing window do not show a significant effect either. There is evidence for this claim coming from experiment 2 as masking interacts with the drug condition. Evidence for the second claim (about task relevance) is not presented, as there is no interaction with the task condition. A classical error seems to be made here, where interactions are not properly tested. Instead, the presence of a significant effect in one condition but not the other is taken as sufficient evidence for an interaction, which is not appropriate. I therefore urge the authors to dampen the claim about the importance of attending to the decoded features. Alternatively, I suggest the authors run their interactions of interest on the time-courses and conduct the appropriate clusterbased analyses.

      We thank the reviewer for pointing out the importance of key interaction effects. Following the reviewer’s suggestion, we dampened our claims about the role of attention. For experiment 1, we changed the heading of the relevant results section from “Memantine’s effect on illusion decoding requires attention” to “The role of consciousness and attention in memantine’s effect on illusion decoding”, and we added the following in the results section:

      “Also our time window-based analyses showed a significant effect of memantine only when the illusion was both unmasked and presented outside the AB (t_28\=-2.76, _P\=0.010, BF<sub>10</sub>=4.53; Fig. 3F). Note, however, that although these post-hoc tests of the effect of memantine on illusion decoding were significant, for our time window-based analyses we did not obtain a statistically significant interaction between the AB and memantine, and the interaction between masking and memantine only approached significance (P\= 0.068). Thus, although these memantine effects were slightly less robust than for T1, probably due to reduced trial counts, these results point to (but do not conclusively demonstrate) a selective effect of memantine on illusion-related feedback processing that depends on the availability of attention. In addition to the lack of the interaction effect, another potential concern…”

      For experiment 2, we added the following in the results section:

      “Note that, for our time window-based analyses of illusion decoding, although the specificity of the memantine effect to the unmasked condition was supported by a significant interaction between drug and masking, we did not obtain a statistically significant interaction between memantine and task-relevance. Thus, although the memantine effect was significant only when the illusion was unmasked and taskrelevant, just like for the effect of temporal attention in experiment 1, these results do not conclusively demonstrate a selective effect of memantine that depends attention (task-relevance).”

      In the discussion, we toned down claims about memantine’s effects being specific to attended conditions, we are highlighting the “preliminary” nature of these findings, and we are now alerting the reader explicitly to be careful with interpreting these effects, e.g.:

      “Although these results have to be interpreted with caution because the key interaction effects were not statistically significant, …”

      How were the length of the peak-timing windows established in Figure 1E? My understanding is that this forms the training-time window for the further decoding analyses, so it is important to justify why they have different lengths, and how they are determined. The same goes for the peak AUC time windows for the interaction analyses. A number of claims in the paper rely on the interactions found in these posthoc analyses, so the 223- to 323 time window needs justification.

      Thanks for this question. The length of these peak-timing windows is different because the decoding of rotation is temporarily very precise and short-lived, whereas the decoding of the other features last much longer and is more temporally variable. In fact, we have followed the same procedure as in a previously published study (Noorman et al., elife 2025) for defining the peak-timing and length of the windows. We followed the same procedure for both experiments reported in this paper, replicating the crucial findings and therefore excluding the possibility that these findings are in any way dependent on the time windows that are selected. We have added that information to the revised version of the manuscript.

      Reviewer #3:

      First, despite its clear pattern of neural effects, there is no corresponding perceptual effect. Although the manipulation fits neatly within the conceptual framework, and there are many reasons for not finding such an effect (floor and ceiling effects, narrow perceptual tasks, etc), this does leave open the possibility that the observation is entirely epiphenomenal, and that the mechanisms being recorded here are not actually causally involved in perception per se.

      We thank the reviewer for the positive assessment of our work. The reviewer rightly points out that, to our surprise, we did not obtain a correlate of the effect of memantine in our behavioral data. We agree with the possible reasons for the absence of such an effect highlighted by the reviewer, and expanded our discussion section accordingly:

      “There are several possible reasons for this lack of behavioral correlate.  For example, EEG decoding may be a more sensitive measure of the neural effects of memantine, in particular given that perceptual sensitivity may have been at floor (masked condition, experiment 1) or ceiling (unmasked condition, experiment 1, and experiment 2). It is also possible that the present decoding results are merely epiphenomenal, not mapping onto functional improvements (e.g., Williams et al., 2007). However, given that in our previous work we found a tight link between these EEG decoding markers and behavioral performance (Fahrenfort et al., 2017; Noorman et al., 2023), it is possible that the effect of memantine in the present study was just too subtle to show up in changes in overt behavior.”

      Second, although it is clear that there is an effect on decoding in this particular condition, what that means is not entirely clear - particularly since performance improves, rather than decreases. It should be noted here that improvements in decoding performance do not necessarily need to map onto functional improvements, and we should all be careful to remain agnostic about what is driving classifier performance. Here too, the effect of memantine on decoding might be epiphenomenal - unrelated to the information carried in the neural population, but somehow changing the balance of how that is electrically aggregated on the surface of the skull. *Something* is changing, but that might be a neurochemical or electrical side-effect unrelated to actual processing (particularly since no corresponding behavioural impact is observed.)

      We would like to refer to our reply to the previous point, and we would like to add that in our previous work (Fahrenfort et al., 2017; Noorman et al., 2023) similar EEG decoding markers were often tightly linked to changes in behavioral performance. This indicates that these particular EEG decoding markers do not simply reflect some sideeffect not related to neural processing. However, as stated in the revised discussion section, “it is possible that the effect of memantine in the present study was just too subtle to show up in changes in overt behavior.”

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public Review):

      (…) In my view, the part about NF-YA1 is less strong - although I realize this is a compelling candidate to be a regulator of cell cycle progression, the experimental approaches used to address this question falls a bit short, in particular, compared to the very detailed approaches shown in the rest of the manuscript. The authors show that the transcription factor NF-YA1 regulates cell division in tobacco leaves; however, there is no experimental validation in the experimental system (nodules). All conclusions are based on a heterologous cell division system in tobacco leaves. The authors state that NF-YA1 has a nodule-specific role as a regulator of cell differentiation. I am concerned the tobacco system may not allow for adequate testing of this hypothesis.

      Reviewer #1 makes a valid point by asking to focus the manuscript more explicitly on the role of NF-YA1 as a differentiation factor in a symbiotic context. We have now addressed this formally and experimentally.

      The involvement of A-type NF-Y subunits in the transition to the early differentiation of nodule cells has been documented in model legumes through several publications that we refer to in the revised version of the discussion (lines 617/623). We fully agree that the CDEL system, because it is heterologous, does not allow us more than to propose a parallel explanation for these observations - i.e_., that the Medicago NF-YA1 subunit presumably acts in post-replicative cell-cycle regulation at the G2/M transition. Considering your recommendations and those of reviewer #2, we sought to support this conclusion by testing the impact of localized over-expression of _NF-YA1 on cortical cell division and infection competence at an early stage of root colonization. The results of these experiments are now presented in the new Figure 9 and Figure 9-figure supplement 1-5 and described from line 435 to 495.

      With the fluorescent tools the authors have at hand (in particular tools to detect G2/M transition, which the authors suggest is regulated by NF-YA1), it would be interesting to test what happens to cell division if NF-YA1 is over-expressed in Medicago roots?

      To limit pleiotropic effects of an ectopic over-expression, we used the symbiosis-induced, ENOD11 promoter to increase NF-YA1 expression levels more specifically along the trajectory of infected cells. We chose to remain in continuity with the experiments performed in the CDEL system by opting for a destabilized version of the KNOLLE transcriptional reporter to detect the G2/M transition. The results obtained are presented in Figure 9B (quantification of split infected cells), in Figure 9-figure supplement 1B (ENOD11 expression profile), in Figure 9-figure supplement 3B (representative confocal images) and Figure 9-figure supplement 4D (quantification of pKNOLLE reporter signal). There, we show that mitosis remains inhibited in cells accommodating infection threads, but is completed in a higher proportion of outer cortical cells positioned on the infection trajectory, where ENOD11 gene transcription is active before their physical colonization.

      Based on NF-YA1 expression data published previously and their results in tobacco epidermal cells, the authors hypothesize that NF-YA regulates the mitotic entry of nodule primordial cells. Given that much of the manuscript deals with earlier stages of the infection, I wonder if NF-YA1 could also have a role in regulating mitotic entry in cells adjacent to the infection thread?

      The expression profile of NF-YA1 at early stages of cortical infection (Laporte et al., 2014) is indeed similar to the one of ENOD11 (as shown in Figure 9-figure supplement 1C) in wild-type Medicago roots, with corresponding transcriptional reporters being both activated in cells adjacent to the infection thread. Under our experimental conditions, additional expression of NF-YA1 (driven by the ENOD11 promoter) in these neighbouring cells did not impact their propensity to enter mitosis and to complete cell division. These results are presented in Figure 9-figure supplement 4D (quantification of pKNOLLE reporter signal) and Figure 9-figure supplement 5 (quantification of split neighbouring cells).

      Reviewer #1 (Recommendations For The Authors):

      - In the first part, images show the qualitative presence/absence of H3.1 or H3.3 histones.

      Upon closer inspection, many cells seem to have both histones. In Fig1-S1 for example (root meristem), it is evident that there are many cells with low but clearly present H3.1 content in the green channel; however, in the overlay, the green is lost and H3.3 (pink) is mainly visible. What does this mean in terms of the cell cycle? 

      We fully agree with reviewer #1 on these points. Independent of whether they have low or high proliferation potential, most cells retain histone H3.1 particularly in silent regions of the genome, while H3.3 is constitutively produced and enriched at transcriptionally active regions. When channels are overlaid, cells in an active proliferation or endoreduplication state (in G1, S or G2, depending on the size of their nuclei) will appear mainly "green" (H3.1-eGFP positive). Cells with a low proliferation potential (e.g., in the QC), G2-arrested (e.g., IT-traversed) or terminally differentiating (e.g., containing symbiosomes or arbuscules) will appear mainly "magenta" (H3.1-low, medium to high H3.3-mCherry content).

      Furthermore, all nodule images only display the overlay image, and individual fluorescence channels are not shown. Does the same masking effect happen here? It may be helpful to quantify fluoresce intensity not only in green but also in red channels as done for other experiments.

      Quantifying fluorescence intensity in the mCherry channel may indeed help to highlight the likely replacement of H3.1-eGFP by H3.3-mCherry in infected cells, as described by Otero and colleagues (2016) at the onset of cellular differentiation. However, the quantification method as established (i.e., measuring the corrected total nuclear fluorescence at the equatorial plane) cannot be applied, most of the time, to infected cells' nuclei due to the overlapping presence of mCherry-producing S. meliloti in the same channel (e.g., in Figure 2B). Nevertheless, and to avoid this masking effect when the eGFP and mCherry channels are overlaid, we now present them as isolated channels in revised Figures 1-3 and associated figure supplements. As the cell-wall staining is regularly included and displayed in grayscale, we assigned to both of them the Green Fire Blue lookup table, which maps intensity values to a multiple-colour sequential scheme (with blue or yellow indicating low or high fluorescence levels, respectively). We hope that this will allow a better appreciation of the respective levels of H3.1- and H3.3-fusions in our confocal images.

      - Fig 1 B - it is hard to differentiate between S. meliloti-mCherry and H3.3-mCherry. Is there a way to label the different structures?

      In the revised version of Figure 1B, we used filled or empty arrowheads to point to histone H3-containing nuclei. To label rhizobia-associated structures, we used dashed lines to delineate nodule cells hosting symbiosomes and included the annotation “IT” for infection threads. We also indicated proliferating, endoreduplicating and differentiating tissues and cells using the following annotations: “CD” for cell division, “En” for endoreduplication and “TD” for terminal differentiation. All annotations are explained in the figure legend.

      - Fig 1 - supplement E and F - no statistics are shown.

      We performed non-parametric tests using the latest version of the GraphPad Prism software (version 10.4.1). Stars (Figure 1-figure supplement 1F) or different letters (Figure 1-figure supplement 1G) now indicate statistically significant differences. Results of the normality and non-parametric tests were included in the corresponding Source Data Files (Figure 1 – figure supplement 1 – source data 1 and 2). We have also updated the compact display of letters in other figures as indicated by the new software version. The raw data and the results of the statistical analyses remain unchanged and can be viewed in the corresponding source files.

      - Fig 2 A - overview and close-up image do not seem to be in the same focal plane. This is confusing because the nuclei position is different (so is the infection thread position).

      We fully agree that our former Figure may have confused reviewers #1 and #2 as well as readers. Figure 2A was designed to highlight, from the same nodule primordium, actively dividing cells of the inner cortex (optical section z 6-14) and cells of the outer cortex traversed, penetrated by or neighbouring an infection thread (optical section z 11-19). We initially wanted to show different magnification views of the same confocal image (i.e_._, a full-view of the inner cortex and a zoomed-view of the outer layers) to ensure that audiences can identify these details. In the revised version of Figure 2A, we displayed these full- and zoomed-views in upper and lower panels, respectively and we removed the solid-line inset to avoid confusion. 

      - Fig 1A and Fig 2E could be combined and shown at the beginning of the manuscript. Also, consider making the cell size increase more extreme, as it is important to differentiate G2 cells after H3.1 eviction and cells in G1. You have to look very closely at the graph to see the size differences.

      We have taken each of your suggestions into account. A combined version of our schematic representation with more pronounced nuclei size differences is now presented in Figure 1A.

      - Fig. 3 C is difficult to interpret. Can this be split into different panels?

      We realized that our previous choice of representation may have been confusing. Each value corresponds only to the H3.1-eGFP content, measured in an infected cell and reported to that of the neighbouring cell (IC / NC) within individual root samples. Therefore, we removed the green-magenta colour code and changed the legend accordingly. We hope that these slight modifications will facilitate the interpretation of the results - namely, that the relative level of H3.1 increases significantly in infected cells in the selected mutants compared to the wild-type. This mode of representation also highlights that in the mutants, there are more individual cases where the H3.1 content in an infected cell exceeds that of the neighbouring cell by more than two times. These cases would be masked if the couples of infected cells and associated neighbours would be split into different panels as in Figure 3B.

      - Line 357/359. I assume you mean ...'through the G2 phase can commit to nuclear division'.

      We have edited this sentence according to your suggestion, which now appears in line 370. 

      Reviewer #2 (Recommendations For The Authors):

      Cell cycle control during the nitrogen-fixing symbiosis is an important question but only poorly understood. This manuscript uses largely cell biological methods, which are always of the highest quality - to investigate host cell cycle progression during the early stages of nodule formation, where cortical infection threads penetrate the nodule primordium. The experiments were carefully conducted, the observations were detail oriented, and the results were thought-provoking. The study should be supported by mechanistic insights. 

      (1) One thought provoked by the authors' work is that while the study was carried out at an unprecedented resolution, the relationship between control of the cell cycle and infection thread penetration remains correlative. Is this reduced replicative potential among cells in the infection thread trajectory a consequence of hosting an infection thread, or a prerequisite to do so?

      We understand and share the point of view of reviewer #2. At this stage, we believe that our data won’t enable us to fully answer the question, thus this relationship remains rather correlative. The reasons are that 1) the access to the status of cortical cells below C2 is restricted to fixed material and therefore only represents a snapshot of the situation, and 2) we are currently unable to significantly interfere with mechanisms as intertwined as cell cycle control and infection control. What we can reasonably suggest from our images is that the most favorable window of the cell cycle for cells about to be crossed by an infection thread is post-replicative, i.e., the G2 phase. Typical markers of the G2 phase were recurrently observed at the onset of physical colonization – enlarged nucleus, containing less histone H3.1 than neighbouring cells in S phase (e.g., in Figure 2A). Reaching the G2 phase could therefore be a prerequisite for infection (and associated cellular rearrangements), while prolonged arrest in this same phase is likely a consequence of transcellular passage towards a forming nodule primordium.

      More importantly, in either scenario, what is the functional significance of exiting the cell cycle or endocycle? By stating that "local control of mitotic activity could be especially important for rhizobia to timely cross the middle cortex, where sustained cellular proliferation gives rise to the nodule meristem" (Line 239), the authors seem to believe that cortical cells need to stop the cell cycle to prepare for rhizobia infection. This is certainly reasonable, but the current study provides no proof, yet. To test the functional importance of cell cycle exit, one would interfere with G2/M transition in nodule cells,  and examine the effect on infection.

      We fully agree with reviewer #2 that the functional importance of a cell-cycle arrest on the infection thread trajectory remains to be demonstrated. Interfering with cell-cycle progression in a system as complex and fine-tuned as infected legume roots certainly requires the right timing – at the level of the tissue and of individual cells; the right dose; and the right molecular player(s) (i.e., bona fide activators or repressors of the G2/M transition). Using the symbiosis-specific NPL promoter, activated in the direct vicinity of cortical infection threads (Figure 9-figure supplement 1B), we tried to force infectable cells to recruit the cell division program by ectopically over-expressing the Arabidopsis CYCD3.1, “mimicking” the CDEL system. So far, this strategy has not resulted in a significant increase in the number of uninfected nodules in transgenic hairy roots - though the effect on symbiosome release remains to be investigated. Provided that a suitable promoter-cell cycle regulator combination is identified, we hope to be able to answer this question in the future.

      Given that the authors have already identified a candidate, and showed it represses cell division in the CDEL system, not testing the same gene in a more relevant context seems a lost opportunity. If one ectopically expressed NY-YA1 in hairy roots, thus repressing mitosis in general, would more cells become competent to host infection threads? This seems a straightforward experiment and readily feasible with the constructs that the authors already have. If this view is too naive, the authors should explain why such a functional investigation does not belong in this manuscript.

      Reviewer #2's point is entirely valid, and we decided to address it through additional experiments. To avoid possible side effects on development by affecting cell division in general, we placed NF-YA1 under control of the symbiosis-induced ENOD11 promoter. Based on the results obtained in the CDEL system, the pENOD11::FLAG-NF-YA1 cassette was coupled to a destabilized version of the KNOLLE transcriptional reporter to detect the G2/M transition. Competence for transcellular infection was maintained upon local NFYA1 overexpression, the latter leading to a slight (non-significant) increase in the number of infected cells per cortical layer. These results are presented in Figure 9-figure supplement 3A-B (representative confocal images) and in Figure 9-figure supplement 4A-

      G.

      (1b) A related comment: on Line 183, it was stated that "The H3.1-eGFP fusion protein was also visible in cells penetrated but not fully passed by an infection thread". Presumably, the authors were talking about the cell marked by the arrowhead. But its H3.1-GFP signal looks no different from the cell immediately to its left. It is hard to say which cells are ones "preparing for intracellular infection pass through S-phase", and which ones are just "regularly dividing cortical cells forming the nodule primordium". What can be concluded is that once a cell has been fully transversed by an infection thread, its H3.1 level is low. Whether this is the cause or consequence of infection cannot be resolved simply by timing the appearance or disappearance of H3.1-GFP.

      We basically agree with comment 1b. In an unsynchronized system such as infected hairy roots, it is challenging to detect the event where a cell is penetrated, but not yet completely crossed by an infection thread. What we wanted to emphasize in Figure 2A, is that host cells in the path of an infection thread re-enter the cell cycle and pass through S-phase just as their neighbours do (as pointed out by reviewer #2 in his summary). The larger nucleus with slightly lower H3.1-eGFP signal than the neighbouring cell (as indicated by the use of the Green Fire Blue lookup table) suggests that the infected cell marked by the arrowhead in Figure 2A is actually in the G2 phase. The main difference is indeed that cells allowing complete infection thread passage exit the cell cycle and largely evict H3.1 while their neighbours proceed to cell division (as exemplified by PlaCCI reporters in Figure 4CD and the new Figure 5-figure supplement 2). Whether cell-cycle exit in G2 is a cause, or a consequence of cortical infection is a question that cannot be easily answered from fixed samples, which is a limitation of our study.

      (2) The authors have convincingly demonstrated that cortical cells accommodating infection threads exit the cell cycle, inhibit cell division, and down-regulate KNOLLE expression. How do these observations reconcile with the feature called the pre-infection thread? The authors devoted one paragraph to this question in the Discussion, but this does seem sufficient given that the pre-infection thread is a prominent concept. Is the resemblance to the cell division plane superficial, or does it reflect a co-option of the normal cytokinesis machinery for accommodating rhizobia?

      From our point of view, cortical cells forming pre-infection threads are likely in an intermediate state. PIT structures undoubtedly share many similarities with cells establishing a cell division plane. The recruitment of at least some of the players normally associated with cytokinesis has been demonstrated and is consistent with the maintenance of infectable cells in a pre-mitotic phase in Medicago, as discussed in lines 558 to 568. We nevertheless think that the arrest of the cell cycle in the G2 phase, presumably occurring in crossed cortical cells, constitutes an event of cellular differentiation and specialization in transcellular infection. 

      The following are mainly points of presentation and description: 

      (3) Line 158: I can't see "subnuclear foci" in Figure 1-figure supplement 1C-E. However, they are visible in Fig. 1C.

      We hope that presenting the eGFP and mCherry channels in separate panels and assigning them the Green Fire Blue colour scheme provides better visibility and contrast of these detailed structures. We now refer to Figure 1C in addition to Figure 1–figure supplement 1E in the main text (line 161). 

      (4) Line 160: The authors should outline a larger region containing multiple QC cells, rather than pointing to a single cell, as there are other areas in the image containing cells with the same pattern.

      We updated Figure 1-figure supplement 1E accordingly.

      (5) Fig. 1B should include single channels, since within a single plant cell, the nucleus, the infection thread, and sometimes symbiosomes all have the same color. This makes it hard to see whether the nuclei in these cells are less green, or are simply overwhelmed by the magenta color.

      To improve the readability of Figure 1B and to address suggestions from individual reviewers, we now include separate channels and have annotated the different structures labeled by mCherry.

      (6) Fig. 2A: the close-up does not match the boxed area in the left panel. Based on the labeling, it seems that the two panels are different optical sections. But why choose a different optical depth for the left panel? This can be disorienting to the author, because one expects the close-up to be the same image, just under higher magnification.

      We fully agree that our previous choice of representation may have been confusing. As we also specified to reviewer #1, we wanted to show a full-view of proliferating cells in the inner cortex and a zoomed-view of infected cells in the outer layers of the same nodule primordium. In the revised version of Figure 2A, we displayed these full- and zoomedviews in separate panels and removed the boxed area to avoid confusion. 

      (7) Figure 2-figure supplement 1B: the cell indicated by the empty arrowhead has a striking pattern of H3.1 and H3.3 distribution on condensed chromosomes. Can you comment on that?

      Reviewer #2 may be referring to the apparent enrichment of H3.3 at telomeres, previously described in Arabidopsis, while pericentromeric regions are enriched in H3.1. This distribution is indeed visible on most of the condensed chromosomes shown in Figure 2-figure supplement 1B. We included this comment in the corresponding caption.

      (8) Fig. 4: It is not very easy to distinguish M phase. Can the authors describe how each phase is supposed to look like with the reporters?

      We agree with reviewer #2 and attempted to improve Figure 4, which is now dedicated to the Arabidopsis PlaCCI reporter. ECFP, mCherry, and YFP channels were presented separately and the corresponding cell-cycle phases (in interphase and mitosis) were annotated. The Green Fire Blue lookup table was assigned to each reporter to provide the best visibility of, for example, chromosomes in early prophase. We included a schematic representation corresponding to the distribution of each reporter, using the colors of the overlaid image to facilitate its interpretation.

      (9) Line 298: what is endopolyploid? This term is used at least three times throughout the manuscript. How is it different from polyploid?

      In the manuscript, we aimed to differentiate the (poly)ploidy of an organism (reflecting the number of copies of the basic genome and inherited through the germline) from endopolyploidy produced by individual somatic cells. As reviewed by Scholes and Paige, polyploidy and endopolyploidy differ in important ways, including allelic diversity and chromosome structural differences. In the Medicago truncatula root cortex for example, a tetraploid cell generated via endoreduplication from the diploid state would contain at most two alleles at any locus. The effects of endopolyploidy on cell size, gene expression, cell metabolism and the duration of the mitotic cell cycle are not shared among individual cells or organs, contrasting to a polyploid individual (Scholes and Paige, 2015).

      See Scholes, D. R., & Paige, K. N. (2015). Plasticity in ploidy : A generalized response to stress. Trends in Plant Science, 20(3), 165‑175. https://doi.org/10.1016/j.tplants.2014.11.007

      (10) Line 332: "chromosomes on mitotic figures" - what does this mean?

      Reviewer #2 is right to point out this redundant wording. Mitotic “figures” are recognized, by definition, based on chromosome condensation. We now use the term "mitotic chromosomes" (line 344).

      (11) Fig. 6A: could the authors consider labeling the doublets, at least some of them? I understand that this nucleus contains many doublets. However, this is the first image where one is supposed to recognize these doublets, and pointing out these features can facilitate understanding. Otherwise, a reader might think the image is comparable to nuclei with no doublets in the rest of the figure.

      Following this suggestion, five of these doublets are now labeled in Figure 7A (formerly Figure 6A).

  2. May 2025
    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      (1) A previously determined 2:2 heterodimeric complex of LGI1-ADAM22 was suggested to play a role in trans interactions. Could the authors discuss if the heterohexameric 3:3 LGI1-ADAM22 is more likely to represent a cis complex or a trans complex, or if both are possible?

      We noticed that there was no obvious structural feature strongly suggesting that the heterohexameric 3:3 LGI1-ADAM22 is more likely to represent a cis complex or a trans complex. Both are possible at the synapse (and similarly, for LGI3-ADAM23 at the jaxtaparanode of myelinated axons). Therefore, we revised the Introduction and Discussion sections as follows:

      Introduction: (about potential structural mechanisms of the 3:3 complex)

      “Similarly to the 2:2 complex, the 3:3 complex might serve as an extracellular scaffold to stabilize Kv1 channels or AMPA receptors in a trans-synaptic fashion. In addition, the 3:3 assembly in a cis fashion on the same membrane might regulate the accumulation of Kv1 channel complexes at axon initial segment. However, no clear evidence to prove these potential mechanistic roles of the 3:3 assembly has been provided, and the three-dimensional structure of the 3:3 complex has not yet been determined.”

      Discussion: (about a role of the LGI3–ADAM23 complex at the jaxtaparanode of myelinated axons)

      “In this context, as discussed in (30), either or both of the 2:2 and 3:3 complexes might be formed in a trans fashion at the juxtaparanode of myelinated axons and bridge the axon and the innermost myelin membrane. Alternatively, the 3:3 complex formed in a cis fashion might positively regulate the clustering of the axonal Kv channels at the juxtaparanode, possibly in a similar manner at the axon initial segment.”

      *Ref. 30: Y. Miyazaki et al., Oligodendrocyte-derived LGI3 and its receptor ADAM23 organize juxtaparanodal Kv1 channel clustering for short-term synaptic plasticity. Cell Rep 43, 113634 (2024).

      (2) It is not entirely clear to me if the LGI1-ADAM22 complex is also crosslinked in the HS-AFM experiments. Could this be more clearly indicated? In addition, if this is the case, could an explanation be given about how the complex can still dissociate?

      Thank you for the constructive suggestions. A non-crosslinked 3:3 LGI-ADAM22 complex was used for HS-AFM observations. To clarify the sample used for HS-AFM, we have modified the text as follows.

      P.8 “Dynamics of the LGI1‒ADAM22 higher-order complex observed by HS-AFM

      HS-AFM images of gel filtration chromatography fractions containing the 3:3 LGI1-ADAM22<sub>ECD</sub> complex (not chemically crosslinked with glutaraldehyde) predominantly…”

      P.10 Materials and methods

      “HS-AFM observations of the LGI1–ADAM22<sub>ECD</sub> complex (not chemically crosslinked with glutaraldehyde) were conducted on AP-mica,…”

      (3) The LGI1 and ADAM22 are of similar size. To me, this complicates the interpretation of dissociation of the complex in the HS-AFM data. How is the overinterpretation of this data prevented? In other words, what confidence do the authors have in the dissociation steps in the HS-AFM data?

      Our criteria for assigning HS-AFM images to the 3:3 LGI1–ADAM22<sub>ECD</sub> complex were based on a comparison of the simulated AFM image of the 3:3 complex obtained by cryo-EM. The automatized fitting process (42) identifies the optimal orientation of cryo-EM images that closely matches the HS-AFM image. In the present study, the concordance coefficient (CC) reached 0.8, indicating that the protein orientation in HS-AFM images of the 3:3 complex was objectively satisfactory.

      Regarding the dissociation step of ADAM22 from the 3:3 complex, we carefully analyzed the HS-AFM videos frame by frame and observed that the protrusion corresponding to ADAM22 in the 3:3 complex disappeared at a specific frame (4.5 s in the third molecule in Movie S1). The dissociation steps of ADAM22 were further confirmed by integrating multiple independent HS-AFM experiments and observations. Thus, although HS-AFM images alone cannot determine the orientation of LGI1 and ADAM22 in the 3:3 complex, the comparison of cryo-EM images with simulated AFM images enables objective assignment and orientation of proteins in the 3:3 complex through automated fitting.

      *Ref. 42: R. Amyot et al., Flechsig, Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images. PLoS Comput Biol 18, e1009970 (2022).

      (4) What is the "LGI1 collapse" mentioned in Figure 4c?

      Thank you for the constructive suggestions. The term “LGI1 collapse” was intended the dissociation of LGI1 from the 3:3 complex. To avoid confusion, we have revised it to “LGI1 release”.

      (5) Am I correct that the structure indicates that the trimerization is entirely organized by LGI1? This would suggest LGI1 trimerizes on its own. Can this be discussed? Has this been observed?

      Yes. The present cryo-EM structure of the 3:3 complex indicates that the trimerization can be entirely organized by LGI1. In addition, during the HS-AFM imaging, the triangle shape seems to be maintained even if one ADAM22<sub>ECD</sub> molecule is released. These findings suggest the possibility that LGI1 could trimerize on its own although this possibility could not be tested due to the difficulty in the expression of the full-length LGI1 alone for biophysical analysis in our hands. On the other hand, considering the dynamic property of the 3:3 complex and spatial alignment of LGI1LRR and ADAM22, we cannot exclude the possibility that ADAM22 could act as a platform to facilitate the intermolecular interaction between LGI1<sub>LRR</sub> and LGI1*<sub>EPTP</sub> for the trimerization of LGI1. This discussion was added in the first paragraph of the subsection "Dynamics of the LGI1–ADAM22 higher-order complex by HS-AFM".

      (6) C3 symmetry was not applied in the cryo-EM reconstruction of the heterohexameric 3:3 LGI1-ADAM22 complex. How much is the complex deviating from C3 symmetry? What interactions stabilize the specific trimeric conformation reconstructed here, compared to other trimeric conformations?

      According to this comment, we compared the non-symmetric, present cryo-EM structure to the previously calculated _C_3 symmetry-restrained structure based on small-angle X-ray scattering analysis and the _C_3 symmetric structure generated by AlphaFold3. Their differences in the domain or protomer configuration are illustrated in Fig. S9.

      We did not find interactions that could obviously stabilize the specific trimeric conformation but the closure motion of LGI1<sub>LRR</sub> (relative to LGI1<sub>EPTP</sub>) in chain F appears to locate it in close proximity to LGI1LRR in chain D to make the triangular assembly slightly more compact. This (partly) compact configuration might stabilize the non-symmetric trimeric configuration observed in the cryo-EM structure. This was described in the last sentence in the subsection "Cryo-EM structure of the 3:3 LGI1– ADAM22<sub>ECD</sub> complex".

      Reviewer #2 (public review):

      The functional significance of these two complexes in the context of synapse remains speculative.

      To assess the functional significance of the 3:3 complex, we spent time and effort designing mutations that solely inhibit the 3:3 assembly but failed to find such mutations. In this paper, we just focused on structural characterization of the 3:3 complex.

      Additionally, the structural presentations in Figures 1-3 (especially Figures 2-3) lack the clarity needed for general readers to fully understand the authors' key points. Enhancing the quality of these visual representations would greatly improve accessibility and comprehension.

      We made an effort to improve Figures 1-3 accordingly. Specifically, we revised them based on the strategy suggested in the Editorial comment regarding this reviewer's comment.

      Editorial comments:

      We noticed that in the reconstruction of the 3:3 complex, which is claimed to be at 3.8A resolution, beta-strands are not separated in the map and local resolution estimates vary from 6-10A. Please clarify.

      We revised Fig. S8 to show the local resolution and volume quality, which correspond to nominal resolution of 3.8 Å, estimated from gold-standard FSC.

      Reviewer #1 (Recommendations for the authors):

      (1) PDB validation reports should be presented to allow further validation

      The PDB validation reports were attached to the revised manuscript (uploaded as "related manuscript file").

      (2) In Figure 4, models below the AFM figures are difficult to see because of the light coloring. In addition, in panel c, the orientation of some of the parts of the models below the 19.2 and 34.5 s. panels do not seem to correlate with the AFM figures. Could the models be adjusted so that they represent the data better?

      Thank you for the constructive suggestions. According to the Reviewer’s comments, we have revised the AFM figures (Fig. 4).

      (3) References are sometimes missing for important statements. Please check throughout.

      Some examples:

      P3, "it has been suggested that the 3:3 complex regulates the density of synaptic molecules such as scaffolding proteins and synaptic vesicles".

      P3. "Furthermore, LGI1 forms a complex with the voltage-gated potassium channel (VGKC) through ADAM22/23".

      According to this comment, we rewrote the description about potential physiological roles of the 3:3 complex and added references as follows:

      "Similarly to the 2:2 complex, the 3:3 complex might serve as an extracellular scaffold to stabilize Kv1 channels or AMPA receptors in a trans-synaptic fashion (9, 17, 19). In addition, the 3:3 assembly in a cis fashion on the same membrane might regulate the accumulation of Kv1 channel complexes at axon initial segment (18, 20). However, no clear evidence to prove these potential mechanistic roles of the 3:3 assembly has been provided, and the three-dimensional structure of the 3:3 complex has not yet been determined."

      We also added references to the following sentences:

      p.2, (the last sentence in the first paragraph of the Introduction) “Additionally, some epilepsy-related mutations have been identified in genes encoding non-ion channel proteins such as LGI1 (4-7).”

      p.3, ln 4-5, “The metalloprotease-like domain interacts with the EPTP domain of LGI1 in the extracellular space (11, 14).”

      p.3, ln 9-10, “Furthermore, LGI1 forms a complex with the voltage-gated potassium channel (VGKC) through ADAM22/23 (9, 17, 18)”

      p.3, ln 20-22, “The results revealed the structural basis of the interaction between the EPTP domain of one LGI1 and the LRR domain of the other LGI1, as well as the interaction between the EPTP domain of LGI1 and the metalloproteinase-like domain of ADAM22 (14)”

      (4) S5 for clarity please add an overview of the complex highlighting where the different parts shown in the panels are located.

      Fig. S5 was modified accordingly. Every panel showing a zoom-up view was indicated by a box in an overview of the complex.

      (5) S7 a+b, also here add models for the structures to indicate which parts are shown.

      Could labels be added to highlight important parts?

      We added an overview of the complex with boxes that indicate the parts shown as the panels, according to this comment. We also added labels to highlight residues that are important for the LGI1<sub>EPTP</sub>–ADAM22<sub>ECD</sub> interaction in the panel showing the LGI1<sub>EPTP</sub>–ADAM22<sub>ECD</sub> interface.

      (6) S7c also shows the cartoon of the structure. How is it possible that the local resolution is not much higher than 6 Å? The overall resolution was 3.8 Å? This looks like a figure of the density plotted at a low level, and not as stated a "surface representation". Could an extra panel be shown of the density plotted at a higher level? Also, please add Å to the legend in this figure.

      Local resolution maps of the 3:3 LGI1-ADAM22<sub>ECD</sub> complex were shown as Fig. S8 in the revised manuscript. According to this comment, the distribution of the resolution was plotted onto the density at high (0.06) and low (0.03) levels. "Å" was added to the legend in the figure.

      Reviewer #2 (Recommendations for the authors):

      (1) The study was conducted using the ectodomain (ECD) of ADAM22. It remains unclear whether the 3:3 complex could form if the transmembrane domain (TMD) of ADAM22 were included. In other words, it is difficult to assess whether the observed 3:3 complex represents plausible cis interactions.

      As mentioned in our reply to the first comment from Reviewer #1, we noticed that there was no obvious structural feature strongly suggesting that the heterohexameric 3:3 LGI1–ADAM22 is more likely to represent a cis complex or a trans complex. Both are possible at the synapse (and similarly, for LGI3–ADAM23 at the jaxtaparanode of myelinated axons). Therefore, we revised the Introduction and Discussion sections as follows:

      Introduction: (about potential structural mechanisms of the 3:3 complex)

      “Similarly to the 2:2 complex, the 3:3 complex might serve as an extracellular scaffold to stabilize Kv1 channels or AMPA receptors in a trans-synaptic fashion. In addition, the 3:3 assembly in a cis fashion on the same membrane might regulate the accumulation of Kv1 channel complexes at axon initial segment. However, no clear evidence to prove these potential mechanistic roles of the 3:3 assembly has been provided, and the three-dimensional structure of the 3:3 complex has not yet been determined.”

      Discussion: (about a role of the LGI3–ADAM23 complex at the jaxtaparanode of myelinated axons)

      “In this context, as discussed in (30), either or both of the 2:2 and 3:3 complexes might be formed in a trans fashion at the juxtaparanode of myelinated axons and bridge the axon and the innermost myelin membrane. Alternatively, the 3:3 complex formed in a cis fashion might positively regulate the clustering of the axonal Kv channels at the juxtaparanode, possibly in a similar manner at the axon initial segment.”

      *Ref. 30: Y. Miyazaki et al., Oligodendrocyte-derived LGI3 and its receptor ADAM23 organize juxtaparanodal Kv1 channel clustering for short-term synaptic plasticity. Cell Rep 43, 113634 (2024).

      (2) Page 2, line 1: "...caused by genetic mutations." - Specify the mutations involved. Which genes are mutated? Providing this information would enhance clarity and context.

      According to this comment, we rephrased the sentence as follows:

      "LGI1 is linked to epilepsy, a neurological disorder that can be caused by genetic mutations of genes regulating neuronal excitability (e.g., voltage- or ligand-gated ion channels)."

      (3) The experimental strategy and data for both cryo-EM and HS-AFM are of high quality. However, improvements are needed in the cryo-EM/structural figures to enhance clarity. Structural components should be labeled, and the protein interfaces should be identified within the overall complex figures in Figures 2 and 3, as the current presentation is challenging for general readers to follow. For example, in Figure 2, panel a would benefit from clear labeling to indicate the locations of ADAM22 and LGI1. Panels b and c lack context unless the authors specify which interface corresponds to panel a. Additionally, panels e and f are unlabelled, making it difficult to interpret the figures. Improved annotations and descriptions would significantly enhance figure accessibility and comprehension.

      Thank you for the constructive suggestion for enhancing accessibility and comprehension of cryo-EM/structural figures. According to this comment, we labeled structural components and indicated the protein interfaces as boxes in the overall complex figures in Figures 2 and 3. Further, in Figure 2, the locations that panels b and c show were indicated as two boxes in the close-up view in panel a.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1:

      (1) The data are generated using ATP read-out (CTG assay). For any inhibitor of mitochondrial function, ATP assays are highly sensitive reflecting metabolic stress, yet these do not necessarily translate into cell growth inhibition using standard Trypan blue assays and tend to overestimate the effects. Please show orthogonal more robust assays of cell growth or proliferation.

      We acknowledge the sensitivity of the ATP read-out assay in reflecting metabolic stress. While additional cell growth assays such as Trypan blue exclusion could provide further insights, we believe that the current ATP assay data robustly demonstrate the effect of the IMT and venetoclax combination on cellular metabolism, which is a critical aspect of our study. The scope of our current work focused on metabolic inhibition, and we suggest that future studies could further explore cell proliferation assays to complement these findings.

      (2) It is concluded that AML cells do not utilize glucose for ATP production. Please provide formal measurements of glycolysis/lactate upon combinatorial treatment.

      We appreciate the reviewer’s suggestion to include glycolysis and lactate measurements, which could indeed add further granularity to our metabolic analysis. However, the primary focus of our study is on mitochondrial function and oxidative phosphorylation (OXPHOS) in AML cells treated with IMT and venetoclax. We believe the data presented in Figure 3 provide strong support for the conclusion that glycolysis is not a major energy source in these cells.

      Specifically, in Figure 3C, we demonstrate that AML cells maintain ATP levels and viability when cultured in galactose, a condition that restricts ATP production through glycolysis and forces cells to rely on OXPHOS. This result strongly suggests that these AML cells are not dependent on glycolysis for ATP production. Furthermore, in Supplementary Figure S3B, we show that oxygen consumption rate (OCR) measurements remain stable in the presence of excess glucose, further supporting our conclusion that the cells do not switch to glycolysis when OXPHOS is inhibited.

      These findings collectively indicate a primary reliance on OXPHOS for energy generation in AML cells, consistent with our study’s objectives to explore mitochondrial dependency and the therapeutic potential of targeting mitochondrial transcription in AML. Future studies could certainly expand on these insights by incorporating a more detailed analysis of glycolytic flux and lactate production under combinatorial treatment, but we believe the current data are sufficient to support our main conclusions.

      (3) The transcriptome data are shown without any analysis of pathways. The conclusion from this data beyond the higher number of genes impacted in the combination arm is unclear. Please provide analysis for example GO pathways and interpret in the context of the drugs' mechanism of action.

      In response to the reviewer’s question, we have added gene ontology (GO) pathway analysis to clarify the transcriptomic impact of our combination treatment with IMT and venetoclax. Functional annotation identified significant enrichment in pathways relevant to innate immune response, mitochondrial function, and cellular signaling processes. Specifically, pathways associated with immune defense, mitochondrial signaling, and intracellular signaling were notably affected. These findings suggest that the combination treatment not only disrupts cellular energy metabolism but also potentially primes immune signaling mechanisms. This aligns with the proposed mechanism, where IMT targets mitochondrial transcription and venetoclax induces apoptosis, together enhancing sensitivity in AML cells. The enriched pathways, therefore, support the mechanism of action of both drugs, showing how the combined inhibition of BCL-2 and mitochondrial transcription creates a compounded cellular disruption that enhances the therapeutic effect.

      (4) Please demonstrate (could be in supplement) matrix of combination to support the statement that the combination is synergistic using Bliss index. The actual Bliss values are missing.

      For the revision, we have now included a matrix of combination treatment effects with the corresponding Bliss synergy index values to substantiate our claim of synergy between IMT and venetoclax. This analysis, provided in the supplement, demonstrates that the observed effects exceed the expected additive impact of each drug alone, as calculated by the Bliss independence model. Specifically, the Bliss values confirm a synergistic interaction in venetoclax-sensitive AML cell lines, highlighting that the combined treatment significantly enhances inhibition of cell viability and apoptosis induction compared to single treatments. This data supports our interpretation of synergy and strengthens the mechanistic conclusions drawn from our findings on the combination therapy’s efficacy.

      (5) Please show KG1 data (OCR), here or in Supplement.

      In response to the reviewer’s request to include OCR data for the KG-1 cell line, we would like to clarify that OCR measurements were attempted; however, they did not yield conclusive results. This is noted in the revised manuscript (Results section), where we explain that the KG-1 cell line did not provide usable OCR data, likely due to limitations in detecting reliable mitochondrial respiration in this particular line under our experimental conditions. Therefore, we were unable to include KG-1 OCR data in the main figures or the supplement.

      Reviewer #2:

      (1) It's important that the authors show that the drug's effects in AML are due to on-target inhibition. It's critical that they show that IMT actually inhibits the mito polymerase in the AML cells in the dose range employed.

      We appreciate the importance of demonstrating on-target inhibition of mitochondrial RNA polymerase by IMT1, especially in light of the detailed characterization of IMT1b, a closely related compound, as presented in Bonekamp et al., Nature 2020. The work by Bonekamp et al. established the specificity and efficacy of IMT1b in targeting mitochondrial RNA polymerase across various tumor models. Building on these findings, we designed our study to primarily evaluate the combinatorial efficacy of IMT1 with venetoclax in AML models, assuming a similar mechanism of action as described for IMT1b. While direct confirmation of on-target inhibition in AML cells by IMT1 would undoubtedly provide additional mechanistic insight, we focused on translational aspects in this study. We believe that the foundational work provided by Bonekamp et al. supports the assumption of on-target effects by IMT1, and we suggest that future studies could explicitly verify this in the context of AML.

      (2) For Fig 1, the stated synergism between Venetoclax (Vex) and IMT in p53 mutant THP1 cells is really not evident, despite what the statistical analysis says. In some ways, the more interesting conclusion is that inhibiting mitochondrial transcription does NOT potentiate the efficacy of Bcl2 inhibition in TP53 mutant AML.

      We appreciate the reviewer’s observation regarding the lack of evident synergy between IMT and venetoclax in TP53 mutant THP-1 cells. In line with this comment, we have now expanded the discussion to emphasize that, while statistical analysis suggested a potential interaction, the biological response in TP53 mutant cells was minimal. This contrasts with the strong synergy observed in TP53 wild-type cell lines, such as MV4-11 and MOLM-13. We have now highlighted that TP53 mutation status may limit the effectiveness of mitochondrial transcription inhibition in potentiating BCL-2 inhibition. This addition underscores the importance of mutation profiles, such as TP53 status, in predicting response to combination therapies in AML and is now clearly addressed in the revised discussion.

      (3) They combine IMT with Vex, but Vex plus azacytidine or decitabine is the approved therapy for AML. Any clinical trial would likely start with this backbone (like Vex+Aza). They should test combinations of IMT with Vex/Aza or Vex/Dec.

      While we recognize the importance of testing IMT in combination with clinically approved therapies like Vex+Aza, our current study was designed to explore the potential of IMT in combination with venetoclax alone. Expanding to other combinations would be an excellent direction for future research but is beyond the scope of our current investigation.

      (4) It's interesting that AML cell lines do not show any reliance on ATP generation from glycolysis, but would this still be the case when OxPhos is inhibited with IMT? Such a simple experiment would be much more interesting and could help them better understand the mechanism of IMT efficacy.

      We thank the reviewer for highlighting this point regarding the reliance of AML cell lines on glycolysis under OxPhos inhibition. In our study, we observed that AML cells predominantly rely on OxPhos, and we did test for ATP production in conditions that favored glycolysis by growing AML cells with galactose instead of glucose in the medium. As described in the manuscript, we did not observe significant ATP production or cell viability from glycolysis, even under these conditions. This finding suggests that AML cells have a low capacity to adapt to glycolytic ATP generation when OxPhos is disrupted by IMT, reinforcing the view that they are highly dependent on mitochondrial function for energy production. We agree that this adaptation—or lack thereof—is an intriguing aspect of IMT efficacy in targeting energy metabolism in AML cells, and we have clarified this point in the discussion.

      (5) OxPhos measurements need statistical analyses.

      We appreciate the reviewer’s suggestion to include statistical analyses for the OXPHOS measurements. We would like to clarify that statistical analyses were included in the initial submission. These are detailed in Figure 3 and its legend, as well as in the Statistical Analysis section, where we specify methods such as the calculation of standard error across replicates. This approach was implemented to ensure the rigor of our OCR data and its conclusions on OXPHOS inhibition in AML cells.

      (6) Given that the combo-treated mice do not exhibit much leukemia in the blood through ~180 days, and yet start dying after 100 days, the authors should comment on this, given that the bone marrow has been shown to be a refuge that protects leukemia cells from various therapies.

      We thank the reviewer for highlighting the observed discrepancy between peripheral blood leukemia levels and survival in combo-treated mice. While leukemic cells were minimally detected in the blood up to approximately 180 days, treated mice began to show signs of disease progression and reduced survival around 100 days. This may suggest that residual leukemic cells persist within the bone marrow, which has been established as a sanctuary site for leukemic cells, providing protection from various therapies. The bone marrow environment likely supports a survival niche, enabling these residual cells to evade treatment effects and potentially initiate disease relapse. We have added this interpretation to the discussion to acknowledge the possibility of bone marrow as a protective refuge, which may limit the full eradication of leukemia in these models despite apparent peripheral blood clearance.

      (7) For Fig 5C, the authors should statistically compare the Combo with Vex alone.

      We have now included statistical comparisons between the combination treatment and venetoclax alone in Fig 5C to provide a clearer interpretation of the data.

      (8) The analyses of gene expression using RNAseq of harvested leukemia cells from the PDX model (Table S2), some more discussion of these results would be helpful, particularly given that neither drug is directly targeting nuclear gene expression.

      We thank the reviewer for their suggestion to discuss the RNAseq findings in more detail. In the revised manuscript, we have expanded on the functional annotation of the gene expression changes observed in leukemia cells from the PDX model following combination treatment (Table S2). The enriched pathways include innate immune involvement, mitochondrial function and immune signaling, and intracellular signaling. This suggests that while neither IMT nor venetoclax directly targets nuclear gene expression, the combined treatment induces secondary effects that alter these pathways, potentially contributing to the treatment’s efficacy in AML. This expanded discussion provides greater insight into how the drug combination impacts gene expression and cellular pathways.

      (9) We need more information on the PDX models, in terms of the classification (M1 to M6) of the patient AMLs and genetics (specific mutations, not just the genes mutated, and chromosomal alterations).

      Additional details regarding the classification and genetic background of the PDX models have been included in the manuscript to better contextualize our findings.

      (10) The authors should discuss whether or not IMT represents an improvement over other therapies intended to target Oxphos in AML (clearly, the low toxicity of IMT is a plus, at least in mice).

      We appreciate the reviewer’s suggestion to discuss IMT in comparison with other OXPHOS-targeting therapies for AML. In the revised discussion, we highlight IMT’s unique properties, particularly its low toxicity profile, which may offer advantages over other OXPHOS inhibitors. This low toxicity, demonstrated in preclinical studies, suggests that IMT might improve patient tolerability compared to existing therapies that target mitochondrial function.

      (11) The authors examined toxicity by weighing the mice and performing CBCs. Measurements of liver and kidney toxicity will be necessary for further clinical development.

      We thank the reviewer for the suggestion to further investigate liver and kidney toxicity. In our study, we assessed toxicity through regular weight monitoring and complete blood counts (CBCs) to evaluate overall health status. While additional liver and kidney toxicity measurements will indeed be important in future studies, resource limitations currently prevent us from performing these additional analyses in this model. We agree that these assessments will be essential as we progress towards clinical development, and we plan to address them in upcoming preclinical studies.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The study by Deng et al reports single-cell expression analysis of developing mouse hearts and examines the requirements for cardiac fibroblasts in heart maturation. Much of this work is overlapping with previous studies, but the single-cell gene expression data may be useful to investigators in the field. The significance and scope of new findings are limited and major conclusions are largely based on correlative data.

      Strengths:

      The strengths of the manuscript are the new single-cell datasets and comprehensive approach to ablating cardiac fibroblasts in pre and postnatal development in mice.

      Weaknesses:

      There are several major weaknesses in the analysis and interpretation of the results.

      (1) The major conclusions regarding collagen signaling and heart maturation are based on gene expression patterns and are not functionally validated. The potential downstream signaling pathways were not examined and known structural contributions of fibrillar collagen to heart maturation are not discussed.

      We thank the reviewer for the comment. In this study, we mainly focused on the functional analysis of fibroblasts in heart development at embryonic and neonatal stages by using cell ablation system and single cell mRNA sequencing analysis. The further functional analysis of collagen pathway is interesting but out of the scope of this study. We will continue this line of research and share the results in the future. Moreover, through the analysis of single cell mRNA-sequencing data, we have predicted the downstream genes that are regulated by the collagen pathway in Fig 5C. We have also added sentences to highlight the structural role of collagen in affecting the related heart developmental processes.

      (2) The heterogeneity of fibroblast populations and contributions to multiple structures in the developing heart are not well-considered in the analysis. The developmental targeting of fibroblasts will likely affect multiple structures in the embryonic heart and other organs. Lethality is described in some of these studies, but additional analysis is needed to determine the effects on heart morphogenesis or other organs beyond the focus on cardiomyocyte maturation being reported. In particular, the endocardial cushions and developing valves are likely to be affected in the prenatal ablations, but these structures are not included in the analyses.

      We thank the reviewer for the comment. We have included a new figure presenting the fibroblast heterogeneity in developing hearts (Fig S3). We have also compared the valve structural differences at E18.5 (Fig S11).

      (3) ECM complexity and extensive previous work on specific ECM proteins in heart development and maturation are not incorporated into the current study. Different types of collagen (basement membrane Col4, filamentous Col6, and fibrillar Col1) are known to be expressed in fibroblast populations in the developing heart and have been studied extensively. Much also has been reported for other ECM components mentioned in the current work.

      We thank the reviewer for the comment. We agree that the ECM is complex, and the functions of many of its components have been previously reported, as mentioned in the introduction. In this study, our focus is to analyze the spatial and temporal expression patterns of various ECM genes in fibroblasts throughout developmental progression (Fig. S5–7). To further acknowledge previous work, we have added additional sentences and cited relevant literature on the role of collagen genes in developing hearts (page 4).

      Reviewer #2 (Public review):

      This study aims to elucidate the role of fibroblasts in regulating myocardium and vascular development through signaling to cardiomyocytes and endothelial cells. This focus is significant, given that fibroblasts, cardiomyocytes, and vascular endothelial cells are the three primary cell types in the heart. The authors employed a Pdgfra-CreER-controlled diphtheria toxin A (DTA) system to ablate fibroblasts at various embryonic and postnatal stages, characterizing the resulting cardiac defects, particularly in myocardium and vasculature development. scRNA-seq analysis of the ablated hearts identified collagen as a crucial signaling molecule from fibroblasts that influences the development of cardiomyocytes and vascular endothelial cells. This is an interesting manuscript; however, there are several major issues, including an over-reliance on the scRNA-seq data, which shows inconsistencies between replicates. Some of the major issues are described below.

      The comments are the same as the comments for “Recommendations for the authors”. Please see the responses below.

      Reviewer #3 (Public review):

      The authors investigated fibroblasts' communication with key cell types in developing and neonatal hearts, with a focus on the critical roles of fibroblast-cardiomyocyte and fibroblast-endothelial cell networks in cardiac morphogenesis. They tried to map the spatial distribution of these cell types and reported the major pathways and signaling molecules driving the communication. They also used Cre-DTA system to ablate Pdgfra labeled cells and observed myocardial and endothelial cell defects at development. They screened the pathways and genes using sequencing data of ablated hearts. Lastly, they reported compensatory collagen expression in long-term ablated neonate hearts. Overall, this study provides us with important insight into fibroblasts' roles in cardiac development and will be a powerful resource for collagens and ECM-focused research.

      Strengths:

      The authors utilized good analyzing tools to investigate multiple databases of single-cell sequencing and Multiseq. They identified significant pathways and cellular and molecular interactions of fibroblasts. Additionally, they compared some of their analytic findings with a human database, and identified several groups of ECM genes with varying roles in mice.

      Weaknesses:

      This study is majorly based on sequencing data analysis. At the bench, they used a very strident technique to study fibroblast functions by ablating one of the major cell populations of the heart. Considering the importance of the fibroblast population, intriguing in vivo findings were expected. Also, they analyzed the downstream genes in ablated hearts, but did not execute any experimental validation for any of the targets.

      Recommendations for the authors:

      Reviewing Editor Comments:

      All three reviewers found the large amount of scRNA-Seq data compelling and valuable, and they noted that the study's conclusions based on the scRNA Seq and fibroblast ablating align closely with previously published studies. Therefore, a more thorough discussion and integration of the current findings with prior studies are recommended. Each reviewer provided specific feedback to improve the manuscript, correct errors, and strengthen the overall presentation, and please edit the manuscript accordingly. Additionally, further validation of the scRNA-Seq data through more data analysis, reference comparisons, or additional experiments is encouraged.

      Reviewer #1 (Recommendations for the authors):

      (1) The heterogeneity of fibroblasts and ECM components in the developing heart needs to be considered in the analysis and description of results. There are extensive reports in both of these areas that would inform the gene expression and ablation studies being reported.

      We thank the reviewer for the comment. We have added a supplemental figure (Fig. S3) analyzing the heterogeneity of fibroblasts during development and described the results on page 3 and 4. Through the analysis of single-cell mRNA sequencing data, we identified four distinct populations of fibroblasts and further performed RNA scope to examine their spatial locations. Additionally, we agree with the reviewer that there are many types of ECM components, which we have addressed in the introduction (page 2). Furthermore, we have conducted a detailed analysis of the spatial and temporal expression patterns of ECM genes throughout developmental progression (Figs. S5–7).

      (2) One of the novel aspects of the work is the prenatal ablation of cardiac fibroblasts. Embryonic lethality was observed in some cases, but the specific cardiac structural anomalies or potential vascular effects were not described. The contributing role of cardiac fibroblasts to valvuloseptal development, which was likely affected in these studies, was not described.

      We thank the reviewer for the comment. Since the heart sections were not initially prepared to compare valve differences between control and ablation conditions, most sections do not include valve structures. However, in the small subset of sections that do contain valves, we have compared valve structures in control and ablated hearts at E18.5 following three doses of tamoxifen treatment from E15.5 to E17.5. In mutants, the valves appear shorter compared to controls. Specifically, we observed that in control hearts, the mitral valve was already connected to the papillary muscle, whereas in ablated hearts, the valve leaflet at similar position was not. We have included these images as a new supplemental figure (Fig. S11). Regarding vascular defects, we have described them in Fig. 3C and 3F.

      (3) The major conclusions regarding collagen signaling and heart development are based on correlations in gene expression and are not validated by functional data. What are the downstream signaling pathways affected and are they affected during development or with ablation? The main conclusions of the study do not take into account well-known structural functions of collagen in the developing heart.

      We thank the reviewer for the comment. Through regulatory prediction analysis, we identified the collagen ligands Col1a1, Col5a1, and Col4a1 from the collagen family (Fig. 5C), which regulate multiple genes in cardiomyocytes, including Masp1. Masp1 is a member of the lectin complement pathway and potentially regulates cardiomyocyte migration during development. These collagen ligands also regulate multiple mitochondria-related genes, such as Etfa, Ndufb10, Ndufs6, and Slc25a4, which are potentially important for cardiomyocyte development and maturation. Moreover, we agree with the reviewer that collagen is an important structural ECM protein, and its deletion or reduction could cause heart developmental defects due to its structural role. We have added a discussion on this possibility (page 8).

      (4) The postnatal ablation studies are very similar to studies with the same mouse lines reported by Kurabara et al 2022 in JMCC (PMID 35569524) which came to similar conclusions and was not cited in the current work.

      We thank the reviewer for the comment and apologize for overlooking this study. We have now included the citation on page 8.

      (5) The discussion of a regenerative response with DTA ablation of fibroblasts is confusing. Proliferation was examined in cardiomyocytes which lose their regenerative capacity after birth in mice. However, cardiac fibroblasts can proliferate in response to injury throughout life which is not really a regenerative process.

      We appreciate the reviewer’s comment. To avoid confusion, we have replaced the term "regeneration" with "response to cell loss" and "compensation."

      (6) Some of the descriptions of single-cell expression data are overstated (Page 7). Regulatory interactions, signaling pathway activation, or function cannot be determined from gene expression data alone.

      We thank the reviewer for the comment. We agree that these conclusions rely on results from multiple assays. We have weakened the description of the analysis by emphasizing that the findings are predictive results from scRNA-seq analysis.

      (7) In the last paragraph of the discussion "data not shown" should be shown or this information should be deleted. As written, the discussion does not present a clear description of what major new findings are being reported or why they are significant. The new insights into heart development are not specified.

      We thank the reviewer for the comment. We have added the data as a supplemental figure (Fig. S19). Since this paragraph is part of the discussion, we believe the results are not conclusive at this stage and require further research to explore the potential protective role of fibroblast ablation in neonatal hearts.

      Minor comments.

      (1) Figure legends are missing information needed to understand what is being shown. For example, in Figure 2, collagen is visualized using CHP staining.

      Thanks. We have gone through all figure legends to ensure that all necessary information has been provided.

      (2) The hearts in Figure S15 are upside down.

      Thanks. We have updated the figure.

      (3) In Figure S16A, "brian" should be "brain".

      Thanks. We have updated it.

      Reviewer #2 (Recommendations for the authors):

      This is an interesting manuscript; however, there are several major issues, including an overreliance on the scRNA-seq data, which shows inconsistencies between replicates. Some of the major issues are described below.

      (1) The CD31 immunostaining data (Figures 3B-G) indicate a reduction in endothelial cell numbers following fibroblast deletion using PdgfraCreER+/-; RosaDTA+/- mice. However, the scRNA-seq data show no percentage change in the endothelial cell population (Figure 4D). Furthermore, while the percentage of Vas_ECs decreased in ablated samples at E16.5, the results at E18.5 were inconsistent, showing an increase in one replicate and a decrease in another, raising concerns about the reliability of the RNA-seq findings.

      We thank the reviewer for the comment. We believe that measuring cell proportions in scRNA-seq results is sensitive and relies on a high number of total and target cells, similar to other cell counting assays such as FACS. As the reviewer pointed out, the proportions of Vas_EC in E18.5 replicates are inconsistent. Specifically, Col_4 at E18.5 showed a relatively low proportion of Vas_EC. Upon examining the cell numbers in each sample, we found that Col_4 had the lowest number of recovered cells, with approximately 760 in total, whereas the other samples had more than 920 cells each. Additionally, since immunofluorescence staining for CD31 marks both Vas_EC and Endo_EC, we combined these two cell types to increase the number of targeted cells. This analysis consistently showed that the ablated samples had lower proportions. However, given that the quantifications have also produced inconsistent results for other cell types, such as Ven_CM, as mentioned in the reviewer’s next question, we have decided to delete this plot to avoid confusion.

      Author response image 1.

      (2) Similarly, while the percentage of Ven_CMs increased at E18.5, it exhibited differing trends at E16.5 (Figure 4E), further highlighting the inconsistency of the scRNA-seq analysis with the other data.

      We thank the reviewer for the comment. Please see the response above.

      (3) Furthermore, the authors noted that the ablated samples had slightly higher percentages of cardiomyocytes in the G1 phase compared to controls (Figures 4H, S11D), which aligns with the enrichment of pathways related to heart development, sarcomere organization, heart tube morphogenesis, and cell proliferation. However, it is unclear how this correlates with heart development, given that the hearts of ablated mice are significantly smaller than those of controls (Figure 3E). Additionally, the heart sections from ablated samples used for CD31/DAPI staining in Figure 3F appear much larger than those of the controls, raising further inconsistencies in the manuscript.

      We thank the reviewer for the comment. We observed changes in G1-phase cardiomyocytes at both E16.5 and E18.5, with pathway enrichment primarily identified in E16.5 cardiomyocytes. At E16.5, the ablated hearts exhibited myocardial defects, including an increased trabecular-to-compact myocardium ratio and reduced vascular density. By E18.5, the ablated embryos had smaller hearts with reduced vascular density, although the trabecular-to-compact myocardium ratio showed no obvious changes. Regarding the larger section size in the ablated hearts compared to the control hearts, there are two reasons contributing to this discrepancy. First, the control and ablated heart sections have different scale bars. The ablated hearts were enlarged compared to control section. Secondly, the heart sections vary in size depending on their position. Sections taken from the middle of the heart are larger than those from the edges. In our initial comparison, we used an edge-positioned section from the control hearts and a middle-positioned section from the ablated hearts. To avoid confusion, we have now updated the control section to match the position of the ablated embryos more closely and used the same size of scale bars in the two images (Fig 3F).

      (4) The manuscript relies heavily on the scRNA-seq dataset, which shows inconsistencies between the two replicates. Furthermore, the morphological and histological analyses do not align with the scRNA-seq findings.

      We respectfully disagree with this comment from the reviewer. As shown in Figure 4B, the scRNAseq data from the two replicates are highly consistent. For inconsistencies in cell proportions and tissue section sizes, please refer to our responses above.

      (5) There is a lack of mechanistic insight into how collagen, as a key signaling molecule from fibroblasts, affects the development of cardiomyocytes and vascular endothelial cells.

      We thank the reviewer for the comment. In this study, we primarily focused on analyzing fibroblast function in heart development using cell ablation and single-cell mRNA sequencing. While further mechanistic analysis of the collagen pathway is intriguing, it falls outside the scope of this study. Additionally, our scRNAseq analysis identified multiple collagen ligands derived from fibroblasts that may regulate gene expression in Ven_CM and influence their development, as shown in Figure 5C. Although validating these predictions would be valuable, it is beyond the scope of this study. We will continue this line of research and share our findings in the future.

      (6) In Figure 1B, Col1a1 expression is observed in the epicardial cells (Figure 1A, E11.5), but this is not represented in the accompanying cartoon.

      We thank the reviewer for the comment. As stated in the main text (page 3), based on scRNA-seq and IF staining results, we observed that Col1a1 is also expressed in epicardial cells. In the cartoon, we depicted the pattern of fibroblasts rather than Col1a1-positive cells, which is why we did not include epicardial cells.

      (7) What is the genotype of the control animals used in the study?

      We thank the reviewer for the comment. We have added the genotype information for the control embryos in the legends of the relevant figures.

      (8) Do the PdgfraCreER+/-; RosaDTA+/- mice survive after birth when induced at E15.5, and do they exhibit any cardiac defects?

      We thank the reviewer for the comment. This is an interesting question; however, we did not perform the experiment because administering tamoxifen to pregnant mice from E15.5 to E18.5 causes delivery complications, as reported in the literature (PMID: 23139287). Unfortunately, this prevents us from exploring this question further.

      Reviewer #3 (Recommendations for the authors):

      Overall, this is a comprehensive study substantiated by the evidence the authors provided in their findings. However, I have a few concerns to be addressed.

      (1) The claim by the authors that "at E17.5 and P3, each FB was in contact with approximately one Vas_EC and four CMs at both stages" is not fully convincing. RNA scope images for Actn2 are not clear enough to lead the quantification (RNA scope images for Cdh5 look better). I suggest performing imaging at higher magnification and the Z stack technique to provide a better understanding of their localization. Also, no changes in FBs adjacent cell numbers (CM&EC) with ages (P3) compared to E17.5? Any thoughts on the explanation?

      We thank the reviewer for the comment. We imaged the staining results using a confocal microscope at 20X resolution. We also considered imaging them at 40X; however, due to the large areas that need to be imaged in these sections, it was challenging to do so. Additionally, we identified each CM based on Actn2 and DAPI staining information and are confident in the accuracy of our quantification results. Moreover, since each FB interacts with multiple CMs and Vas_ECs in 3D projections, but our calculations are based only on 2D imaging sections, there may be discrepancies compared to a true 3D environment. We have added a sentence to address this limitation (page 9). Regarding the similar number of interactions observed at E17.5 and P3, we think there are two possibilities. First, the three cell types may proliferate in a synchronized manner, maintaining a consistent number of interactions. Second, these cell types may exhibit minimal proliferation during late embryonic and early neonatal stages. Instead, heart growth primarily occurs through CM hypertrophy, which does not significantly alter the number of interactions.

      (2) Fix the Capitalized font of RNA markers in Figure S2.

      Thanks. We have updated them.

      (3) I appreciate the visualization of ligand-receptor interactions in collagen network comparison between FB to CM and FB to EC, and predictive analysis on the FB ligands that regulate differentially expressed genes in ablated heart CM and ECs.

      We appreciate the reviewer for the comment.

      (4) The authors depleted Pdgfra-Cre cells at E10.5, and reported 100% DTA+ lethality after 3 days. Induction at E13.5 to ablate Pdgfra-Cre cells resulted in survival at least up to E16.5 age. What could be the possible reasons authors think that lead to embryo lethality when induced at E10.5? Did the authors analyze the expression of Pdgfra at E10.5 to E13.5 using Pdgfra antibody or Pdgfra-Cre labeling, or using the ScRNA seq data?

      We thank the reviewer for the comment. The expression pattern of Pdgfra at E10.5 has been previously reported (PMID: 18297729) and shown to be highly expressed in the atrioventricular region, consistent with the Col1a1 expression pattern we profiled in this study. Therefore, we believe the embryonic lethality observed in the ablated embryos at E10.5 was likely due to the disruption of the atrioventricular structure. However, since Pdgfra is also expressed in other tissues at this stage, we cannot rule out the possibility that the ablation of non-cardiac tissues also contributed to the lethality.

      (5) In terms of the findings on the trabeculation and compaction defects, please provide the images of the ventricles with markers to indicate the compact and trabecular zones and their defects.

      Thanks! We have included images that illustrate the quantification of compact and trabecular myocardium thickness in control and ablated hearts (FigS10C).

      (6) Did the author check the expression of any other marker for the vascular system in addition to CD31 to see the effects of ablated FB on coronary vasculature development?

      We thank the reviewer for the comment. We analyzed only Cd31 to assess the effects of fibroblast ablation on the overall endothelial cell population. We did not separately examine the subpopulations, but this would be an interesting direction for future studies.

      (7) Can the authors interpret how findings from PHH3 proliferation explain thinner compact and thicker trabeculae in ablated hearts?

      We thank the reviewer for the comment and apologize for the misinterpretation of the results. We observed that the ablated hearts have a thinner compact myocardium, while the thickness of the trabecular myocardium remains unchanged, leading to an increased trabecular-to-compact myocardium ratio (Fig 3D). We have corrected the description in the manuscript accordingly. Moreover, since the compact myocardium has a higher proliferation rate than the trabecular myocardium, a reduction in overall cell proliferation is expected to have a more pronounced impact on the compact myocardium. Inhibition of compact myocardium proliferation has been reported to lead thinner compact myocardium and non-compaction defects (PMID: 31342111).

      (8) The authors did not execute experiments to find the downstream target that causes compaction defects and endothelial cell density defects upon ablation of FBs. Can you project from your sequencing analysis what could be the potential downstream if you could execute bench-side experiments on this?

      We appreciate the reviewer for the comment. We believe that the regulatory predictive results in Figures 5C and D from the scRNA-seq data analysis have provided a set of downstream candidates for validation. We could select some of the ligands, such as the collagen ligands Col1a1, Col4a1, and Col5a1, to treat the ablated embryos in vivo to assess whether they could partially rescue the myocardium defects. Additionally, we could conduct ex vivo experiments by co-culturing CM and FB, comparing them with CM alone and CM treated with the identified ligands. This would allow us to evaluate CM proliferation and the expression of downstream genes identified in the prediction results. However, as the reviewer suggested, these experiments are planned for future studies.

      (9) Please provide the echocardiographic M mode images with a comparable number of cardiac cycles in control and ablated (Fig. 6H). Also, the heart rate of the ablated heart is too low to compare other parameters with the control. If you could stabilize the heart rate at comparable values to control the heart, it is possible that EF and FS values will be largely changed.

      We thank the reviewer for the comment. As the echocardiographic analysis was performed on conscious mice, the lower heart rates in the ablated mice are a phenotype associated with the ablation. Unfortunately, we are unable to adjust them to the same as the control mice.

      (10) Can you provide a numerical dataset for any one of the cell chat figures? Like in figure 2A, supporting the claim "However, in terms of interaction strength, FB exhibited the highest values compared to those of other cell types (Fig. 2A)".

      Yes, we have added a supplemental table (Table S2) containing the numerical interaction weights. As shown in the table, the interactions between FB and other cell types have the highest values.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1:

      The Reviewer asks that we provide the source of PDGF-AB/BB proteins.

      We apologize for omitting such information. We now provide the source of PDGF-AB/BB in the Methods as PeproTech. In our revised manuscript we clearly state in Page 7, line 142: “Cells were then treated with recombinant human PDGF-AB (40ng/ml; PeproTech, 10770584) or -BB (20ng/ml; PeproTech, 10771918) for 5 days. “

      The Reviewer asks that we adequately report our chosen irradiation parameters suggesting that we consider (PMCID: PMC5495460) for appropriate parameter reporting.

      We thank the Reviewer for this excellent suggestion. We now provide a more detailed irradiation reporting based on the shared manuscript in Page 9, line 10, line 204.

      The Reviewer requests more details about the age range to distinguish young from old donors.

      In the Methods section of our revised manuscript, we now provide the age range for our old donors being between 53 and 67 while our younger donor population ranged between 19 and 27 years of age. These changes are reflected in Page 6, line 128: “Human degenerated NP and AF tissues (Grade IV or V on Pfirrman grade; 64.6 ±8.5 years old)) were obtained as the surgical waste from donors with discogenic pain, with each donor providing written informed consent. Healthy NP and AF cells (23.0 ±3.7 years old) were gifted by Professor Lisbet Haglund from McGill University (Tissue Biobank #2019-4896).”

      The Reviewer wonders about the rationale for using different concentrations of PDGF-AB/BB in the degenerate cell and irradiation experiments.

      We apologize for our lack of clarity. We initially treated cells with different concentrations (20 and 40 ng/ml) of PDGF-AB/BB to first establish a dose-response. From our MTT and gene expression analyses we determined that 20ng/ml was sufficient to elicit significant changes in cell proliferation markers, including MKI67, CCNB1 and CCND1. Increasing the concentration to 40 ng/ml of either growth factor did not significantly influence these parameters. However, we felt that for our bulk RNA seq experiments, we may see better changes in signaling molecules under 40ng/ml of PDGF-AB since its effects on cell growth at this concentration were maximal while PDGF-BB was maintained at 20ng/ml based on its efficacy in our mitogenic response.

      The Reviewer asks that we consider describing the effects of PDGF-AB/BB as mitigating or therapeutic rather than protective both in the title and throughout the manuscript.

      We agree with the Reviewer’s recommendation, and we have now changed the title to “Therapeutic effects of PDGF-AB/BB against cellular senescence in human intervertebral disc”. Moreover, we implemented this change in the revised manuscript as requested.

      The Reviewer believes that changes in the NP are more clinically evident (by imaging methods), despite degeneration often initiating from the AF (annulus fibrosus), e,g. through tears/microtears and would like for us to reflect this in our revised manuscript.

      We agree with the Reviewer’s comment, and we thank them for this added accuracy. On this basis, we now corrected our language in the introduction by stating in Page 4, line 68 that: “To date, the main focus of IVD cell studies has been on the NP, as changes in the NP are easily detected through imaging techniques like MRI, making it the most visible indicator of disc degeneration in clinical practice. In addition, NP plays a crucial role in the progression of IVD degeneration due to its susceptibility to significant structural and functional changes during aging and degeneration.”

      The Reviewer points out a prior study which examined the effects of X-ray irradiation on NF-kB signaling in young and aged IVDs (PMCID: PMC5495460) suggesting that we include this reference in our revised manuscript.

      We thank the Reviewer for this suggestion, and we are now referencing this elegant study in the discussion section of our revised manuscript. Thus, in page 20, line 440 we state: “ In fact, it has been shown that NF-kB signaling was elevated in mouse IVDs exposed to a single 20 Gy dose of irradiation in an ex vivo culture model.”

      The Reviewer asks that our experimental methods are described in the order of the experimental workflow. For example, section 2.2 describes RNA sequencing, which is a terminal assay. Section 2.2 may be more appropriate for detailing the methods of PDGF-AB/BB treatment, along with the rationale.

      We thank the Reviewer for pointing this out and have reorganized the Methods section accordingly.

      Reviewer #2:

      The Reviewer requests more experimental details in the methodology including the rationale for such methods/conditions as well as specific culture models utilized, substrates, cell density, and media components.

      We apologize for our lack of clarity. We now revised the methods section based on the comments.

      The Reviewer asks about the quantitative data for b-galactosidase assay and immunofluorescence of senescence-associated proteins such as P21 and P16.

      We apologize for omitting this information. We now included the quantification of P21 and P16 positive cells, which is presented in the revised Figures 4. For b-galactosidase assay, we were unable to quantify the percentage of positive cells because we did not perform nuclei staining, making it difficult to accurately determine the total cell number. Instead, we provided representative images showing the full field of view at 10X magnification using Echo microscope.

      The Reviewer requests the protein level data of PDGFRA to determine if the transcripts are being translated to protein.

      We thank the Reviewer for this suggestion. The protein expression of PDGFRA has been included in the Supplementary Figure 2. We found that PDGFRA protein levels were decreased in both NP and AF cells in response to PDGF treatments. It is known that upon binding with PDGF ligands, PDGFRA undergoes rapid internalization and degradation, a mechanism that prevents overstimulation of the signaling pathway (doi: 10.1042/BST20200004). The upregulated gene expression probably attempting to compensate for this degradation and supports continued activation of PDGFRA signaling activation, emphasizing its crucial role in response to the PDGF treatment. Thus, we implemented it in the discussion section in page 22, line486:” Interestingly, while mRNA level was increased in PDGF treated NP cells, its protein level was decreased, highlighting the complexity in PDGF receptor dynamics. Upon binding with PDGF ligands, PDGFRA is known to undergo rapid internalization and degradation, a mechanism that prevents overstimulation of the signaling pathway (Rogers and Fantauzzo 2020). The upregulated gene expression probably attempting to compensate for this degradation and supports continued activation of PDGFRA signaling activation, emphasizing its crucial role in response to the PDGF treatment.”

      The Reviewer points out that our conclusion that “PDGF do not mediate their effects via the PDGFRA” is not supported by the current data asking that further discussion, interpretation, and direct comparison of the nucleus pulposus and annulus fibrosus data sets be presented to the readers.

      We thank the Reviewer for the insightful comment. In page 20, line 432, we have corrected our language to now state: “In contrast, while PDGF treatment alleviated the senescent phenotype in AF cells, it also induced changes in pathways such as response to mechanical stimuli and neurogenesis, which were distinct from those in NP cells. This indicates that the treatment enhanced IVD functionality through different mechanisms within the two compartments.”

      The Reviewer cannot appreciate the changes in S-phase between control and treated groups.

      We apologize for the poor quality of the figure in our initial submission. We analyzed the data in S phase and included them in our revised Figures 5C and 5F.

      The Reviewer believes that discectomies are typically not performed on patients with discogenic back pain but on patients who are undergoing surgery for a herniated disc.

      We agree with the Reviewer, and we corrected our language in the revised manuscript. In Page 6, line 128, we now stated: “Human degenerated NP and AF tissues (Grade IV or V on Pfirrman grade; 64.6 ±8.5 years old)) were obtained as the surgical waste from donors with disc herniation, with each donor providing written informed consent.”

      The Reviewer asks about the protein-protein interactions in AF cells.

      We thank the Reviewer for this suggestion, and we now included it in Figure 3.

      The Reviewer requests more details about the protocol and doses for the irradiation studies.

      In the revised manuscript, we added this information in page 10, line 204.

      The Reviewer asks whether the gene expression of PDGFRA was increased or decreased in irradiated cells compared to non-irradiated cells.

      The gene expression of PDGFRA was decreased in NP cells exposed to irradiation compared to non-irradiated cells. The data are shown in Figure 4 and their description in the text is in page 17, line 411.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      Zhao and colleagues employ Drosophila nephrocytes as a model to investigate the effects of a high-fat diet on these podocyte-like cells. Through a highly focused analysis, they initially confirm previous research in their hands demonstrating impaired nephrocyte function and move on to observe the mislocalization of a slit diaphragmassociated protein (pyd). Employing a reporter construct, they identify the activation of the JAK/STAT signaling pathway in nephrocytes. Subsequently, the authors demonstrate the involvement of this pathway in nephrocyte function from multiple angles, using a gain-of-function construct, silencing of an inhibitor, and ectopic overexpression of a ligand. Silencing the effector Stat92E via RNAi or inhibiting JAK/ STAT with Methotrexate effectively restored impaired nephrocyte function induced by a high-fat diet, while showing no impact under normal dietary conditions.

      Strengths:

      The findings establish a link between JAK/STAT activity and the impact of a high-fat diet on nephrocytes. This nicely underscores the importance of organ crosstalk for nephrocytes and supports a potential role for JAK/STAT in diabetic nephropathy, as previously suggested by other models.

      Weaknesses:

      The analysis is overly reliant on tracer endocytosis and single lines. Immunofluorescence of slit diaphragm proteins would provide a more specific assessment of the phenotypes.

      We thank the reviewer for the positive comments and pointing out that slit diaphragm markers would provide a more specific assessment of the phenotypes. In our revised manuscript, we used Sns-mRuby3, in which mRuby3 was tagged endogenously at the C-terminal of Sns (PMID: 39195240 and PMID: 39431457), to show the slit diaphragm pattern.

      Reviewer #2 (Public Review):

      Summary:

      In their manuscript, Zhao et al. describe a link between JAK-STAT pathway activation in nephrocytes on a high-fat diet. Nephrocytes are the homologs to mammalian podocytes and it has been previously shown, that metabolic syndrome and obesity are associated with worse outcomes for chronic kidney disease. A study from 2021 (Lubojemska et al.) could already confirm a severe nephrocyte phenotype upon feeding Drosophila a high-fat diet and also linking lipid overflow by expressing adipose triglyceride lipase in the fat body to nephrocyte dysfunction. In this study, the authors identified a second pathway and mechanism, how lipid dysregulation impact on nephrocyte function. In detail, they show activation of JAK-STAT signaling in nephrocytes upon feeding them a high-fat diet, which was induced by Upd2 expression (a leptin-like hormone) in the fat body, and the adipose tissue in Drosophila. Further, they could show genetic and pharmacological interventions can reduce JAK-STAT activation and thereby prevent the nephrocyte phenotype in the high-fat diet model.

      Strengths:

      The strength of this study is the combination of genetic tools and pharmacological intervention to confirm a mechanistic link between the fat body/adipose tissue and nephrocytes. Inter-organ communication is crucial in the development of several diseases, but the underlying mechanisms are only poorly understood. Using Drosophila, it is possible to investigate several players of one pathway, here JAK-STAT. This was done, by investigating the functional role of Hop, Socs36E, and Stat92E in nephrocytes and has also been combined with feeding a high-fat diet, to assess restoration of nephrocyte function by inhibiting JAK-STAT signaling. Adding a translational approach was done by inhibiting JAK-STAT signaling with methotrexate, which also resulted in attenuated nephrocyte dysfunction. Expression of the leptin-like hormone upd2 in the fat body is a good approach to studying inter-organ communication and the impact of other organs/tissue on nephrocyte function and expands their findings from nephrocyte function towards whole animal physiology.

      Weaknesses:

      Although the general findings of this study are of great interest, there are some weaknesses in the study, which should be addressed. Overall, the number of flies investigated for the majority of the experiments is very low (6 flies) and it is not clear whether the flies used, are from independent experiments to exclude problems with food/diet. For the analysis, the mean values of flies should be calculated, as one fly can be considered a biological replicate, but not all individual cells. By increasing the number of flies investigated, statistical analysis will become more solid. In addition, the morphological assessment is rather preliminary, by only using a Pyd antibody. Duf or Sns should be visualized as well, also the investigation of the different transgenic fly strains studying the importance of JAK-STAT signaling in nephrocytes needs to include a morphological assessment. Moreover, the expected effect of feeding a high-fat diet on nephrocytes needs to be shown (e.g. by lipid droplet formation) and whether upd2 is actually increased here should also be assessed. The time points of assessment vary between 1, 3, and 7 days and should be consistent throughout the study or the authors should describe why they use different time points.

      We thank the reviewer for the comments and suggestions. HFD causes enlarged crop (Liao et al, 2021, PMID: 33171202) and accumulation of lipid droplets in the intestine. To exclude the problems with different batches of food/diet, we checked crop and the intestine during the sample preparation as indications of food consistency.

      We followed the suggestion to take the mean values of flies in the data analysis, one was considered a biological replicate in the revised version. We added in another slit diaphragm protein reporter Sns-mRuby3, in which mRuby3 fluorescent protein was tagged at the C-terminal of endogenous Sns. This reporter was used to show the effect of HFD on slit diaphragm protein, manipulation of Jak/Stat pathway (ppl-Gal4>upd2 and dot-Gal4>UAS-Stat92E-RNAi), and drug treatment.

      Lubojemska et al 2021 (PMID: 33945525) showed that HFD leads to lipid droplet accumulation in larval nephrocytes. Following the reviewer’s suggestion, we stained the adult nephrocytes with Nile red and found lipid droplet formation caused by HFD, verifying the HFD effects on lipid droplet accumulation.

      Regarding the timepoints, the newly eclosed flies (1-day old) were treated for 7 days (transferred to fresh diet or shifted from 18 to 29 °C for 7 days to induce target gene expression). Thus, the flies were 7 days old. In the revised manuscript, we changed “1-day-old females” to “7-day-old females” in the figure legend. The exception was Figure 4 panel G and H, we used Day 3 for the UAS-hop.Tum overexpression in the flp-out clones, which is different from the HFD approach (Day 7). This is because Hop.Tum is a strong gain of function mutation. UAS-hop.Tum overexpression in the eye imaginal disc leads to apoptosis via up-regulating a proapoptotic gene hid (Bhawana Maurya et al, 2021, PMID: 33824299). Thus, we used Day 3 for this experiment.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      There are relevant issues, that should be addressed:

      Major:

      - The analysis of JAK/STAT signaling in nephrocytes is limited to nephrocyte function, despite the nice slit diaphragm phenotype shown in Figure 2A. What happens to the slit diaphragm in the other genotypes, the rescue settings in particular? Immunofluorescence of Pyd should be explored for all conditions to evaluate proper phenocopy. Tracer endocytosis is much less specific.

      We thank the reviewer for the suggestion. We made a transgenic line Sns-mRuby3, in which mRuby3 was tagged to the endogenous Sns C-terminal. It has been used as a slit diaphragm reporter (PMID: 39195240 and PMID: 39431457). Apart from the tracer assays, we used Sns-mRuby3 reporter and/or Pyd staining to visualize the changes in slit-diaphragm structures.

      - The interventions are restricted to single RNAi lines and reporters, raising concerns about specificity/potential off-targets. Additional lines should be tested for verification.

      Different versions of RNAi lines are available for targeting fly genes. For UAS-Socs36E-RNAi, we chose the one that was generated with a short hairpin, which is known to restrict the off-target effects (Ni et al, 2011, PMID: 21460824). For UAS-Stat92E-RNAi, we added in an independent RNAi line (Figure 6 - figure supplement 1 and 2).   

      Minor:

      - In Figure 2C, the image of HFD shows a section that cuts through the surface at a shallower angle, making everything appear blurry. This image should be replaced.

      We replaced Figure 2C (the image of HFD) with another one.

      - What is the relevance (if any) of reduced electrodense vacuoles with a high-fat diet? An effect on endocytic trafficking/endosome architecture remains unexplored.

      Lubojemska et al (PMID: 33945525) studied the endocytic trafficking/endosome architecture of the larval nephrocytes and found that HFD impaired the endocytosis. We studied the adult pericardial nephrocytes. It is very likely that the endocytic trafficking/endosome architecture is affected by HFD in the adult nephrocytes.  

      - How do the findings presented in this manuscript correlate with a similar study by Lubojemska et al.? At least the discussion should provide more evaluation of this aspect.

      Lubojemska et al (PMID: 33945525) assayed the larval nephrocytes and found that a HFD leads to the ectopic accumulation of lipid droplets in the nephrocytes and decreased endocytosis. They further demonstrated that lipid droplet lipolysis and PGC1α counteracts the harmful effects of a HFD. We performed Nile red staining and verified the accumulation of lipid droplets in the adult pericardial nephrocytes upon HFD feeding, which agrees with Lubojemska discovery. We found that a HFD activates Jak/Stat pathway, which mediates the nephrocyte functional defects. A previous study showed that Stat1 has an inhibitory effect on PGC1α transcription (PMID: 26689548). Further study is needed to investigate the interaction between Jak/Stat pathway and PGC1α transcription. We added the information to the discussion.

      - Please check spelling and grammar.

      Reviewer #2 (Recommendations For The Authors):

      (1) Which cells are investigated? Please state.

      Pericardial nephrocytes were used in this study. The information was added to the result parts.

      (2) Rephrase 'chronic kidney disease model'. Feeding for 7 days and assessment after 7 days cannot be considered chronic as flies can live more than 60 days.

      Lubojemska et al (PMID: 33945525) fed the newly hatched larvae with a HFD and used the third instar larvae for the experiments. The term “chronic kidney disease” has been used in the reference PMID: 33945525. It takes about 4 days for fly larvae to develop from the first instar to the third instar. Thus, the animals were fed on the HFD for only 4 days. In this regard, feeding for seven days might be considered as chronic.

      (3) Line 89: Curran et al., 2014). with risk increasing risk as BMI increases (Hsu et al., 2006). Please correct this sentence.

      We thank the reviewer for finding the error. In the revised version, the sentence was changed as “with increasing risk as BMI increases (Hsu et al., 2006)”.

      (4) Figure 1: The authors should explain why they use FITC-Albumin and 10kDA dextran, what are the differences, and why are both used?

      The tracers are different in size (70kD FITC-Albumin and 10kDA dextran). Both FITC-Albumin and 10kDA dextran have been used in previous publications (Zhao et al 2024, PMID: 39431457 and Weavers et al 2009, PMID: 18971929) to show that the nephrocytes can efficiently take up the tracers of different sizes.

      (5) Figure 3: The JAK-STAT sensor was used on Day 1 to confirm activation of JAKSTAT signaling, which means a very fast response towards the HFD after 24hrs. How is the activation after 7 days? The nephrocyte assessment in Figures 1 and 2 is done at the later time point, how about earlier time points in HFD? One would expect an earlier phenotype as well if JAK-STAT signaling is causative.

      In Figure 3C, newly eclosed flies (1-day old) were fed on a control diet or a HFD for 7 days. Thus, in the legend it shall be “7-day-old females”. Sorry for misleading. The caption was updated as “7-day-old females”.

      (6) Figure 4H: I don't understand how many cells or flies are depicted and analysed? Are the dots one nephrocyte from 4 flies? If yes, the numbers need to be increased.

      In figure 4H, we quantified 5 UAS-hop.Tum clones and 5 neighbor cells. We only found 5 clones from 4 flies. We didn’t quantify all the nephrocytes, since we compared the clone with its neighbor cell. To make it easier to follow, we changed the description as “n= 5 clones and 5 neighbor cells”.

      (7) Figure 4: Why are flies investigated at different ages? Day 1 vs Day 3? This should be consistent with the HFD approach and day 7. Or investigate the HFD at earlier time points as well.

      In Figure 4, the newly eclosed flies (1-day old) were shifted from 18 to 29 °C for 7 days to induce target gene expression. Thus, the flies were 7-day old. In the revised manuscript, we changed “1-day-old females” to “7-day-old females” in the figure legend. We used Day 3 for the UAS-hop.Tum overexpression in the flp-out clones, which is different from the HFD approach (Day 7). This is because Hop.Tum is a strong gain of function mutation. UAS-hop.Tum overexpression in the eye imaginal disc leads to apoptosis via up-regulating a proapoptotic gene hid (Bhawana Maurya et al, 2021, PMID: 33824299). Thus, we used Day 3 for this experiment.

      (8) Figure 5: Do the authors see upd2-GFP in the nephrocyte or at the nephrocyte? Is upd2 filtered to bind the JAK-STAT-receptor? They should show this, which is easy to do due to the GFP label.

      We thank the reviewer for the suggestion. We looked into the nephrocyte from ppl-Gal4>upd2-GFP flies and found Upd2-GFP in the nephrocytes. We further showed that ppl-Gal4 was not expressed in the nephrocytes, suggesting that Upd2-GFP is secreted from the fat body and transported to the nephrocytes. We stained the nephrocytes for Pyd and found compromised fingerprint pattern caused by Upd2-GFP expression in the fat body. The data was added to Figure 5 - figure supplement 1.

      (9) Figure 5: What are the upd2 levels after day 1 and compared to HFD at day 7? In the Rajan et al manuscript, upd2 levels have been assessed by qPCR, this can be done here as well. Although there is a mechanistic link shown here, I think it would be interesting to test the upd2 levels at the different time points assessed.

      In the Rajan et al manuscript, they showed that the expression of upd2 was up regulated by HFD. My previous work showed that HFD changes taste perception. We performed qPCR to determine the expression of upd2 and verified that upd2 was upregulated in HFD fed flies (Yunpo Zhao et al. 2023. PMID: 37934669). We included the reference in the revised version.

      (10) Figure 6: Does a Socs36E overexpression e.g. with the Bloomington strain 91352 also rescue the HFD phenotype, by blocking JAK-STAT signaling?

      We thank the reviewer for the suggestion. We tested the effect of Socs36E overexpression and observed that UAS-Socs36E can partially rescue HFD caused nephrocyte functional decline. The data was not included in the revised manuscript. Notably, apart from having an inhibitory effect on the Jak/Stat, Socs36E represses MAPK pathway (Amoyel et al, 2016, PMID: 26807580).    

      (11) Figure 7: What is the control for the methotrexate treatment? What is the solvent?

      We used DMSO as the solvent for methotrexate and used it as the control for the methotrexate treatment. We added the following sentences to the method parts, “Methotrexate (06563, Sigma-Aldrich, MO) was dissolved in DMSO to make a 10mM stock solution”, and “The samples incubated in Schneider’s Medium supplemented with DMSO vehicle were used a control”.

      (12) Why did the authors use Dot-Gal4 for the Socs36E knockdown and Dot-Gal4ts for the Stat92E knockdown?

      We used Dot-Gal4ts and temperature shifting to restrict the Stat92E knockdown at adult stages.

      (13) Supplementary Figure 1: Please add the individual data to the figure as done for all other figures.

      We thank the reviewer for this comment. The figure individual data was added according to the suggestion.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary

      The authors use microscopy experiments to track the gliding motion of filaments of the cyanobacteria Fluctiforma draycotensis. They find that filament motion consists of back-and-forth trajectories along a "track", interspersed with reversals of movement direction, with no clear dependence between filament speed and length. It is also observed that longer filaments can buckle and form plectonemes. A computational model is used to rationalise these findings.

      We thank the reviewer for this accurate summary of the presented work.

      Strengths:

      Much work in this field focuses on molecular mechanisms of motility; by tracking filament dynamics this work helps to connect molecular mechanisms to environmentally and industrially relevant ecological behavior such as aggregate formation.

      The observation that filaments move on tracks is interesting and potentially ecologically significant.

      The observation of rotating membrane-bound protein complexes and tubular arrangement of slime around the filament provides important clues to the mechanism of motion.

      The observation that long filaments buckle has the potential to shed light on the nature of mechanical forces in the filaments, e.g. through the study of the length dependence of buckling.

      We thank the reviewer for listing these positive aspects of the presented work.

      Weaknesses:

      The manuscript makes the interesting statement that the distribution of speed vs filament length is uniform, which would constrain the possibilities for mechanical coupling between the filaments. However, Figure 1C does not show a uniform distribution but rather an apparent lack of correlation between speed and filament length, while Figure S3 shows a dependence that is clearly increasing with filament length. Also, although it is claimed that the computational model reproduces the key features of the experiments, no data is shown for the dependence of speed on filament length in the computational model. The statement that is made about the model "all or most cells contribute to propulsive force generation, as seen from a uniform distribution of mean speed across different filament lengths", seems to be contradictory, since if each cell contributes to the force one might expect that speed would increase with filament length.

      We agree that the data shows in general a lack of correlation, rather than strictly being uniform. In the revised manuscript, we intend to collect more data from observations on glass to better understand the relation between filament length and speed.

      In considering longer filaments, one also needs to consider the increased drag created by each additional cell - in other words, overall friction will either increase or be constant as filament length increases. Therefore, if only one cell (or few cells) are generating motility forces, then adding more cells in longer filaments would decrease speed.

      Since the current data does not show any decrease in speed with increasing filament length, we stand by the argument that the data supports that all (or most) cells in a filament are involved in force generation for motility. We would revise the manuscript to make this point - and our arguments about assuming multiple / most cells in a filament contributing to motility - clear.

      The computational model misses perhaps the most interesting aspect of the experimental results which is the coupling between rotation, slime generation, and motion. While the dependence of synchronization and reversal efficiency on internal model parameters are explored (Figure 2D), these model parameters cannot be connected with biological reality. The model predictions seem somewhat simplistic: that less coupling leads to more erratic reversal and that the number of reversals matches the expected number (which appears to be simply consistent with a filament moving backwards and forwards on a track at constant speed).

      We agree that the coupling between rotation, slime generation and motion is interesting and important when studying the specific mechanism leading to filament motion. However, we believe it is even more fundamental to consider the intercellular coordination that is needed to realise this motion. Individual filaments are a collection of independent cells. This raises the question of how they can coordinate their thrust generation in such a way that the whole filament can both move and reverse direction of motion as a single unit. With the presented model, we want to start addressing precisely this point.

      The model allows us to qualitatively understand the relation between coupling strength and reversals (erratic vs. coordinated motion of the filament). It also provides a hint about the possibility of de-coordination, which we then look for and identify in longer filaments.

      While the model’s results seem obvious in hindsight, the analysis of the model allows phrasing the question of cell-to-cell coordination, which so far has not been brought up when considering the inherently multi-cell process of filament motility.

      Filament buckling is not analysed in quantitative detail, which seems to be a missed opportunity to connect with the computational model, eg by predicting the length dependence of buckling.

      Please note that Figure S10 provides an analysis of filament length and number of buckling instances observed. This suggests that buckling happens only in filaments above a certain length.

      We do agree that further analyses of buckling - both experimentally and through modelling would be interesting. This study, however, focussed on cell-to-cell coupling / coordination during filament motility. We have identified the possibility of de-coordination through the use of a simple 1D model of motion, and found evidence of such de-coordination in experiments. Notice that the buckling we report does not depend on the filament hitting an external object. It is a direct result of a filament activity which, in this context, serves as evidence of cellular de-coordination.

      Now that we have observed buckling and plectoneme formation, these processes need to be analysed with additional experiments and modelling. The appropriate model for this process needs to be 3D, and should ideally include torques arising from filament rotation. Experimentally, we need to identify means of influencing filament length and motion and see if we can measure buckling frequency and position across different filament lengths. These works are ongoing and will have to be summarised in a separate, future publication.

      Reviewer #2 (Public review):

      Summary:

      The authors combined time-lapse microscopy with biophysical modeling to study the mechanisms and timescales of gliding and reversals in filamentous cyanobacterium Fluctiforma draycotensis. They observed the highly coordinated behavior of protein complexes moving in a helical fashion on cells' surfaces and along individual filaments as well as their de-coordination, which induces buckling in long filaments.

      We thank the reviewer for this accurate summary of the presented work.

      Strengths:

      The authors provided concrete experimental evidence of cellular coordination and de-coordination of motility between cells along individual filaments. The evidence is comprised of individual trajectories of filaments that glide and reverse on surfaces as well as the helical trajectories of membrane-bound protein complexes that move on individual filaments and are implicated in generating propulsive forces.

      We thank the reviewer for listing these positive aspects of the presented work.

      Limitations:

      The biophysical model is one-dimensional and thus does not capture the buckling observed in long filaments. I expect that the buckling contains useful information since it reflects the competition between bending rigidity, the speed at which cell synchronization occurs, and the strength of the propulsion forces.

      Cell-to-cell coordination is a more fundamental phenomenon than the buckling and twisting of longer filaments, in that the latter is a consequence of limits of the former. In this sense, we are focussing here on something that we think is the necessary first step to understand filament gliding. The 3D motion of filaments (bending, plectoneme formation) is fascinating and can have important consequences for collective behaviour and macroscopic structure formation. As a consequence of cellular coupling, however, it is beyond the scope of the present paper.

      Please also see our response above. We believe that the detailed analysis of buckling and plectoneme formation requires (and merits) dedicated experiments and modelling which go beyond the focus of the current study (on cellular coordination) and will constitute a separate analysis that stands on its own. We are currently working in that direction.

      Future directions:

      The study highlights the need to identify molecular and mechanical signaling pathways of cellular coordination. In analogy to the many works on the mechanisms and functions of multi-ciliary coordination, elucidating coordination in cyanobacteria may reveal a variety of dynamic strategies in different filamentous cyanobacteria.

      We thank the reviewer for highlighting this point again and seeing the value in combining molecular and dynamical approaches.

      Reviewer #3 (Public review):

      Summary:

      The authors present new observations related to the gliding motility of the multicellular filamentous cyanobacteria Fluctiforma draycotensis. The bacteria move forward by rotating their about their long axis, which causes points on the cell surface to move along helical paths. As filaments glide forward they form visible tracks. Filaments preferentially move within the tracks. The authors devise a simple model in which each cell in a filament exerts a force that either pushes forward or backwards. Mechanical interactions between cells cause neighboring cells to align the forces they exert. The model qualitatively reproduces the tendency of filaments to move in a concerted direction and reverse at the end of tracks.

      We thank the reviewer for this accurate summary of the presented work.

      Strengths:

      The observations of the helical motion of the filament are compelling. The biophysical model used to describe cell-cell coordination of locomotion is clear and reasonable. The qualitative consistency between theory and observation suggests that this model captures some essential qualities of the true system.

      The authors suggest that molecular studies should be directly coupled to the analysis and modeling of motion. I agree.

      We thank the reviewer for listing these positive aspects of the presented work and highlighting the need for combining molecular and biophysical approaches.

      Weaknesses:

      There is very little quantitative comparison between theory and experiment. It seems plausible that mechanisms other than mechano-sensing could lead to equations similar to those in the proposed model. As there is no comparison of model parameters to measurements or similar experiments, it is not certain that the mechanisms proposed here are an accurate description of reality. Rather the model appears to be a promising hypothesis.

      We agree with the referee that the model we put forward is one of several possible. We note, however, that the assumption of mechanosensing by each cell - as done in this model - results in capturing both the alignment of cells within a filament (with some flexibility) and reversal dynamics. We have explored an even more minimal 1D model, where the cell’s direction of force generation is treated as an Ising-like spin and coupled between nearest neighbours (without assuming any specific physico-chemical basis). We found that this model was not fully able to capture both phenomena. In that model, we found that alignment required high levels of coupling (which is hard to justify except for mechanical coupling) and reversals were not readily explainable (and required additional assumptions). These points led us to the current, mechanically motivated model.

      The parameterisation of the current model would require measuring cellular forces. To this end, a recent study has attempted to measure some of the physical parameters in a different filamentous cyanobacteria [1] and in our revision we will re-evaluate model parameters and dynamics in light of that study. We will also attempt to directly verify the presence of mechano-sensing by obstructing the movement of filaments.

      Summary from the Reviewing Editor:

      The authors present a simple one-dimensional biophysical model to describe the gliding motion and the observed statistics of trajectory reversals. However, the model does not capture some important experimental findings, such as the buckling occurring in long filaments, and the coupling between rotation, slime generation, and motion. More effort is recommended to integrate the information gathered on these different aspects to provide a more unified understanding of filament motility. In particular, the referees suggest performing a more quantitative analysis of the buckling in long filaments. Finally, it is also recommended to discuss the results in the context of previous literature, in order to better explain their relevance. Please find below the detailed individual recommendations of the three reviewers.

      We thank the editor for this accurate summary of the presented work and for highlighting the key points raised by the reviewers. We have provided below point-by-point replies to these.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The relevance of the study organism Fluctiforma draycotensis is not clearly explained, and the results are not discussed in the context of previous literature. The motivation would be clearer if the manuscript explained why this model organism was chosen and how the results compare with those previously observed for this or other organisms.

      We have extended the introduction and discussion sections to make it clearer why we have worked with this organism and how the findings from this work relate to previous ones. In brief, Flucitforma draycotensis is a useful organism to work with as it not only displays significant motility but it also displays intriguing collective behaviour at different scales. Previous works on gliding motility in filamentous cyanobacteria have mostly focussed on the model organism Nostoc punctiforme, which only displays motility after differentiation into hormogonia [1]. There have also been studies in a range of different filamentous species, including those of the non-monophyletic genus, Phormidium, but these studies mostly looked at effects of genetic deletions on motility [2] or utilised electron microscopy to identify proteins (or surface features) involved in motility [3-5]. It must be noted that motility is also described and studied in non-filamentous cyanobacteria, but the dynamics of motion and molecular mechanisms there are different to filamentous cyanobacteria [6,7]. These previous studies are now cited / summarised in the revised introduction and discussion sections.

      The inferred tracks, probably associated with secreted slime, play a key role since it is supposed that the tracks provide the external force that keeps the filaments straight. Movie S3, in phase contrast, provides convincing evidence for the tracks, but they cannot be seen in the fluorescence images presented in the main text. Clearer evidence of them should be shown in the main text. An especially important aspect of the tracks is where they start and end since the computational model assumes that reversal happens due to forces generated by reaching the end of a track. Therefore it seems important to comment on what produces the tracks, to check whether reversals actually happen at the end of a track, etc. Perhaps tracks could be strained with Concanavalin-A?

      To confirm that reversals happen on track ends, we have now performed an analysis on agar, where we can see tracks on phase microscopy. This analysis confirms that, on agar, reversals indeed happen on track ends. We added this analysis, along with images showing tracks clearly as a new Fig in the main text (see new Fig. 1).

      Further confirming the reversal at track ends, we note that filaments on circular tracks do not not reverse over durations longer than the ‘expected reversal interval’ of a filament on a straight track (see details in response to Reviewer 2).

      Regarding what produces the tracks on agar, we are still analysing this using different methods and these results will be part of a future study. Fluorescent staining can be used to visualise slime tubes using TIRF microscopy, as shown in Fig. S8, however, visualising tracks on agar using low magnification microscopy has been difficult due to background fluorescence from agar.

      We would also like to clarify that the model does not incorporate any assumptions regarding the track-filament interaction, other than that the track ends behave akin to a physical boundary for the filament. The observed reversal at track ends and “what” produces the track are distinct aspects of filament motion. We do not think that the model’s assumption of filament reversal at the end of the track requires understanding of the mechanism of slime production.

      Reviewer #3 (Recommendations for the authors):

      The manuscript combines three distinct topics: (1) the difference in locomotion on glass vs agar, (2) the development of a biophysical model, and (3) the helical motion of filament. It is not clear what insight one can gain from any one of these topics about the two others. The manuscript would be strengthened by more clearly connecting these three aspects of the work. A stronger comparison of theory to observation would be very useful. Some suggestions:

      (1) The observation that it is only the longest filaments that buckle is interesting. It should be possible to predict the critical length from the biophysical model. Doing so could allow fits of some model parameters.

      (2) What model parameters change between glass and agar? Can you explain these qualitative differences in motility by changing one model parameter?

      (3) Is it possible to exert a force on one end of a filament to see if it is really mechano-sensing that couples their motion?

      We thank the reviewer for this comment and agree with them that a better connection between model and experiment should be sought. We believe that the new analyses, presented below in response to the 2nd suggestion of the reviewer, provide such a connection in the context of reversal frequency. As stated below, we think that the 1st suggestion falls outside of the scope of the current work, but should form the basis of a future study.

      Regarding suggestion (1) - addressing buckling:

      We agree with the reviewer that using a model to predict a critical buckling length would be useful. We note, however, that the presented study focussed on cell-to-cell coupling / coordination during filament motility using a 1D, beadchain model. The buckling observations served, in this context, as evidence of cellular de-coordination. Now that we have observed buckling (and plectoneme formation), these processes need to be analysed with further experiments and modelling. The appropriate model for studying buckling would have to be at least 2D (ideally 3D) and consider elastic forces and torques relating to filament bending, rotation, and twisting. Experimentally, we need to identify means of influencing filament length and motion and undertake further measurements of buckling frequency and position across different filament lengths. These investigations are ongoing and will be summarised in a separate, future publication.

      Regarding suggestion (2) - addressing differences in motility on agar vs. glass:

      We believe that the two key differences between agar and glass experiments are the occasional detachment of filaments from substrate on glass and the lack of confining tracks on glass. These differences might arise from the interactions between the filament, the slime, and the surface. As both slime and agar contain polysaccharides, the slime-agar interaction can be expected to be different from the slime-glass interaction. Additionally, in the agar experiments, the filaments are confined between the agar and a glass slide, while they are not confined on the glass, leaving them free to lift up from the glass surface. We expect these factors to alter reversal frequency between the two conditions. To explore this possibility, we have now extended the analysis of experimental data from glass and present that (see details below):

      (i) dwell times are similar between agar and glass, and

      (ii) reversal frequency distribution is different between glass and agar, and remains constant across filament length on glass.

      We were able to explore these experimental findings with new model simulations, by removing the assumption of an “external bounding frame”. We then analysed reversal frequency within against model parameters, as detailed below.

      “The movement of the filaments on glass. We have extended our analysis of motility on glass resulting in the following noted features. Firstly, the median speed shows a weak positive correlation with filament length on glass (see original Fig S3B vs. updated Fig. S3A). This is slightly different to agar, where we do not observe any strong correlation in either direction (see original, Fig. 1 vs. updated Fig 2). Both the cases of positive, and no correlation, support our original hypothesis that the propulsion force is generated by multiple cells within the filament.

      Secondly, the filaments on glass display ‘stopping’ events that are not followed by a reversal, but are instead followed by a continuation in the original direction of motion, which we term ‘stop-go’ events, in contrast to the reversals. The dwell times associated with reversals and ‘stop-go’ events are similarly distributed (see original Fig S3A vs. updated Fig S3B). Furthermore, the dwell time distributions are similar between agar and glass (compare old Fig. 1C vs. new Fig 2C and new Fig. S3B). This suggests that the reversal process is the same on both agar and glass.

      Thirdly, we find that the frequencies of both reversal and stop-go events on glass are uncorrelated with the filament length (see new Fig. S4A) and there are approximately twice as many reversals as stop-go events. In contrast, the filaments on agar reverse with a frequency that is inversely proportional to the filament length (which is in turn proportional to the track length) (see original Fig. S1). The distribution of reversal frequencies on agar is broader and flatter than the distribution on glass (see new Fig. S4B). These findings are inline with the idea that tracks on agar (which are defined by filament length) dictate reversal frequency, resulting in the strong correlations we observe between reversal frequency, track length, and filament length. On glass, filament movement is not constrained by tracks, and we have a specific reversal frequency independent of filament length.”

      “Model can capture movement of filaments on glass and provides hypotheses regarding constancy of reversal frequency with length. We believe the model parameters controlling cellular memory (ω<sub>max</sub>) and strength of cellular coupling (K<sub>ω</sub>) describe the internal behaviour of a filament and therefore should not change depending on the substrate. Thus, we expect the model to be able to capture movement on glass just by removal of any ‘confining tracks’, i.e external forces, from the simulations. Indeed, we find that the model displays both stop-go and reversal events when simulated without any external force and can capture the dwell time distribution under this condition (compare new Figs. S12,S13 with S3).

      In terms of reversal frequency, however, the model shows a reduction in reversal frequency with filament length (see new Fig. S15). This is in contrast to the experimental data. We find, however, that model results also show a reduction in reversal frequency with increasing (ω<sub>max</sub> and K<sub>ω</sub> (see new Fig. S14 and S15). This effect is stronger with (ω<sub>max</sub>, while it quickly saturates with K<sub>ω</sub> (see new Fig. S14). Therefore, one possibility of reconciling the model and experiment results in terms of constant reversal frequency with filament length would be to assume that (ω<sub>max</sub> is decreasing with filament length (see new Fig. S16). Testing this hypothesis - or adding additional mechanisms into the model - will constitute the basis of future studies.”

      Regarding suggestion (3) - role of mechanosensing:

      We have tried several experiments to evaluate mechanosensing. First, we have used a micropipette or a thin wire placed on the agar, to create a physical barrier in the way of the filaments. The micropipette approach was not quite feasible in our current setup. The wire approach was possible to implement, but the wire caused a significant undulation / perturbation on agar. Possibly relating to this, filaments tended to continue moving alongside the wire barrier. Therefore, these experiments were inconclusive at this stage with regards to mechanosensing a physical barrier. As an alternative, we have attempted trapping gliding filaments using an optical trap with a far red laser that should not affect the physiology of the cells. This did not cause an immediate reversal in filament motion. However, this could be due to the optical trap strength being below the threshold value for mechanosensing. The force per unit length generated by filamentous cyanobacteria has been calculated via a model of self-buckling rods, giving a value of ≈1nN/μm [8]. In comparison, the optical trap generates forces on the scale of pN. Thus, the trap force is several orders of magnitude lower than the propulsive force generated by a filament, given filament lengths in the range of ten to several hundreds μm. We conclude that the lack of observed response may be due to the optical trap force being too weak.

      Thus, the experiments we can perform using our current available methods and equipment are not able to prove either the presence or the absence of mechanosensing in the filament. We plan to perform further experiments in this direction, involving new and/or improved experimental setups, such as use of Atomic Force Microscopy.

      We would like to note that there is an additional observation that supports the idea of reversals being mediated by mechanosensing at the end of a track, instead of the locations of the track ends being caused by the intrinsic reversal frequency of the filament. In a few instances (N = 4), filaments on agar ended up on a circular track (see Movie S4 for an example). These filaments did not reverse over durations a few times longer than the ‘expected reversal interval’ of a filament on a straight track.

      Should $N$ following eq 7 and in eq 9 be $N_f$?

      We have corrected this typo.

      It would be useful to include references to what is known about mechanosensing in cyanobacteria.

      We agree with the reviewer, and we have not updated the discussion section to include this information. Mechanosensing has not yet been shown directly in any cyanobacteria, but several species are shown to harbor genes that are implicated (by homology) to be involved in mechanosensing. In particular, analysis of cyanobacterial genomes predicts the presence of a significant number of homologues of the Escherichia coli mechanosensory ion channels MscS and MscL [9]. We have also identified similar MscS protein sequences in F. draycotensis. These channels open when the membrane tension increases, allowing the cell to protect itself from swelling and rupturing when subject to extreme osmotic shock. [10,11]

      We also note that F. draycotensis, as with other filamentous cyanobacteria, have genes associated with the type IV pili, which may be involved in the surface-based motility [1]. Type IV pili have been shown to be mechanosensitive. For example, in cells of Pseudomonas aeruginosa that ‘twitch’ on a surface using type IV pili, application of mechanical shear stress results in increased production of an intracellular signalling molecule involved in promoting biofilm production. The pilus retraction motor has been shown to be involved in this shear-sensing response [12]. Additionally, twitching P. aeruginosa cells often reverse in response to collisions with other cells. Reversal is also caused by collisions with inert glass microfibres, which suggests that the pili-based motility can be affected by a mechanical stimulus [13].

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      (9) S.C. Johnson, J. Veres, H. R. Malcolm, Exploring the diversity of mechanosensitive channels in bacterial genomes. Eur Biophys J 50, 25–36 (2021).

      (10) S.I. Sukharev, W.J. Sigurdson, C. Kung, F. Sachs, Energetic and spatial parameters for gating of the bacterial large conductance mechanosensitive channel, MscL. Journal of General Physiology, 113(4), 525-540 (1999).

      (11) N. Levina, S. Tötemeyer, N.R. Stoke, P. Louis, M.A. Jones, I.R. Boot. Protection of Escherichia coli cells against extreme turgor by activation of MscS and MscL mechanosensitive channels: identification of genes required for MscS activity. The EMBO journal (1999).

      (12) V.D. Gordon, L. Wang, Bacterial mechanosensing: the force will be with you, always. Journal of cell science 132(7):jcs227694 (2019).

      (13) M.J. Kühn, L. Talà, Y.F. Inclan, R. Patino, X. Pierrat, I. Vos, Z. Al-Mayyah, H. Macmillan, J. Negrete Jr, J.N. Engel, A. Persat, Mechanotaxis directs Pseudomonas aeruginosa twitching motility. Proceedings of the National Academy of Sciences. 118(30):e2101759118 (2021).

    1. Author response:

      We sincerely thank the editor and all three reviewers for their constructive comments. We deeply appreciate the reviewers’ efforts in highlighting both the strengths and the weaknesses of our study. To enhance the quality and clarity of our work, we plan to address the concerns raised in the public reviews through the following actions:

      (1) Improving the tone and language of the manuscript

      We will revise the manuscript thoroughly, incorporating additional explanations and clarifications where necessary, and improving the tone and language to enhance readability and precision. Especially, we will pay careful attention on the terms “positional information,” “positional value,” and “positional cue,” and we plan to explain them in a historical context.

      (2) Extending analysis to regular blastemas

      To validate the applicability of our proposed model beyond the accessory limb model (ALM), we will examine the gene expression patterns of key signaling molecules in regular blastemas generated by limb amputation. This will allow us to test whether the mechanisms we describe are also active during normal limb regeneration.

      (3) Increasing sample sizes in critical experiments

      In order to ensure reproducibility and statistical reliability, we will increase the number of biological replicates in key experiments within the limitations regulated by our animal ethics approval. Additionally, we will collect data that clearly defines the dorsal/ventral axis within the structures, as far as possible. We will also revise the manuscript to pay closer attention to the anterior/posterior/dorsal/ventral axis in the existing data, ensuring that it is clearly described.

      (4) Adding quantitative gene expression data

      To support and reinforce our in situ hybridization results, we will include additional quantitative gene expression analyses (e.g., qRT-PCR), thereby strengthening the conclusions drawn from our expression data.

      We are grateful for the reviewers’ insights and are confident that these revisions will significantly strengthen our manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews:

      We sincerely thank the reviewers for their thoughtful review and feedback. We believe that our work will provide valuable insights into how MRSA evolves under bacteriophage predation and stimulate efforts to use genetic trade-offs to combat drug resistance. We have substantially revised the paper and performed several additional experiments to address the reviewers' questions and concerns.

      Summary:

      (1) Testing for genetic trade-offs in additional S. aureus strains

      We obtained 30 clinical isolates of the S. aureus USA300 strain that were isolated between 2008 and 2011 (see Table S1). We first tested the FStaph1N, Evo2, and FNM1g6 phages against this expanded strain panel and found that Evo2 showed strong activity against all 30 strains (Table S4). We tested whether Evo2 infection could elicit trade-offs in b-lactam resistance for a subset of these strains. We found that Evo2 infection caused a ~10-100-fold reduction in their MIC against oxacillin. This data is now incorporated into a revised Figure 2 in panel C.

      (2) Testing additional staphylococcal phages

      We isolated from the environment a phage called SATA8505. Similar to FStaph1N and Evo2, SATA8505 belongs to the Kayvirus genus and infects the MRSA strains MRSA252, MW2, and LAC. Phage-resistant MRSA recovered following SATA8505 infection also showed a strong reduction in oxacillin resistance (Figure S5). Furthermore, we confirmed that resistance against FNM1g6, which belongs to the Dubowvirus genes, does not elicit tradeoffs in b-lactam resistance (Figure S4). Sequencing analysis of FNM1g6 - resistant LAC strains showed a different mutation fmhC, which was not observed with the FStaph1N and Evo2 phages (Table 1). We have added this new data into the main text and supplemental figures and tables. Future work will focus on obtaining comprehensive analysis of a wide range of phage families. 

      (3) Testing additional antibiotics

      We also expanded our trade-off analysis include wider range of antibiotic classes (Table S3). Overall, the loss of resistance appears to be confined to b-lactams.

      (4) Genetic analysis of ORF141

      In order determine the function of ORF141, which is mutated in Evo2, we attempted to clone wild-type ORF141 into a staphylococcal plasmid and perform complementation assays with Evo2. Unfortunately, obtaining the plasmid-borne wild-type ORF141 has proven to be tricky, as all clones developed frameshift or deletions in the open reading frame. We posit that the gene product of ORF141 is toxic to the bacteria. We are currently working on placing the gene under more stringent expression conditions but feel that these efforts fall outside of the scope of this paper.  

      (5) Testing the effect of single mutants  

      Our genomic analysis showed that phage-resistant MRSA evolved multiple mutations following phage infection, making it difficult to determine the mechanism of each mutation alone. For example, phage-resistant MW2 and LAC evolved nonsense mutations in transcriptional regulators mgrA, arlR, and sarA. To test whether these mutations alone were sufficient to confer resistance, we obtained MRSA strains with single-gene knockouts of mgrA, arlR, and sarA and tested their ability to resist phage. We observed that deletion of mgrA in the MW2 resulted in a modest reduction in phage sensitivity (Figure S7). However, we did not the observe any changes in the other mutant strains. These results suggest that phage resistance in these strains is likely caused by a combination of mutations. Determining the mechanisms of these mutations is the focus if our future work.

      (6) Transcriptomics of phage-resistant MRSA strains

      To further assess the effects of the phage resistance mutations, we performed bulk RNA-seq on phage-resistant MW2 and LAC strains and compared their differential expression levels to the respective wild-type strains. We picked these strains because our genomic data showed that they had evolved mutations in known transcriptional regulators (e.g. mgrA). Our analysis shows that both strains significantly modulate their gene expression (Figure 4). Notably, both strains upregulate the cell wall-associated protein ebh, while downregulating several genes involved in quorum sensing, virulence, and secretion. We have included this new data in Figure 4 and Table S5 and added an entire section in the manuscript discussing these results and their implications.  

      (7) Co-treatment of MRSA with phage and b-lactam

      We performed checkerboard experiments on MRSA strains with phage and b-lactam gradients (Figure 6). We found that under most conditions, MRSA cells were only able to recover under low phage and b-lactam concentrations. Notably, these recovered cells were still phage resistant and b-lactam sensitive. However, under one condition where MW2 was treated with FStaph1N and b-lactam, we found that some recovered cells still had high levels of b-lactam resistance, showing a distinct mutational profile. We discuss these results in detail in the main text.

      Reviewer # 1:

      Strengths:

      Phage-mediated re-sensitization to antibiotics has been reported previously but the underlying mutational analyses have not been described. These studies suggest that phages and antibiotics may target similar pathways in bacteria.

      We thank Reviewer 1 for this assessment. We hope that the data provided in this work will help stimulate further inquiries into this area and help in the development of better phage-based therapies to combat MRSA.

      Weaknesses:

      One limitation is the lack of mechanistic investigations linking particular mutations to the phenotypes reported here. This limits the impact of the work.

      We acknowledge the limitations of our initial analysis. We note (and cite) that separate studies have already linked mutations in femA, mgrA, arlR, and sarA with reduced b-lactam resistance and virulence phenotypes in MRSA, but not to phage resistance. For the other mutations, we could not find literature linking them to our observed phenotypes. We analyzed the effects of single gene knockouts of mgrA, arlR, and sarA on MRSA’s phage resistance. However, as shown above, the results only showed modest effects on phage resistance in the MW2 strain (see Figure S7 and lines 309-317). We therefore believe that mutations in single genes are not sufficient to cause the trade-offs in phage/ b-lactam resistance. Because each MRSA strain evolved multiple mutations (e.g. MW2 evolved 6 or more mutations), we feel that determining the effects of all possible permutations of those mutations was beyond the scope of the paper.

      However, to bridge the mutational data with our phenotypic observations, we performed RNAseq and compared the transcriptomes of un-treated and phage-treated MRSA strains (see Figure 4, Table S5, and lines 337-391). Our results show that phage-treated MRSA strains significantly modulate their transcript levels. Indeed, some of the changes in gene expression can explain for the phenotypic observations (e.g. overexpression of ebh can lead to reduced clumping). Further, the results shown some unexpected patterns, such as the downregulation of quorum sensing genes or genes involved in type VII secretion.

      Another limitation of this work is the use of lab strains and a single pair of phages. However, while incorporation of clinical isolates would increase the translational relevance of this work it is unlikely to change the conclusions.

      We thank the reviewer for this suggestion. We would like to clarify that MW2, MRSA252, and LAC are pathogenic clinical isolates that were isolated between 1997 and 2000’s. However, we acknowledge that, because these 3 strains have been propagated for many generations, they might have acquired laboratory adaptations. We therefore obtained 30 USA300 clinical strains that were isolated in more recent years (~2008-2011) and tested our phages against them. We note that these clinical isolates (generously provided by Dr. Petra Levin’s lab) were preserved with minimal passaging to reduce the effects of laboratory adaptation. We found that the Evo2 phage was able to elicit oxacillin trade-offs in those strains as well. (see Table S1, Table S7, Fig 2C, and lines 210 – 225)

      For the phages, we had to work with phage(s) that could infect all three MRSA strains. That is why in our initial tests, we focused on FStaph1N and Evo2, both members of the Kayvirus genus. Now in our revised work, we extend our analysis to FNM1g6, a member of the Dubowvirus genus, that also infects the LAC strain, but not MW2 and MRSA252. We find that FNM1g6 is unable to drive trade-offs in b-lactam resistance (see lines 229 – 238). Next, we analyzed the effects of SATA8505, also a member of the Kayvirus genus. Here, we observed that SATA8505 can elicit trade-offs in b-lactam resistance (see Figure S5 and lines 238 – 246). These results suggest that not all staphylococcal phages can elicit these trade-offs and call for more comprehensive analyses of different types of phages.

      Reviewer #1 (Recommendations for the authors):

      Specific questions:

      (1) The Evo2 isolate is an evolved version of phage Staph1N with more potent lytic activity. Is this reflected in more pronounced antibiotic sensitivity?

      We did not observe that Evo2-treated MRSA cells showed more sensitivity towards b-lactams. However, we did observe that Evo2 was able to elicit these trade-offs at lower multiplicities of infection (MOI) (see lines 173 – 176 and Figure S2). Further, we did observe that Evo2 caused a greater trade-off in virulence phenotypes (hemolysis and cell agglutination) (see lines 416 - 419 lines 433 – 435, and Figure 5)

      In our revisions, we also tested Evo2-treated MRSA against a wide range of antibiotics. We did not observe significant changes in MICs against those agents.   

      (2) Are there mutations in the SCCmec cassette or the MecA gene after selection against ΦStaph1N?

      We did not observe any mutations in known resistance genes SCCmec or blaZ. Furthermore, we did not see any differential expression of those genes in our transcriptomic data (see lines 344 and 346).  

      (3) The authors report that phage ΦNM1γ6 does not induce antibiotic sensitivity changes despite being effective against bacterial strain LAC. Were mutational sequencing studies performed with the resistant isolates that emerged against this strain? Can the authors hypothesize why these did not impact the virulence or resistance of LAC despite effective killing? How does this align with their models for ΦStaph1N?

      We thank the reviewer for that insightful question. In our revised manuscript, we found that ΦNM1γ6 elicits a point mutation in the fmhC gene, which is involved in cell wall maintenance (see lines 326 – 335). To our knowledge, this point mutation has not been linked to phage resistance or drug sensitivity MRSA. Notably this mutation was not observed with ΦStaph1N or Evo2. We therefore speculate that ΦNM1γ6 binds to a different receptor molecule on the MRSA cell wall.   

      (4) If I understand correctly, the authors attribute these effects of phage predation on antibiotic sensitivity and virulence to orthogonal selection pressures. A good test of this model would be to examine the mutations that emerge in antibiotic/phage co-treatment. This should be done.

      We thank the reviewer for this suggestion. As described in the summary section above, we performed checkerboard experiments on MRSA strains with phage and b-lactam gradients (see lines 440 – 494 and Figure 6). We found that under most conditions, MRSA cells were only able to recover under low phage and b-lactam concentrations. Notably, these recovered cells were still phage resistant and b-lactam sensitive. However, under one condition where MW2 was treated with FStaph1N and b-lactam, we found that some recovered cells still had high levels of b-lactam resistance and only limited phage resistance, showing a distinct mutational profile (Figure S6). Under these conditions, we think that the selective pressure exerted by FStaph1N is “overcome” by the selective pressure of the high oxacillin concentration, a point that we discuss in the main text.

      Reviewer #2 (Public review):

      Summary:

      The work presented in the manuscript by Tran et al deals with bacterial evolution in the presence of bacteriophage. Here, the authors have taken three methicillin-resistant S. aureus strains that are also resistant to beta-lactams. Eventually, upon being exposed to phage, these strains develop beta-lactam sensitivity. Besides this, the strains also show other changes in their phenotype such as reduced binding to fibrinogen and hemolysis.

      Strengths:

      The experiments carried out are convincing to suggest such in vitro development of sensitivity to the antibiotics. Authors were also able to "evolve" phage in a similar fashion thus showing enhanced virulence against the bacterium. In the end, authors carry out DNA sequencing of both evolved bacteria and phage and show mutations occurring in various genes. Overall, the experiments that have been carried out are convincing.

      We thank Reviewer 2 for their positive comments.

      Weaknesses:

      Although more experiments are not needed, additional experiments could add more information. For example, the phage gene showing the HTH motif could be reintroduced in the bacterial genome and such a strain can then be assayed with wildtype phage infection to see enhanced virulence as suggested. At least one such experiment proves the discoveries regarding the identification of mutations and their outcome.

      We thank the reviewer for this suggestion. We attempted to clone ORF141 into an expression plasmid and perform complementation experiments with Evo2 phage; however, all transformants that were isolated had premature stop-codons and frameshifts in the wild-type ORF141 insert that would disrupt protein function. We therefore think that the gene product of ORF141 might be toxic to the cells. We are currently working on placing the gene under more stringent transcriptional control but feel that these efforts fall outside of the scope of this paper.  

      Secondly, I also feel that authors looked for beta-lactam sensitivity and they found it. I am sure that if they look for rifampicin resistance in these strains, they will find that too. In this case, I cannot say that the evolution was directed to beta-lactam sensitivity; this is perhaps just one trait that was observed. This is the only weakness I find in the work. Nevertheless, I find the experiments convincing enough; more experiments only add value to the work.  

      We thank the reviewer for their comments. Because both phages and β-lactams interface with the bacterial cell wall, we posited that phage resistance would reduce resistance in cell wall targeting antibiotics. In our revisions, we have expanded our analysis to include a much wider range of antibiotic classes, including rifampicin, mupirocin, erythromycin, and other cell wall disruptors, such as daptomycin and teicoplanin. We did not observe any significant changes to the MICs of these other antibiotics (see Table S3 and lines 191-199). It therefore appears that the effects of these trade-offs are confined to beta-lactams.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #2 (Public review):

      Summary:

      This study uses in vivo multimodal high-resolution imaging to track how microglia and neutrophils respond to light-induced retinal injury from soon after injury to 2 months post-injury. The in vivo imaging finding was subsequently verified by ex vivo study. The results suggest that despite the highly active microglia at the injury site, neutrophils were not recruited in response to acute light-induced retinal injury.

      Strengths:

      An extremely thorough examination of the cellular-level immune activity at the injury site. In vivo imaging observations being verified using ex vivo techniques is a strong plus.

      Thank you!

      Weaknesses:

      This paper is extremely long, and in the perspective of this reviewer, needs to be better organized. Update: Modifications have been made throughout, which has made the manuscript easier to follow.

      Thank you!

      Study weakness: though the finding prompts more questions and future studies, the findings discussed in this paper is potentially important for us to understand how the immune cells respond differently to different severity level of injury. The study also demonstrated an imaging technology which may help us better understand cellular activity in living tissue during earlier time points.

      We agree that AOSLO has much to offer and this represents some of the earliest reports of its kind.  

      Comments on revisions:

      I appreciate the thorough clarification and re-organization by the authors, and the messages in the manuscript are now more apparent. I recommend also briefly discussing limitations/future improvements in the discussion or conclusion.

      We have added a section to the discussion entitled “Limitations and future improvements”, please see lines 665 – 677.

      Reviewer #3 (Public review):

      Summary

      This work investigated the immune response in the murine retina after focal laser lesions. These lesions are made with close to 2 orders of magnitude lower laser power than the more prevalent choroidal neovascularization model of laser ablation. Histology and OCT together show that the laser insult is localized to the photoreceptors and spares the inner retina, the vasculature and the pigment epithelium. As early as 1-day after injury, a loss of cell bodies in the outer nuclear layer is observed. This is accompanied by strong microglial proliferation to the site of injury in the outer retina where microglia do not typically reside. The injury did not seem to result in the extravasation of neutrophils from the capillary network, constituting one of the main findings of the paper. The demonstrated paradigm of studying the immune response and potentially retinal remodeling in the future in vivo is valuable and would appeal to a broad audience in visual neuroscience.

      Strengths

      Adaptive optics imaging of murine retina is cutting edge and enables non-destructive visualization of fluorescently labeled cells in the milieu of retinal injury. As may be obvious, this in vivo approach is a benefit for studying fast and dynamic immune processes on a local time scale - minutes and hours, and also for the longer days-to-months follow-up of retinal remodeling as demonstrated in the article. In certain cases, the in vivo findings are corroborated with histology.

      Thank you!

      The analysis is sound and accompanied by stunning video and static imagery. A few different sets of mouse models are used, a) two different mouse lines, each with a fluorescent tag for neutrophils and microglia, b) two different models of inflammation - endotoxin-induced uveitis (EAU) and laser ablation are used to study differences in the immune interaction.

      Thank you!

      One of the major advances in this article is the development of the laser ablation model for 'mild' retinal damage as an alternative to the more severe neovascularization models. This model would potentially allow for controlling the size, depth and severity of the laser injury opening interesting avenues for future study.

      Thank you!

      The time-course, 2D and 3D spatial activation pattern of microglial activation are striking and provide an unprecedented view of the retinal response to mild injury.

      We agree that this more complete spatial and temporal evaluation made possible by in vivo imaging is novel.

      Weaknesses

      Generalization of the (lack of) neutrophil response to photoreceptor loss - there is ample evidence in literature that neutrophils are heavily recruited in response to severe retinal damage that includes photoreceptor loss. Why the same was not observed here in this article remains an open question. One could hypothesize that neutrophil recruitment might indeed occur under conditions that are more in line with the more extreme damage models, for example, with a stronger and global ablation (substantially more photoreceptor loss over a larger area). This parameter space is unwieldy and sufficiently large to address the question conclusively in the current article, i.e. how much photoreceptor loss leads to neutrophil recruitment? By the same token, the strong and general conclusion in the title - Photoreceptor loss does not recruit neutrophils - cannot be made until an exhaustive exploration be made of the same parameter space. A scaling back may help here, to reflect the specific, mild form of laser damage explored here, for instance - Mild photoreceptor loss does not recruit neutrophils despite...

      We are striving for clarity and accuracy in our title without adding too many qualifiers.  At present, we feel that the title as submitted is consistent and aligned with the central finding of our manuscript.  The nuance that the reviewer points to is elaborated in the body of the manuscript and we hope the general readership appreciates the same level of detail as appreciated by reviewer #3.

      EIU model - The EIU model was used as a positive control for neutrophil extravasation. Prior work with flow cytometry has shown a substantial increase in neutrophil counts in the EIU model. Yet, in all, the entire article shows exactly 2 examples in vivo and 3 ex vivo (Figure 7) of extravasated neutrophils from the EIU model (n = 2 mice). The general conclusion made about neutrophil recruitment (or lack thereof) is built partly upon this positive control experiment. But these limited examples, especially in the case where literature reports a preponderance of extravasated neutrophils, raise a question on the paradigm(s) used to evaluate this effect in the mild laser damage model.

      This is a helpful suggestion. We agree that readers should see more evidence of the positive control. Therefore we have now included two more supplementary files that show that there is a strong neutrophil response to EIU.  In Figure 7 – supplementary figure 1, we show many Ly-6G-positive neutrophils in the retina seen with histology at the 24 hour time point. In Figure 7 – video 3, we show massive Catchup-positive neutrophil presence in vivo at 24hrs as well.  This aligns with our positive control and also the literature.

      Overall, the strengths outweigh the weaknesses, provided the conclusions/interpretations are reconsidered.

      With the added clarification about the magnitude of the neutrophil response in EIU, we feel that the conclusions presented in the manuscript as-is are valid and appropriate.

      Recommendations for the authors:

      Reviewer #3 (Recommendations for the authors):

      The authors are applauded for embracing the reviewers' feedback and making substantial revisions. Some minor comments below:

      The weakness noted in the public review encourages the authors to reconsider the interpretations drawn based on the results. One would have expected to see far more examples of extravasated neutrophils from the EIU model. That this was not seen weakens the neutrophil recruitment claim substantially. Even without this claim, the methods, laser damage model, time-course and spatial activation pattern of microglial activation are all striking and unprecedented. So, as stated in the public review, the strengths do indeed outweigh the weaknesses once the neutrophil claim is softened.

      We address this in the response above. A strong neutrophil response was observed to EIU. This was confirmed with both histology and in vivo imaging.

      This was alluded to by Reviewer 1 in the prior review - at times, there is an overemphasis on imaging technology that distracts from the scientific questions. The imaging is undoubtedly cutting-edge but also documented in prior work by the authors. Any efforts to reduce or balance the emphasis would help with the general flow.

      Given that these discoveries are made possible partly through new technology, we prefer to keep the details of the innovation in the current manuscript. Given the exceptionally large readership of eLife, we feel some description of the AOSLO imaging is warranted in the manuscript.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      In this study, the authors explored how galanin affects whole-brain activity in larval zebrafish using wide-field Ca2+ imaging, genetic modifications, and drugs that increase brain activity. The authors conclude that galanin has a sedative effect on the brain under normal conditions and during seizures, mainly through the galanin receptor 1a (galr1a). However, acute "stressors(?)" like pentylenetetrazole (PTZ) reduce galanin's effects, leading to increased brain activity and more seizures. The authors claim that galanin can reduce seizure severity while increasing seizure occurrence, speculated to occur through different receptor subtypes. This study confirms galanin's complex role in brain activity, supporting its potential impact on epilepsy.

      Strengths:

      The overall strength of the study lies primarily in its methodological approach using whole-brain Calcium imaging facilitated by the transparency of zebrafish larvae. Additionally, the use of transgenic zebrafish models is an advantage, as it enables genetic manipulations to investigate specific aspects of galanin signaling. This combination of advanced imaging and genetic tools allows for addressing galanin's role in regulating brain activity.

      Weaknesses:

      The weaknesses of the study also stem from the methodological approach, particularly the use of whole-brain Calcium imaging as a measure of brain activity. While epilepsy and seizures involve network interactions, they typically do not originate across the entire brain simultaneously. Seizures often begin in specific regions or even within specific populations of neurons within those regions. Therefore, a whole-brain approach, especially with Calcium imaging with inherited limitations, may not fully capture the localized nature of seizure initiation and propagation, potentially limiting the understanding of Galanin's role in epilepsy.

      Furthermore, Galanin's effects may vary across different brain areas, likely influenced by the predominant receptor types expressed in those regions. Additionally, the use of PTZ as a "stressor" is questionable since PTZ induces seizures rather than conventional stress. Referring to seizures induced by PTZ as "stress" might be a misinterpretation intended to fit the proposed model of stress regulation by receptors other than Galanin receptor 1 (GalR1).

      The description of the EAAT2 mutants is missing crucial details. EAAT2 plays a significant role in the uptake of glutamate from the synaptic cleft, thereby regulating excitatory neurotransmission and preventing excitotoxicity. Authors suggest that in EAAT2 knockout (KO) mice galanin expression is upregulated 15-fold compared to wild-type (WT) mice, which could be interpreted as galanin playing a role in the hypoactivity observed in these animals.

      Indeed, our observation of the unexpected hypoactivity in EAAT2a mutants, described in our description of this mutant (Hotz et al., 2022), prompted us to initiate this study formulating the hypothesis that the observed upregulation of galanin is a neuroprotective response to epilepsy.

      However, the study does not explore the misregulation of other genes that could be contributing to the observed phenotype. For instance, if AMPA receptors are significantly downregulated, or if there are alterations in other genes critical for brain activity, these changes could be more important than the upregulation of galanin. The lack of wider gene expression analysis leaves open the possibility that the observed hypoactivity could be due to factors other than, or in addition to, galanin upregulation.

      We have performed a transcriptome analysis that we are still evaluation. We can already state that AMPA receptor genes are not significantly altered in the mutant.

      Moreover, the observation that in double KO mice for both EAAT2 and galanin, there was little difference in seizure susceptibility compared to EAAT2 KO mice alone further supports the idea that galanin upregulation might not be the reason for the observed phenotype. This indicates that other regulatory mechanisms or gene expressions might be playing a more pivotal role in the manifestation of hypoactivity in EAAT2 mutants.

      We agree that upregulation of galanin transcripts is at best one of a suite of regulatory mechanisms that lead to hypoactivity in EAAT2 zebrafish mutants.

      These methodological shortcomings and conceptual inconsistencies undermine the perceived strengths of the study, and hinders understanding of Galanin's role in epilepsy and stress regulation.

      Reviewer #2 (Public Review):

      Summary:

      This study is an investigation of galanin and galanin receptor signaling on whole-brain activity in the context of recurrent seizure activity or under homeostatic basal conditions. The authors primarily use calcium imaging to observe whole-brain neuronal activity accompanied by galanin qPCR to determine how manipulations of galanin or the galr1a receptor affect the activity of the whole-brain under non-ictal or seizure event conditions. The authors' Eaat2a-/- model (introduced in their Glia 2022 paper, PMID 34716961) that shows recurrent seizure activity alongside suppression of neuronal activity and locomotion in the time periods lacking seizures is used in this paper in comparison to the well-known pentylenetetrazole (PTZ) pharmacological model of epilepsy in zebrafish. Given the literature cited in their Introduction, the authors reasonably hypothesize that galanin will exert a net inhibitory effect on brain activity in models of epilepsy and at homeostatic baseline, but were surprised to find that this hypothesis was only moderately supported in their Eaat2a-/- model. In contrast, under PTZ challenge, fish with galanin overexpression showed increased seizure number and reduced duration while fish with galanin KO showed reduced seizure number and increased duration. These results would have been greatly enriched by the inclusion of behavioral analyses of seizure activity and locomotion (similar to the authors' 2022 Glia paper and/or PMIDs 15730879, 24002024). In addition, the authors have not accounted for sex as a biological variable, though they did note that sex sorting zebrafish larvae precludes sex selection at the younger ages used. It would be helpful to include smaller experiments taken from pilot experiments in older, sex-balanced groups of the relevant zebrafish to increase confidence in the findings' robustness across sexes. A possible major caveat is that all of the various genetic manipulations are non-conditional as performed, meaning that developmental impacts of galanin overexpression or galanin or galr1a knockout on the observed results have not been controlled for and may have had a confounding influence on the authors' findings. Overall, this study is important and solid (yet limited), and carries clear value for understanding the multifaceted functions that neuronal galanin can have under homeostatic and disease conditions.

      Strengths:

      - The authors convincingly show that galanin is upregulated across multiple contexts that feature seizure activity or hyperexcitability in zebrafish, and appears to reduce neuronal activity overall, with key identified exceptions (PTZ model).

      - The authors use both genetic and pharmacological models to answer their question, and through this diverse approach, find serendipitous results that suggest novel underexplored functions of galanin and its receptors in basal and disease conditions. Their question is well-informed by the cited literature, though the authors should cite and consider their findings in the context of Mazarati et al., 1998 (PMID:982276). The authors' Discussion places their findings in context, allowing for multiple interpretations and suggesting some convincing explanations.

      - Sample sizes are robust and the methods used are well-characterized, with a few exceptions (as the paper is currently written).

      - Use of a glutamatergic signaling-based genetic model of epilepsy (Eaat2a-/-) is likely the most appropriate selection to test how galanin signaling can alter seizure activity, as galanin is known to reduce glutamatergic release as an inhibitory mechanism in rodent hippocampal neurons via GalR1a (alongside GIRK activation effects). Given that PTZ instead acts through GABAergic signaling pathways, it is reasonable and useful to note that their glutamate-based genetic model showed different effects than did their GABAergic-based model of seizure activity.

      Weaknesses:

      - The authors do not include behavioral assessments of seizure or locomotor activity that would be expected in this paper given their characterizations of their Eaat2a-/- model in the Glia 2022 paper that showed these behavioral data for this zebrafish model. These data would inform the reader of the behavioral phenotypes to expect under the various conditions and would likely further support the authors' findings if obtained and reported.<br />

      We agree that a thorough behavioral assessment would have strengthened the study, but we deemed it outside of the scope of this study.

      - No assessment of sex as a biological variable is included, though it is understood that these specific studied ages of the larvae may preclude sex sorting for experimental balancing as stated by the authors.

      The study was done on larval zebrafish (5 days post fertilization). The first signs of sexual differentiation become apparent at about 17 days post fertilization (reviewed in Ye and Chen, 2020). Hence sex is no biological variable at the stage studied. 

      - The reported results may have been influenced by the loss or overexpression of galanin or loss of galr1a during developmental stages. The authors did attempt to use the hsp70l system to overexpress galanin, but noted that the heat shock induction step led to reduced brain activity on its own (Supplementary Figure 1). Their hsp70l:gal model shows galanin overexpression anyways (8x fold) regardless of heat induction, so this model is still useful as a way to overexpress galanin, but it should be noted that this galanin overexpression is not restricted to post-developmental timepoints and is present during development.

      The developmental perspective is an important point to consider. Due to the rapid development of the zebrafish it is not trivial to untangle this. In the zebrafish we first observe epileptic seizures as early as 3 days post fertilization (dpf), where the brain is clearly not well developed yet (e.g. behaviroal response to light are still minimal). Even the 5 dpf stage, where most of our experiments have been conducted, cannot by far not be considered post-development.  

      Reviewer #3 (Public Review):

      Summary:

      The neuropeptide galanin is primarily expressed in the hypothalamus and has been shown to play critical roles in homeostatic functions such as arousal, sleep, stress, and brain disorders such as epilepsy. Previous work in rodents using galanin analogs and receptor-specific knockout has provided convincing evidence for the anti-convulsant effects of galanin.

      In the present study, the authors sought to determine the relationship between galanin expression and whole-brain activity. The authors took advantage of the transparent nature of larval zebrafish to perform whole-brain neural activity measurements via widefield calcium imaging. Two models of seizures were used (eaat2a-/- and pentylenetetrazol; PTZ). In the eaat2a-/- model, spontaneous seizures occur and the authors found that galanin transcript levels were significantly increased and associated with a reduced frequency of calcium events. Similarly, two hours after PTZ galanin transcript levels roughly doubled and the frequency and amplitude of calcium events were reduced. The authors also used a heat shock protein line (hsp70I:gal) where galanin transcript levels are induced by activation of heat shock protein, but this line also shows higher basal transcript levels of galanin. Again, the higher level of galanin in hsp70I:gal larval zebrafish resulted in a reduction of calcium events and a reduction in the amplitude of events. In contrast, galanin knockout (gal-/-) increased calcium activity, indicated by an increased number of calcium events, but a reduction in amplitude and duration. Knockout of the galanin receptor subtype galr1a via crispants also increased the frequency of calcium events.

      In subsequent experiments in eaat2a-/- mutants were crossed with hsp70I:gal or gal-/- to increase or decrease galanin expression, respectively. These experiments showed modest effects, with eaat2a-/- x gal-/- knockouts showing an increased normalized area under the curve and seizure amplitude.

      Lastly, the authors attempted to study the relationship between galanin and brain activity during a PTZ challenge. The hsp70I:gal larva showed an increased number of seizures and reduced seizure duration during PTZ. In contrast, gal-/- mutants showed an increased normalized area under the curve and a stark reduction in the number of detected seizures, a reduction in seizure amplitude, but an increase in seizure duration. The authors then ruled out the role of Galr1a in modulating this effect during PTZ, since the number of seizures was unaffected, whereas the amplitude and duration of seizures were increased.

      Strengths:

      (1) The gain- and loss-of function galanin manipulations provided convincing evidence that galanin influences brain activity (via calcium imaging) during interictal and/or seizure-free periods. In particular, the relationship between galanin transcript levels and brain activity in Figures 1 & 2 was convincing.

      (2) The authors use two models of epilepsy (eaat2a-/- and PTZ).

      (3) Focus on the galanin receptor subtype galr1a provided good evidence for the important role of this receptor in controlling brain activity during interictal and/or seizure-free periods.

      Weaknesses:

      (1) Although the relationship between galanin and brain activity during interictal or seizure-free periods was clear, the manuscript currently lacks mechanistic insight in the role of galanin during seizure-like activity induced by PTZ.

      We completely agree and concede that this study constitutes only a first attempt to understand the (at least for us) perplexing complexity of galanin function on the brain.

      (2) Calcium imaging is the primary data for the paper, but there are no representative time-series images or movies of GCaMP signal in the various mutants used.

      We have now added various movies in supplementary data.

      (3) For Figure 3, the authors suggest that hsp70I:gal x eaat2a-/-mutants would further increase galanin transcript levels, which were hypothesized to further reduce brain activity. However, the authors failed to measure galanin transcript levels in this cross to show that galanin is actually increased more than the eaat2a-/- mutant or the hsp70I:gal mutant alone.

      After a couple of unsuccessful mating attempts with our older mutants, we finally decided not to wait for a new generation to grow up, deeming the experiment not crucial (but still nice to have).

      (4) Similarly, transcript levels of galanin are not provided in Figure 2 for Gal-/- mutants and galr1a KOs. Transcript levels would help validate the knockout and any potential compensatory effects of subtype-specific knockout.

      To validate the gal-/- mutant line, we decided to show loss of protein expression (Suppl. Figure 2), which we deem to more relevant to argue for loss of function. Galanin transcript levels in galr1a KOs were also added into the same Figure. However, validation of the galr1a KO could not be performed due to transcript levels being close to the detection limit and lack of available antibodies.

      (5) The authors very heavily rely on calcium imaging of different mutant lines. Additional methods could strengthen the data, translational relevance, and interpretation (e.g., acute pharmacology using galanin agonists or antagonists, brain or cell recordings, biochemistry, etc).

      Again, we agree and concede that a number of additional approaches are needed to get more insight into the complex role of galanin in regulation overall brain activity. These include, among others, also behavioral, multiple single cell recordings and pharmacological interventions.

      Recommendations for the authors:

      Reviewer #2 (Recommendations For The Authors):

      Minor issues:

      (1) "Sedative" effect of galanin is somewhat vague and seems overapplied without the inclusion of behavioral data showing sedation effects. I would replace "sedative" with something clearer, like the phrase "net inhibitory effect" or similar.

      We have modified the wording as deemed appropriate.

      (2) Include new data that is sufficiently powered to detect or rule out the effects of sex as a biological variable within the various experiments.

      At this stage sex is not a biological variable. Sex determination starts a late larval stage around 14dpf. Our analysis is based on 5pdf larvae.

      (3) Attempt to perform some experiments with galanin/galr1a manipulations that have been induced after the majority of development without using heat shock induction if possible (unknown how feasible this is in current model systems).

      In the current model this is not feasible, but an excellent suggestion for future studies that would then also address more longterm effects in the model.

      (4) Figure 2 should include qPCR results for galanin or galr1a mRNA expression to match Figure 1C, F, and Figure 2C and to confirm reductions in the respective RNA transcript levels of gal or galr1a. It could be useful to perform qPCR for galanin in all galr1aKO mice to ascertain whether compensatory elevations in galanin occur in response to galr1aKO.

      (5) Axes should be made with bolder lines and bolder/larger fonts for readability and consistency throughout.

      Indeed, an excellent suggestion. We have adjusted the axes significantly improving the readability of the graphs.

      (6) The bottom o,f the image for Figure 2 appears to have been cut off by mistake (page 5).

      (7) The ending of the legend text for Figure 3 appears to have been cut off by mistake (page 6).

      Both regrettable mistakes have been corrected (already in the initial posted version)

      Reviewer #3 (Recommendations For The Authors):

      (1) The introduction or first paragraph of the results should be revised to more directly state the hypotheses. Several critical details were only clear after reading the discussion.

      We added some words to the introduction, hoping that the critical points are now more apparent to the reader.

      (2) Galanin is known to be rapidly depleted by seizures (Mazarati et al., 1998; Journal of Neuroscience, PMID #9822761) but this paper did not appear to be cited or considered. Could the rapid depletion of galanin during seizures help explain the confusing effects of galanin manipulations during PTZ?

      We have added a sentence and the reference to the discussion.

      (3) Figure 1 panels are incorrect. For example, Panel 'F' is used twice and the figure legend is also incorrect due to the labeling errors. In-text references to the figure should also be updated accordingly.

      (4) In Figure 2 N-P, the delta F/F threshold wording is partially cropped. The figure should be updated.

      Thank you for pointing out this mistake. Both figures have now been updated (already in the initial posted version)

      (5) The naming and labeling of groups in the manuscript and figures should be updated to more accurately reflect the fish used for each experiment. As it currently stands, I found the labeling confusing and sometimes misleading. For example, Figure 3 'controls' are actually eaat2a-/- mutants, whereas the other group is hsp70I:gal x eaat2a-/- crosses or gal-/- x eaat2a-/- crosses. In other Figures, 'controls' are eaat2a+/+larva, or wild-type siblings (sometimes unclear).

      We have made appropriate changes to the manuscript to make this point clearer to the reader, especially when the controls are eaat2a mutants.

      (6) Figure 4J and 4K only show 5 data points, when the authors clearly indicate that 6 fish had seizures. Continuation of this data in Figure 4L shows 6 data points.

      Indeed the 6 data points in Figure 4J and K are hard to see due to their nearly complete overlap. On larger magnification all six data points become distinguishable. We will try some different plotting approaches for the revision.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1:

      Summary:

      In this manuscript (eLife-RP-RA-2024-103904), the authors identified that NOLC1 was upregulated in gastric cancer samples, which promoted cancer progression and cisplatin resistance. They further found that NOLC1 could bind to p53 and decrease its nuclear transcriptional activity, then inhibit p53-mediated ferroptosis. There are several major concerns regarding the conclusions.

      Strengths:

      This study identified that NOLC1 could bind to p53 and decrease its nuclear transcriptional activity, then inhibit p53-mediated ferroptosis in gastric cancer.

      Weaknesses:

      The major conclusions were not sufficiently supported by the results. The experiments were not conducted in a comprehensive manner.

      Major concerns

      (1) The authors investigated NOLC1 expression in gastric cancer (GC) using clinical samples, which is valuable; however, the sample array includes only 3 patients. This sample size is insufficient to support conclusions for human samples. Please increase the sample size and apply a more robust statistical analysis. Additionally, specify the statistical methods used in the figure legend.

      Thanks very much for the kind comments and great suggestions. As suggested, we have increased the sample size of GC patients, and the new data (six pair samples) was shown in Fig. S1A, further reflecting that NOLC1 was upregulate in gastric cancer (GC). Moreover, the statistical methods have been added in each figure legend.

      (2) These data are not sufficient to support the key conclusion of this study "NOLC1 is significantly upregulated in GC tissues and Cis-resistant GC cells". There is no convincing data showing that NOLC1 upregulation is specific to cancer cells or any other cell types. Based on the following results that NOLC1 expressed in cancer cells can support cancer cell survival and drug resistance, the authors switched to investigating the role of NOLC1 in cancer cells without demonstrating cancer cells indeed highly upregulate NOLC1.

      Thanks for raising this good question. As shown in Fig. 1E-F, the TCGA database have shown that NOLC1 was upregulated in GC. Moreover, we further analyzed the NOLC1 expression level in other cancer type, according to the Human Protein Atlas (https://www.proteinatlas.org/). The results indicated that NOLC1 mRNA level was much higher in almost all cancers except acute myeloid leukemia (LAML). In addition, according to the gene expression profiling interactive analysis (GEPIA, http://gepia.cancer-pku.cn/index.html), NOLC1 mRNA level was above 100 nTPM in most gastric cancer cell lines, however in most non-cancerous cell lines was below 100 nTPM, indicating that NOLC1 was up-regulated in gastric cancer.

      Author response image 1.

      The mRNA level of NOLC1 in different GC cells and non-cancerous cells.

      (3) The authors primarily use MGC-803 cells for experiments; however, MGC-803 is known to be a HeLa-contaminated cell line. Could the authors explain this choice of using this cell line only? Did they validate key findings with additional cell lines? This is particularly important for assays such as cisplatin resistance validation, in vivo experiments, TEM imaging, and MitoPeDPP fluorescence imaging.

      Thanks for raising this good question. We are not only use MGC-803 cells, the key findings in vitro was also validated in MKN-45 cells (Fig. 2), and in vivo experiment also validated in Mouse Forestomach Carcinoma cells (MFC)-tumor bearing 615 mice model (Fig 7). Furthermore, we further added some experiments in MKN-45 cells. The TEM imaging showed that NOLC1 could significantly inhibit cisplatin (Cis) induced lipid membrane damage in MKN-45 cells (Fig. S6A). Moreover, MitoPeDPP fluorescence assay analyzed by FCAs also indicating that rapid ROS was enriched in mitochondria in MKN-45 cells (Fig. 4E, Fig. S6J).

      (4) In Figure 2, did the authors perform assays with NOLC1 overexpression? If so, please include these results to strengthen the conclusions.

      Thanks very much for the kind comments and great suggestions. As suggested, we added new data about NOLC1 overexpression assay Cell counting kit-8 assay shows that NOLC1-overexpression group is more resistance to Cis compared to vector group (Fig. S4E, S5A).

      (5) The authors show in Figures 2A-B that shNOLC1 without cisplatin treatment does not affect cell viability. However, Figures 2D-E suggest increased apoptosis in shNOLC1 cells without cisplatin treatment. Additionally, in vivo studies in Figure 3 show no significant difference between the shNC+PBS and shNOLC1+PBS groups, which appears contradictory to the apoptosis assays. Similarly, Ki67 staining shows decreased scores in the shNOLC1 group compared to shNC. Could the authors clarify this inconsistency?

      Thanks for raising this good question. In Fig 2D-E, the difference in proportion of death cells between shNOLC1 and shNC treated with PBS groups were only 3% (MGC-803) and 7% (MKN-45) which is much lower than that treated with cisplatin in vitro. Moreover, in vivo analysis indicated that the average tumor volume in NOLC1+PBS group was smaller than that in NC group, but there was no statistical significance (p value = 0.3962). Moreover, tumor proliferation is a complex process regulated by many factors [1,2], thus the level of Ki67 is by no means the same as the rate of tumor proliferation, might be positively correlated.

      (6) In Figure 4, NOLC1 knockdown appears to enhance cisplatin-induced ferroptosis rather than apoptosis. Given p53's role in apoptosis, did the authors compare the effects of NOLC1 on cisplatin-induced apoptosis vs. ferroptosis? If so, please clarify whether NOLC1 predominantly regulates apoptosis or ferroptosis.

      Thanks for raising this good question. We do have compared the effects of NOLC1 on cisplatin-induced apoptosis vs. ferroptosis. As shown in Fig. 5A, NOLC1 knockdown obviously increased the BCL-2 protein level which is an anti-apoptotic protein and mediated by p53 via protein interaction in cytoplasm[3,4], this phenomenon may cause by the increasing level of p53 in cytoplasm (Fig. 6I). Also, the TEM imaging showed the classic ferroptotic morphological changes rather than apoptosis (Fig. 5A, S6A). Taken together, NOLC1 mainly regulates p53 mediated ferroptosis rather than apoptosis.

      (7) Did the authors perform co-IP assays with p53 or HA antibodies to immunocapture NOLC1? If not, please add this experiment to support protein interactions. The mechanistic correlation between p53 and NOLC1 can be supported by adding experiments using multiple GC cell lines with various p53 alterations (such as loss-of- function or gain-of-function mutations/deletions). This is critical because the authors specifically claimed that NOLC1 can inhibit p53-mediated ferroptosis, but not other tumor suppressors.

      Thanks very much for the kind comments and great suggestions. As suggested, we had performed Co-IP assay with anti-HA antibodies to immunocapture NOLC1-FLAG. As shown in Fig. 5K, p53 DNA binding domain (DBD)-HA could immunocapture with NOLC1, further indicated that NOLC1 could binding to p53 DBD. Moreover, we concur with the reviewer that adding experiments using multiple p53 alterations, however considering that different p53 mutants have completely different functional changes. Therefore, we using siRNA to knockdown p53 level in MGC-803 cells, the results shown that NOLC1 mediated resistance was disappear and the GPX4 level was increased (Fig. S10). These data have shown that NOLC1 promotes GC resistance via mediated p53 functions.

      (8) In Figure S5B, the LDH release can be blocked by Fer-1?

      Thanks for raising this good question. As suggested, Fer-1 (20 μmol/mL) significantly blocked the LDH release in NOLC1 knockdown group (Fig S6E). This data further confirmed that NOLC1 suppressed Cis-induced ferroptosis.

      (9) How about the ubiquitination assay in MGC-803 cells?

      Thanks for raising this good question. As suggested, we also analyzed the ubiquitination assay in MGC-803 cells. As the result showed that NOLC1 also could increasing level of ubiquitination of p53 (Fig. 6H).

      (10) In Figure 6H, the DBD domain of NOLC1 is required for inhibiting P53 ubiquitination.

      Thanks for your opinion. However, in our paper, we only mentioned that p53 DBD domain, rather than NOLC1 DBD domain. Also, we did not find any DNA binding function of NOLC1 in the Pubmed database. Therefore, we would like to ask whether the revised opinion is correct.

      (11) In Figure 8B, the CD3 antibody is not specific, please change it to a new one.

      Thanks very much for the kind comments and great suggestions. As suggested, we have used new CD3 antibody and the new data was added in Fig. 8B.

      (12) The authors report that NOLC1 influences peripheral blood lymphocytes with cisplatin treatment, with or without PD-1. Could the authors explain why NOLC1 would affect peripheral blood lymphocytes? Additionally, did they assess immune cell infiltration in the tumor microenvironment (TME) by flow cytometry?

      Thanks for raising good question. The tumor size of the knockdown group treated with Cis + PD-1 was too small (less than 100 mg) to extract enough infiltrated immune cells (less than 10000 CD45<sup>+</sup> cells), thus we chose to detect immune cells in the blood of the mice. Considering that the infiltrating immune cells including CTLs were originate from peripheral blood by circulation. Under the normal conditions, serval tumor biology behavior impact the TME to limit immune responses and present barriers to cancer therapy. For example, tumor could express or secret lots of negative regulator like PD-L1. Causing immune cells cannot recognize tumor cells and infiltrate into tumor tissue. Ferroptosis, as a new from of ICD, could damage tumor cell plasm and release amount of tumor associated antigen and tumor-specific antigens causing immune cells priming and activation. Eventually, the activated immune cells in peripheral blood travel towards the tumor site, infiltrating the tumor tissue under favorable co-stimulatory conditions and guided by chemokine gradients. Once within the tumor microenvironment, these activated T cells can control tumor growth through direct tumor cell destruction and cytokine-mediated processes [5–8]

      To assess immune cell infiltration in the TME, we analyzed the tumor infiltrated CD3<sup>+</sup> and CD8<sup>+</sup> immune cells in tumor tissue by immunofluorescence (Fig. 8B). Thus, the peripheral blood lymphocytes could reflect the infiltration of immune cells in the tumor.

      Minor concerns:

      (1) Please clarify the statistical methods in each figure legend.

      Thanks for your opinion. We have added statistical methods in each figure legend.

      (2) In Figure 2D, please provide statistical data of cleaved-caspase3 expression.

      Thanks for your opinion. As is shown in Fig. S5B-C, the relative cleaved-caspase3 were provided.

      (3) Please ensure that the canonical expressions used in the research paper are adhered to.

      Thanks for your opinion. We have carefully modified our expressions in our paper.

      (4) Please pay more attention to the grammar and formatting of texts.

      Thanks for your opinion. We revised our manuscript through the American Journal Experts (AJE) service.

      Reviewer #2:

      Summary:

      Shengsheng Zhao et al. investigated the role of nucleolar and coiled-body phosphoprotein 1 (NOLC1) in relegating gastric cancer (GC) development and cisplatin-induced drug resistance in GC. They found a significant correlation between high NOLC1 expression and the poor prognosis of GC. Meanwhile, upregulation of NOLC1 was associated with cis-resistant GC. Experimentally, the authors demonstrate that knocking down NOLC1 increased GC sensitivity to Cis possibly by regulating ferroptosis. Mechanistically, they found NOLC1 suppressed ferroptosis by blocking the translocation of p53 from the cytoplasm to the nucleus and promoting its degradation. In addition, The authors also evaluated the effect of combinational treatment of anti- PD-1 and cisplatin in NOLC1-knockdown tumor cells, revealing a potential role of NOLC1 in the targeted therapy for GC.

      Strengths:

      Chemoresistance is considered a major reason causing failure of tumor treatment and death of cancer patients. This paper explored the role of NOLC1 in the regulation of Cis-mediated resistance, which involves a regulated cell death named ferroptosis. These findings provide more evidence highlighting the study of regulated cell death to overcome drug resistance in cancer treatment, which could give us more potential strategies or targets for combating cancer.

      Weaknesses:

      More evidence supporting the regulation of ferroptosis induced by Cisplatin by NOLC1 should be added. Particularly, the role of ferroptosis in the cisplatin-resistance should be verified and whether NOLC1 regulates ferroptosis induced by additional FINs should be explored. Besides, the experiments to verify the regulation of ferroptosis sensitivity by NOLC1 are sort of superficial. The role of MDM2/p53 in ferroptosis or cisplatin resistance mediated by NOLC1 should be further studied by genetic manipulation of p53, which is the key evidence to confirm its contribution to NOLC1 regulation of GC and relative cell death.

      Major points:

      (1) More evidence supporting the regulation of ferroptosis induced by Cisplatin by NOLC1 should be added. Particularly, the role of ferroptosis in the cisplatin-resistance should be verified and whether NOLC1 regulates ferroptosis induced by additional FINs should be explored.

      Thanks very much for the kind comments and great suggestions. As suggested, we have further analyzed the ferroptosis inhibit ability of NOLC1 in MGC-45 cells treated with Erastin, a common used ferroptosis activator. As shown in Fig. S6B, the ferroptosis activated by Erastin was also blocked by NOLC1.

      (2) In Figure 1J, the CR cell line should obviously have less apoptosis-maker c-PARP expression, which means these cells are resistant to apoptosis induced by CR. Thus, it would be more rational to study the role of apoptosis regulation by NOLC1. Why did the later data shift to the study of ferroptosis?

      Thanks for raising this good question. In the CR cells, the expression levels of many genes were changed, so it is uncertain whether the decreased expression level of cleaved-PARP in the resistant cells is caused by NOLC1 up-regulated. To explore the specific mechanism of NOLC1 mediated resistant, we performed the TEM imaging (Fig. 4A, S6A) and the results showed that cells exhibited classic ferroptosis morphological changes. Moreover, the BCL-2 (an anti-apoptotic protein, and regulated by p53 via protein interaction in cytoplasm) was increased after NOLC1 knockdown (Fig S5A). This phenomenon may cause by the increasing p53 levels in the cytoplasm[3,4] (Fig 5I). Taken together we shift to study of cisplatin induced ferroptosis.

      (3) Besides, how about the regulation of apoptosis during cis-resistance by NOLC1 in GC?

      Thanks for raising this good question. As mentioned above the Cis induced apoptosis was not as significant as ferroptosis, caused by BCL-2 (a key anti-apoptosis protein) increasing which is mediated by p53 via protein interaction in cytoplasm. NOLC1 increased plasm p53 level subsequently increased BCL-2 level.

      (4) The experiments to verify the regulation of ferroptosis sensitivity by NOLC1 are sort of superficial. The role of MDM2/p53 in ferroptosis or cisplatin resistance mediated by NOLC1 should be further studied by genetic manipulation of p53, which is the key evidence to confirm its contribution to NOLC1 regulation of GC and relative cell death.

      Thanks for raising this good question. As is shown in Fig S10, after knockdown p53 protein level by using siRNA, NOLC1 could not promote Cis-resistance and the GPX4 level was increased reflecting that NOLC1 promotes Cis resistance via mediate p53 function.

      (5) In Figure 2, the data indicated that the knockdown of NOLC1 increased rH2Ax in the presence of Cisplatin, which indicated that NOLC1 might regulate DNA damage-related cellular function. These functions should be more relevant to cisplatin resistance, considering the fundamental effect of this chemo drug.

      Thanks very much for the kind comments and great suggestions. Indeed, we found that DNA damage was more obvious in knockdown groups, but the ferroptotic changes like ROS and mitochondrial membrane damage were also significantly different in knockdown groups. Considering that as a chemo drug, cisplatin not only induces damage DNA but also acts as a stress which could activates various signal pathways including apoptosis, ferroptosis, pyroptosis, necroptosis, etc., under different drug concentrate or time [9–11]. Therefore, it is important to find out the NOLC1 predominantly blocked pathway in GC.

      (6) In Figure.4, ferroptosis inhibitors like Ferr-1 or DFO should be used to verify the regulation of ferroptosis by Cisplatin and NOLC1.

      Thanks very much for the kind comments and great suggestions. As suggested, we performed additional LDH release assay. The results showed that Fer-1 also could block cisplatin induced LDH release in NOLC1 knockdown groups (Fig. S6E).

      (7) In Figure 4H, Cisplatin decreased FSP1 and GPX4, which could be enhanced in the NOLC1-konckdown cell line. Meanwhile, the knockdown of NOLC1 increased the ACSL4 level. These findings could be the key reason for the regulation of ferroptosis by NOLC1 rather than p53 since they all are direct regulators of ferroptosis.

      Thanks very much for the kind comments and great suggestions. We rewrote the text as you suggested. Recently, it also has been reported that ACSL4-regulated ferroptosis is related to p53, but the exact mechanism is still unclear [12]. Moreover, further studies of specific relation between NOLC1 and FSP1/ACSL4 will be conducted in the further

      (8) Whether p53 mediates the regulation of ferroptosis and cisplatin resistance by NOLC1 should be thoroughly studied using p53-KO cell lines.

      Thanks very much for the kind comments and great suggestions. As previously mentioned, by using si-RNA to knockdown p53, the NOLC1 mediate Cis-resistance were blocked (Fig. S10). Meanwhile, the GPX4 level was also increased in p53/NOLC1 double-knockdown groups compared to the NOLC1 knockdown group. These data indicating that NOLC1 suppresses ferroptosis via mediating p53 functions.

      Reviewer #3:

      The authors have put forth a compelling argument that NOLC1 is indispensable for gastric cancer resistance in both in vivo and in vitro models. They have further elucidated that NOLC1 silencing augments cisplatin-induced ferroptosis in gastric cancer cells. The mechanistic underpinning of their findings suggests that NOLC1 modulates the p53 nuclear/plasma ratio by engaging with the p53 DNA Binding Domain, which in turn impedes p53-mediated transcriptional regulation of ferroptosis. Additionally, the authors have shown that NOLC1 knockdown triggers the release of ferroptosis-induced damage-associated molecular patterns (DAMPs), which activate the tumor microenvironment (TME) and enhance the efficacy of the anti-PD-1 and cisplatin combination therapy.

      Strengths:

      The manuscript presents a robust dataset that substantiates the authors' conclusion. They have identified NOLC1 as a potential oncogene that confers resistance to immuno-chemotherapy in gastric cancer through the mediation of ferroptosis and subsequent TME reprogramming. This discovery positions NOLC1 as a promising therapeutic target for gastric cancer treatment. The authors have delineated a novel mechanistic pathway whereby NOLC1 suppresses p53 transcriptional functions by reducing its nuclear/plasma ratio, underscoring the significance of p53 nuclear levels in tumor suppression over total protein levels.

      Weaknesses:

      While the overall findings are commendable, there are specific areas that could benefit from further refinement. The authors have posited that NOLC1 suppresses p53- mediated ferroptosis; however, the mRNA levels of ferroptosis genes regulated by p53 have not been quantified, which is a critical gap in the current study. In Figure 4A, transmission electron microscopy (TEM) results are reported solely for the MGC-803 cell line. It would be beneficial to include TEM data for the MKN-45 cell line to strengthen the findings. The authors have proposed a link between NOLC1-mediated reduction in the p53 nuclear/plasma ratio and gastric cancer resistance, yet the correlation between this ratio and patient prognosis remains unexplored, which is a significant limitation in the context of clinical relevance.

      Thanks very much for the kind comments and great suggestions. As suggested, recently studies have reported that CDKN1A (also called p21, a p53 transcriptional mediated protein) could promotes ferroptosis[13], the mRNA levels of ferroptosis genes regulated by p53 have were quantified in Fig. S8G-H. Moreover, we further proceed TEM imaging in MKN-45 cells, the result was consistent to MGC-803 cells, reflecting that NOLC1 has a broad spectrum of promoting drug resistance in gastric cancer. Also, recently studies have reported that p53 transcriptional active and p53 transcriptional inactive types include patients with intermediate prognosis and recurrence rates, with the p53-acvtie group showing better prognosis[14]. Considering p53 transcriptional activity depends on p53 nuclear accumulation, we assume that the low level of p53 nuclear/plasma may cause poor prognosis in gastric cancer. Meanwhile we will further collect enough samples and their prognostic information to analysis NOLC1-mediated reduction in the p53 nuclear/plasma ratio and gastric cancer resistance.

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    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer 1 (Public review):

      Summary:

      Gene transfer agent (GTA) from Bartonella is a fascinating chimeric GTA that evolved from the domestication of two phages. Not much is known about how the expression of the BaGTA is regulated. In this manuscript, Korotaev et al noted the structural similarity between BrrG (a protein encoded by the ror locus of BaGTA) to a well-known transcriptional anti-termination factor, 21Q, from phage P21. This sparked the investigation into the possibility that BaGTA cluster is also regulated by anti-termination. Using a suite of cell biology, genetics, and genome-wide techniques (ChIP-seq), Korotaev et al convincingly showed that this is most likely the case. The findings offer the first insight into the regulation of GTA cluster (and GTA-mediated gene transfer) particularly in this pathogen Bartonella. Note that anti-termination is a well-known/studied mechanism of transcriptional control. Anti-termination is a very common mechanism for gene expression control of prophages, phages, bacterial gene clusters, and other GTAs, so in this sense, the impact of the findings in this study here is limited to Bartonella.

      Strengths:

      Convincing results that overall support the main claim of the manuscript.

      Weaknesses:

      A few important controls are missing.

      We sincerely appreciate reviewer #1's positive assessment of our manuscript. In response to the concern regarding control samples/experiments, we have addressed this issue in our revision, by providing data of the replicates of our experiments. We acknowledge that antitermination is a well-established mechanism of expression control in bacteria, including bacterial gene clusters, phages, prophages, and at least one other GTA. As reviewer #2 also noted, our study presents a unique example of phage co-domestication, where antitermination integrates both phage remnants at the regulatory level. We have emphasized this original aspect more clearly in the revised manuscript.

      Reviewer 1 (Recommendations for the authors):

      (1) Provide Rsmd and DALI scores to show how similar the AlphaFold-predicted structures of BrrG are to other anti-termination factors. This should be done for Fig1B and also for Suppl. Fig 1 to support the claim that BrrG, GafA, GafZ, Q21 share structural features.

      In the revised manuscript we provide Rsmd and DALI scores in the supplementary Fig. 1A (Suppl. Fig. 1A). In Suppl. Fig. 1B we further include a heatmap of similiarity values.

      (2) Throughout the manuscript, flow cytometry data of gfp expression was used and shown as single replicate. Korotaev et al wrote in the legends that error bars are shown (that is not true for e.g. Figs. 3, 4, and 5). It is difficult for reviewers/readers to gauge how reliable are their experiments.

      In the revised manuscript we show all replicates for the flow cytometry histograms.

      For Fig. 2C, all replicates are provided in Suppl. Fig. 3.

      For Fig. 3B, all replicates are provided in Suppl. Fig. 4.

      For Fig. 4B, all replicates are provided in Suppl. Fig. 5.

      For Fig. 5B, all replicates are provided in Suppl. Fig. 6.

      (3) I am unsure how ChIP-seq in Fig. 2A was performed (with anti-FLAG or anti-HA antibodies? I cannot tell from the Materials & Methods). More importantly, I did not see the control for this ChIP-seq experiment. If a FLAG-tagged BrrG was used for ChIP-seq, then a WT non-tagged version should be used as a negative control (not sequencing INPUT DNA), this is especially important for anti-terminator that can co-travel with RNA polymerase. Please also report the number of replicates for ChIP-seq experiments.

      Fig. 2A presents the coverage plot from the ChIP-Seq of ∆brrG +pPtet:3xFLAG-brrG (N’ in green). As anticipated by the referee, we had used ∆brrG +pTet:brrG (untagged) as control (grey). Each strain was tested in a single replicate. The C-terminal tag produced results similar to the untagged version, suggesting it is non-functional. All tested tags are shown in Supplementary Figure 2.

      (4) Korotaev et al mentioned that BrrG binds to DNA (as well as to RNA polymerase). With the availability of existing ChIP-seq data, the authors should be able to locate the DNA-binding element of BrrG, this additional information will be useful to the community.

      We identified a putative binding site of BrrG using our ChIP-Seq data. The putative binding site is indicated in Fig. 2D of the revised manuscript.

      (5) Mutational experiments to break the potential hairpin structure are required to strengthen the claim that this putative hairpin is the potential transcriptional terminator.

      We did not claim the identified hairpin is a confirmed terminator, but proposed it as a candidate. We agree with the referee that the suggested experiment would be necessary to definitively establish its function. However, our main objective was to show that BrrG acts as a processive terminator, which we demonstrated by replacing the putative terminator with a well-characterized synthetic one that BrrG successfully bypassed. Therefore, we chose not to perform the proposed experiment and have accordingly softened our conclusions regarding the hairpin’s potential terminator function.

      Reviewer 2 (Public review):

      Summary:

      In this study, the authors identified and characterized a regulatory mechanism based on transcriptional anti-termination that connects the two gene clusters, capsid and run-off replication (ROR) locus, of the bipartite Bartonella gene transfer agent (GTA). Among genes essential for GTA functionality identified in a previous transposon sequencing project, they found a potential antiterminatior of phage origin within the ROR locus. They employed fluorescence reporter and gene transfer assays of overexpression and knockout strains in combination with ChiPSeq and promoter-fusions to convincingly show that this protein indeed acts as an antiterminator counteracting attenuation of the capsid gene cluster expression.

      Impact on the field:

      The results provide valuable insights into the evolution of the chimeric BaGTA, a unique example of phage co-domestication by bacteria. A similar system found in the other broadly studied Rhodobacterales/Caulobacterales GTA family suggests that antitermination could be a general mechanism for GTA control.

      Strengths:

      Results of the selected and carefully designed experiments support the main conclusions.

      Weaknesses:

      It remains open why overexpression of the antiterminator does not increase the gene transfer frequency.

      We are grateful for reviewer #2's thoughtful and encouraging feedback on our manuscript. The reviewer raises an important question about why overexpression of the antiterminator does not increase gene transfer frequency. While we acknowledge this point, we consider it beyond the scope of the current study. Our findings clearly demonstrate that the antiterminator induces capsid component expression in a large proportion of cells. However, the fact that this expression plateaus at high levels rather than exhibiting a transient peak, as seen in the wild type, suggests that antiterminators do not regulate GTA particle release via lysis. We are actively investigating this further through additional experiments, which we plan to publish separately from this study.

      Reviewer 2 (Recommendations for the authors):

      (1) The authors wrote "GTAs are not self-transmitting because the DNA packaging capacity of a GTA particle is too small to package the entire gene cluster encoding it" (page 3). I thought that at least the Bartonella capsid gene cluster should be self-transmissible within the 14 kb packaged DNA (https://doi.org/10.1371/journal.pgen.1003393, https://doi.org/10.1371/journal.pgen.1000546). This was also concluded by Lang et al (https://doi.org/10.1146/annurev-virology-101416-041624). In this case the presented results would have important implications. As the gene cluster and the anti-terminator required for its expression are separated on the chromosome, it would not be possible to transfer an active GTA gene cluster, although the DNA coding for the genes required for making the packaging agent itself, theoretically fits into a BaGTA particle. Could the authors comment on that? I think it would be helpful to add the sizes of the different gene clusters and the distance between them in Fig. 2A. The ROR amplified region spans 500kb, is the capsid gene cluster within this region?

      We thank the reviewer for bringing up this interesting point. The ror gene cluster, which encodes the antiterminator BrrG, is approximately 9.2 kb in size and could feasibly be packaged in its entirety into a GTA particle. In contrast, the bgt cluster (capsid cluster) is approximately 20 kb in size —exceeding the packaging limit of GTA particles—and is separated from the bgt cluster by approximately 35 kb. Consequently, if the ror cluster is transferred via a GTA particle into a recipient host that does not encode the bgt gene cluster, the ror cluster would not be expressed.

      We added the sizes of the gene clusters to Fig. 1A.

      (2) Another side-note regarding the introduction: On page three the authors write: "GTAs encode bacteriophage-like particles and in contrast to phages transfer random pieces of host bacterial DNA". While packaging is not specific, certain biases in the packaging frequency are observed in both studied GTA families. For Bartonella this is ROR. In the two GTA-producing strains D. shibae and C. crescentus origin and terminus of replication are not packaged and certain regions are overrepresented (https://doi.org/10.1093/gbe/evy005, https://doi.org/10.1371/journal.pbio.3001790). Furthermore, D. shibae plasmids are not packaged but chromids are. I think the term "random" does not properly describe these observations. I would suggest using "not specific" instead.

      We thank the reviewer for this suggestion and adjusted the wording on p. 3 accordingly.

      (3) Page 5: Remove "To address this". It is not needed as you already state "To test this hypothesis" in the previous sentence.

      We adjusted the working on p.5 accordingly.

      (4) I think the manuscript would greatly benefit from a summary figure to visualize the Q-like antiterminator-dependent regulatory circuit for GTA control and its four components described on pages 15 and 16.

      We thank the reviewer for this valuable suggestion. We included a summary figure (Fig. 6) in the discussion section of the revised manuscript.

      (5) Page 17: It might be worth noting that GafA is highly conserved along GTAs in Rhodobacterales (https://doi.org/10.3389/fmicb.2021.662907) and so is probably regulatory integration into the ctrA network (https://doi.org/10.3389/fmicb.2019.00803). It's an old mechanism. It would be also interesting to know if it is a common feature of the two archetypical GTAs that the regulator is not part of the cluster itself.

      We agree with the reviewer’s comments and have revised the wording to state that GafA is highly conserved.

    1. Author response:

      The following is the authors’ response to the previous reviews

      General Response to Reviewers:

      We thank the Reviewers for their comments, which continue to substantially improve the quality and clarity of the manuscript, and therefore help us to strengthen its message while acknowledging alternative explanations.

      All three reviewers raised the concern that we have not proven that Rab3A is acting on a presynaptic mechanism to increase mEPSC amplitude after TTX treatment of mouse cortical cultures.  The reviewers’ main point is that we have not shown a lack of upregulation of postsynaptic receptors in mouse cortical cultures. We want to stress that we agree that postsynaptic receptors are upregulated after activity block in neuronal cultures.  However, the reviewers are not acknowledging that we have previously presented strong evidence at the mammalian NMJ that there is no increase in AChR after activity blockade, and therefore the requirement for Rab3A in the homeostatic increase in quantal amplitude points to a presynaptic contribution. We agree that we should restrict our firmest conclusions to the data in the current study, but in the Discussion we are proposing interpretations. We have added the following new text:

      “The impetus for our current study was two previous studies in which we examined homeostatic regulation of quantal amplitude at the NMJ.  An advantage of studying the NMJ is that synaptic ACh receptors are easily identified with fluorescently labeled alpha-bungarotoxin, which allows for very accurate quantification of postsynaptic receptor density. We were able to detect a known change due to mixing 2 colors of alpha-BTX to within 1% (Wang et al., 2005).  Using this model synapse, we showed that there was no increase in synaptic AChRs after TTX treatment, whereas miniature endplate current increased 35% (Wang et al., 2005). We further showed that the presynaptic protein Rab3A was necessary for full upregulation of mEPC amplitude (Wang et al., 2011). These data strongly suggested Rab3A contributed to homeostatic upregulation of quantal amplitude via a presynaptic mechanism.  With the current study showing that Rab3A is required for the homeostatic increase in mEPSC amplitude in cortical cultures, one interpretation is that in both situations, Rab3A is required for an increase in the presynaptic quantum.”

      The point we are making is that the current manuscript is an extension of that work and interpretation of our findings regarding the variability of upregulation of postsynaptic receptors in our mouse cortical cultures further supports the idea that there is a Rab3Adependent presynaptic contribution to homeostatic increases in quantal amplitude.

      Public Reviews:

      Reviewer #1 (Public review):

      Koesters and colleagues investigated the role of the small GTPase Rab3A in homeostatic scaling of miniature synaptic transmission in primary mouse cortical cultures using electrophysiology and immunohistochemistry. The major finding is that TTX incubation for 48 hours does not induce an increase in the amplitude of excitatory synaptic miniature events in neuronal cortical cultures derived from Rab3A KO and Rab3A Earlybird mutant mice. NASPM application had comparable effects on mEPSC amplitude in control and after TTX, implying that Ca2+-permeable glutamate receptors are unlikely modulated during synaptic scaling. Immunohistochemical analysis revealed no significant changes in GluA2 puncta size, intensity, and integral after TTX treatment in control and Rab3A KO cultures. Finally, they provide evidence that loss of Rab3A in neurons, but not astrocytes, blocks homeostatic scaling. Based on these data, the authors propose a model in which neuronal Rab3A is required for homeostatic scaling of synaptic transmission, potentially through GluA2-independent mechanisms.

      The major finding - impaired homeostatic up-scaling after TTX treatment in Rab3A KO and Rab3 earlybird mutant neurons - is supported by data of high quality. However, the paper falls short of providing any evidence or direction regarding potential mechanisms. The data on GluA2 modulation after TTX incubation are likely statistically underpowered, and do not allow drawing solid conclusions, such as GluA2-independent mechanisms of up-scaling.

      The study should be of interest to the field because it implicates a presynaptic molecule in homeostatic scaling, which is generally thought to involve postsynaptic neurotransmitter receptor modulation. However, it remains unclear how Rab3A participates in homeostatic plasticity.

      Major (remaining) point:

      (1) Direct quantitative comparison between electrophysiology and GluA2 imaging data is complicated by many factors, such as different signal-to-noise ratios. Hence, comparing the variability of the increase in mini amplitude vs. GluA2 fluorescence area is not valid. Thus, I recommend removing the sentence "We found that the increase in postsynaptic AMPAR levels was more variable than that of mEPSC amplitudes, suggesting other factors may contribute to the homeostatic increase in synaptic strength." from the abstract.

      We have not removed the statement, but altered it to soften the conclusion. It now reads, “We found that the increase in postsynaptic AMPAR levels in wild type cultures was more variable than that of mEPSC amplitudes, which might be explained by a presynaptic contribution, but we cannot rule out variability in the measurement.”.

      Similarly, the data do not directly support the conclusion of GluA2-independent mechanisms of homeostatic scaling. Statements like "We conclude that these data support the idea that there is another contributor to the TTX- induced increase in quantal size." should be thus revised or removed.

      This particular statement is in the previous response to reviewers only, we deleted the sentence that starts, “The simplest explanation Rab3A regulates a presynaptic contributor….”. and “Imaging of immunofluorescence more variable…”. We deleted “ our data suggest….consistently leads to an increase in mEPSC amplitude and sometimes leads to….” We added “…the lack of a robust increase in receptor levels leaves open the possibility that there is a presynaptic contributor to quantal size in mouse cortical cultures. However, the variability could arise from technical factors associated with the immunofluorescence method, and the mechanism of Rab3A-dependent plasticity could be presynaptic for the NMJ and postsynaptic for cortical neurons.”

      Reviewer #2 (Public review):

      I thank the authors for their efforts in the revision. In general, I believe the main conclusion that Rab3A is required for TTX-induced homeostatic synaptic plasticity is wellsupported by the data presented, and this is an important addition to the repertoire of molecular players involved in homeostatic compensations. I also acknowledge that the authors are more cautious in making conclusions based on the current evidence, and the structure and logic have been much improved.

      The only major concern I have still falls on the interpretation of the mismatch between GluA2 cluster size and mEPSC amplitude. The authors argue that they are only trying to say that changes in the cluster size are more variable than those in the mEPSC amplitude, and they provide multiple explanations for this mismatch. It seems incongruous to state that the simplest explanation is a presynaptic factor when you have all these alternative factors that very likely have contributed to the results. Further, the authors speculate in the discussion that Rab3A does not regulate postsynaptic GluA2 but instead regulates a presynaptic contributor. Do the authors mean that, in their model, the mEPSC amplitude increases can be attributed to two factors- postsynaptic GluA2 regulation and a presynaptic contribution (which is regulated by Rab3A)? If so, and Rab3A does not affect GluA2 whatsoever, shouldn't we see GluA2 increase even in the absence of Rab3A? The data in Table 1 seems to indicate otherwise.

      The main body of this comment is addressed in the General Response to Reviewers. In addition, we deleted text “current data, coupled with our previous findings at the mouse neuromuscular junction, support the idea that there are additional sources contributing to the homeostatic increase in quantal size.” We added new text, so the sentence now reads: “Increased receptors likely contribute to increases in mESPC amplitudes in mouse cortical cultures, but because we do not have a significant increase in GluA2 receptors in our experiments, it is impossible to conclude that the increase is lacking in cultures from Rab3A<sup>-/-</sup> neurons.”

      I also question the way the data are presented in Figure 5. The authors first compare 3 cultures and then 5 cultures altogether, if these experiments are all aimed to answer the same research question, then they should be pooled together. Interestingly, the additional two cultures both show increases in GluA2 clusters, which makes the decrease in culture #3 even more perplexing, for which the authors comment in line 261 that this is due to other factors. Shouldn't this be an indicator that something unusual has happened in this culture?

      Data in this figure is sufficient to support that GluA2 increases are variable across cultures, which hardly adds anything new to the paper or to the field. 

      A major goal of performing the immunofluorescence measurements in the same cultures for which we had electrophysiological results was to address the common impression that the homeostatic effect itself is highly variable, as the reviewer notes in the comment “…GluA2 increases are variable across cultures…” Presumably, if GluA2 increases are the mechanism of the mEPSC amplitude increases, then variable GluA2 increases should correlate with variable mEPSC amplitude increases, but that is not what we observed. We are left with the explanation that the immunofluorescence method itself is very variable. We have added the point to the Discussion, which reads, “the variability could arise from technical factors associated with the immunofluorescence method, and the mechanism of Rab3A-dependent homeostatic plasticity could be presynaptic for the NMJ and postsynaptic for cortical neurons.”

      Finally, the implication of “Shouldn’t this be an indicator that something unusual has happened in this culture?” if it is not due to culture to culture variability in the homeostatic response itself, is that there was a technical problem with accurately measuring receptor levels. We have no reason to suspect anything was amiss in this set of coverslips (the values for controls and for TTX-treated were not outside the range of values in other experiments). In any of the coverslips, there may be variability in the amount of primary anti-GluA2 antibody, as this was added directly to the culture rather than prepared as a diluted solution and added to all the coverslips. But to remove this one experiment because it did not give the expected result is to allow bias to direct our data selection.

      The authors further cite a study with comparable sample sizes, which shows a similar mismatch based on p values (Xu and Pozzo-Miller 2007), yet the effect sizes in this study actually match quite well (both ~160%). P values cannot be used to show whether two effects match, but effect sizes can. Therefore, the statement in lines 411-413 "... consistently leads to an increase in mEPSC amplitudes, and sometimes leads to an increase in synaptic GluA2 receptor cluster size" is not very convincing, and can hardly be used to support "the idea that there are additional sources contributing to the homeostatic increase in quantal size.”

      We have the same situation; our effect sizes match (19.7% increase for mEPSC amplitude; 18.1% increase for GluA2 receptor cluster size, see Table 1), but in our case, the p value for receptors does not reach statistical significance. Our point here is that there is published evidence that the variability in receptor measurements is greater than the variability in electrophysiological measurements. But we have softened this point, removing the sentences containing “…consistently leads and sometimes...” and “……additional sources contributing…”.

      I would suggest simply showing mEPSC and immunostaining data from all cultures in this experiment as additional evidence for homeostatic synaptic plasticity in WT cultures, and leave out the argument for "mismatch". The presynaptic location of Rab3A is sufficient to speculate a presynaptic regulation of this form of homeostatic compensation.

      We have removed all uses of the word “mismatch,” but feel the presentation of the 3 matched experiments, 23-24 cells (Figure 5A, D), and the additional 2 experiments for a total of 5 cultures, 48-49 cells (Figure 5C, F), is important in order to demonstrate that the lack of statistically significant receptor response is due neither to a variable homeostatic response in the mEPSC amplitudes, nor to a small number of cultures.

      Minor concerns:

      (1) Line 214, I see the authors cite literature to argue that GluA2 can form homomers and can conduct currents. While GluA2 subunits edited at the Q/R site (they are in nature) can form homomers with very low efficiency in exogenous systems such as HEK293 cells (as done in the cited studies), it's unlikely for this to happen in neurons (they can hardly traffic to synapses if possible at all).

      We were unable to identify a key reference that characterized GluA2 homomers vs. heteromers in native cortical neurons, but we have rewritten the section in the manuscript to acknowledge the low conductance of homomers:

      “…to assess whether GluA2 receptor expression, which will identify GluA2 homomers and GluA2 heteromers (the former unlikely to contribute to mEPSCs given their low conductance relative to heteromers (Swanson et al., 1997; Mansour et al., 2001)…”

      (2) Lines 221-222, the authors may have misinterpreted the results in Turrigiano 1998. This study does not show that the increase in receptors is most dramatic in the apical dendrite, in fact, this is the only region they have tested. The results in Figures 3b-c show that the effect size is independent of the distance from soma.

      Figure 3 in Turrigiano et al., shows that the increase in glutamate responsiveness is higher at the cell body than along the primary dendrite. We have revised our description to indicate that an increase in responsiveness on the primary dendrite has been demonstrated in Turrigiano et al. 1998.

      “We focused on the primary dendrite of pyramidal neurons as a way to reduce variability that might arise from being at widely ranging distances from the cell body, or, from inadvertently sampling dendritic regions arising from inhibitory neurons. In addition, it has been shown that there is a clear increase in response to glutamate in this region (Turrigiano et al., 1998).”

      “…synaptic receptors on the primary dendrite, where a clear increase in sensitivity to exogenously applied glutamate was demonstrated (see Figure 3 in (Turrigiano et al., 1998)).

      (3) Lines 309-310 (and other places mentioning TNFa), the addition of TNFa to this experiment seems out of place. The authors have not performed any experiment to validate the presence/absence of TNFa in their system (citing only 1 study from another lab is insufficient). Although it's convincing that glia Rab3A is not required for homeostatic plasticity here, the data does not suggest Rab3A's role (or the lack of) for TNFa in this process.

      We have modified the paragraph in the Discussion that addresses the glial results, to describe more clearly the data that supported an astrocytic TNF-alpha mechanism: “TNF-alpha accumulates after activity blockade, and directly applied to neuronal cultures, can cause an increase in GluA1 receptors, providing a potential mechanism by which activity blockade leads to the homeostatic upregulation of postsynaptic receptors (Beattie et al., 2002; Stellwagen et al., 2005; Stellwagen and Malenka, 2006).”

      We have also acknowledged that we cannot rule out TNF-alpha coming from neurons in the cortical cultures: “…suggesting the possibility that neuronal Rab3A can act via a non-TNF-alpha mechanism to contribute to homeostatic regulation of quantal amplitude, although we have not ruled out a neuronal Rab3A-mediated TNF-alpha pathway in cortical cultures.”

      Reviewer #3 (Public review):

      This manuscript presents a number of interesting findings that have the potential to increase our understanding of the mechanism underlying homeostatic synaptic plasticity (HSP). The data broadly support that Rab3A plays a role in HSP, although the site and mechanism of action remain uncertain.

      The authors clearly demonstrate that Rab3A plays a role in HSP at excitatory synapses, with substantially less plasticity occurring in the Rab3A KO neurons. There is also no apparent HSP in the Earlybird Rab3A mutation, although baseline synaptic strength is already elevated. In this context, it is unclear if the plasticity is absent, already induced by this mutation, or just occluded by a ceiling effect due to the synapses already being strengthened. Occlusion may also occur in the mixed cultures when Rab3A is missing from neurons but not astrocytes. The authors do appropriately discuss these options. The authors have solid data showing that Rab3A is unlikely to be active in astrocytes, Finally, they attempt to study the linkage between changes in synaptic strength and AMPA receptor trafficking during HSP, and conclude that trafficking may not be solely responsible for the changes in synaptic strength during HSP.

      Strengths:

      This work adds another player into the mechanisms underlying an important form of synaptic plasticity. The plasticity is likely only reduced, suggesting Rab3A is only partially required and perhaps multiple mechanisms contribute. The authors speculate about some possible novel mechanisms, including whether Rab3A is active pre-synaptically to regulate quantal amplitude.

      As Rab3A is primarily known as a pre-synaptic molecule, this possibility is intriguing. However, it is based on the partial dissociation of AMPAR trafficking and synaptic response and lacks strong support. On average, they saw a similar magnitude of change in mEPSC amplitude and GluA2 cluster area and integral, but the GluA2 data was not significant due to higher variability. It is difficult to determine if this is due to biology or methodology - the imaging method involves assessing puncta pairs (GluA2/VGlut1) clearly associated with a MAP2 labeled dendrite. This is a small subset of synapses, with usually less than 20 synapses per neuron analyzed, which would be expected to be more variable than mEPSC recordings averaged across several hundred events. However, when they reduce the mEPSC number of events to similar numbers as the imaging, the mESPC amplitudes are still less variable than the imaging data. The reason for this remains unclear. The pool of sampled synapses is still different between the methods and recent data has shown that synapses have variable responses during HSP. Further, there could be variability in the subunit composition of newly inserted AMPARs, and only assessing GluA2 could mask this (see below). It is intriguing that pre-synaptic changes might contribute to HSP, especially given the likely localization of Rab3A. But it remains difficult to distinguish if the apparent difference in imaging and electrophysiology is a methodological issue rather than a biological one. Stronger data, especially positive data on changes in release, will be necessary to conclude that pre-synaptic factors are required for HSP, beyond the established changes in post-synaptic receptor trafficking.

      Regarding the concern that the lack of increase in receptors is due to a technical issue, please see General Response to Reviewers, above. We have also softened our conclusions throughout, acknowledging we cannot rule out a technical issue.

      Other questions arise from the NASPM experiments, used to justify looking at GluA2 (and not GluA1) in the immunostaining. First, there is a strong frequency effect that is unclear in origin. One would expect NASPM to merely block some fraction of the post-synaptic current, and not affect pre-synaptic release or block whole synapses. But the change in frequency seems to argue (as the authors do) that some synapses only have CP-AMPARs, while the rest of the synapses have few or none. Another possibility is that there are pre-synaptic NASPM-sensitive receptors that influence release probability. Further, the amplitude data show a strong trend towards smaller amplitude following NASPM treatment (Fig 3B). The p value for both control and TTX neurons was 0.08 - it is very difficult to argue that there is no effect. The decrease on average is larger in the TTX neurons, and some cells show a strong effect. It is possible there is some heterogeneity between neurons on whether GluA1/A2 heteromers or GluA1 homomers are added during HSP. This would impact the conclusions about the GluA2 imaging as compared to the mEPSC amplitude data.

      The key finding in Figure 3 is that NASPM did not eliminate the statistically significant increase in mEPSC amplitude after TTX treatment (Fig 3A).  Whether or not NASPM sensitive receptors contribute to mESPC amplitude is a separate question (Fig 3B). We are open to the possibility that NASPM reduces mEPSC amplitude in both control and TTX treated cells (p = 0.08 for both), but that does not change our conclusion that NASPM has no effect on the TTX-induced increase in mEPSC amplitude. The mechanism underlying the decrease in mEPSC frequency following NASPM is interesting, but does not alter our conclusions regarding the role of Rab3A in homeostatic synaptic plasticity of mEPSC amplitude. In addition, the Reviewer does not acknowledge the Supplemental Figure #1, which shows a similar lack of correspondence between homeostatic increases in mEPSC amplitude and GluA1 receptors in two cultures where matched data were obtained. Therefore, we do not think our lack of a robust increase in receptors can be explained by our failing to look at the relevant receptor.

      To understand the role of Rab3A in HSP will require addressing two main issues:

      (1) Is Rab3A acting pre-synaptically, post-synaptically or both? The authors provide good evidence that Rab3A is acting within neurons and not astrocytes. But where it is acting (pre or post) would aid substantially in understanding its role. The general view in the field has been that HSP is regulated post-synaptically via regulation of AMPAR trafficking, and considerable evidence supports this view. More concrete support for the authors' suggestion of a pre-synaptic site of control would be helpful.

      We agree that definitive evidence for a presynaptic role of Rab3A in homeostatic plasticity of mEPSC amplitudes in mouse cortical cultures requires demonstrating that loss of Rab3A in postsynaptic neurons does not disrupt the plasticity, whereas loss in presynaptic neurons does. Without these data, we can only speculate that the Rab3A-dependence of homeostatic plasticity of quantal size in cortical neurons may be similar to that of the neuromuscular junction, where it cannot be receptors. We have added to the Discussion that the mechanism of Rab3A regulation of homeostatic plasticity of quantal amplitude could different between cortical neurons and the neuromuscular junction (lines 448-450 in markup,). Establishing a way to co-culture Rab3A-/- and Rab3A+/+ neurons in ratios that would allow us to record from a Rab3A-/- neuron that has mainly Rab3A+/+ inputs (or vice versa) is not impossible, but requires either transfection or transgenic expression with markers that identify the relevant genotype, and will be the subject of future experiments.

      (2): Rab3A is also found at inhibitory synapses. It would be very informative to know if HSP at inhibitory synapses is similarly affected. This is particularly relevant as at inhibitory synapses, one expects a removal of GABARs or a decrease in GABA release (ie the opposite of whatever is happening at excitatory synapses). If both processes are regulated by Rab3A, this might suggest a role for this protein more upstream in the signaling; an effect only at excitatory synapses would argue for a more specific role just at those synapses.

      We agree with the Reviewer, that it is important to determine the generality of Rab3A function in homeostatic plasticity. Establishing the homeostatic effect on mIPSCs and then examining them in Rab3A-/- cultures is a large undertaking and will be the subject of future experiments.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Minor (remaining) points:

      (1) The figure referenced in the first response to the reviewers (Figure 5G) does not exist.

      We meant Figure 5F, which has been corrected in the current response.

      (2) I recommend showing the data without binning (despite some overlap).

      The box plot in Origin will not allow not binning, but we can make the bin size so small that for all intents and purposes, there is close to 1 sample in each bin. When we do this, the majority of data are overlapped in a straight vertical line. Previously described concerns were regarding the gaps in the data, but it should be noted that these are cell means and we are not depicting the distributions of mEPSC amplitudes within a recording or across multiple recordings.

      (3) Please auto-scale all axes from 0 (e.g., Fig 1E, F).

      We have rescaled all mEPSC amplitude axes in box plots to go from 0 (Figures 1, 2 and 6).

      (4) Typo in Figure legend 3: "NASPM (20 um)" => uM

      Fixed.

      Reviewer #2 (Recommendations for the authors):

      (1) Line 140, frequencies are reported in Hz while other places are in sec-1, while these are essentially the same, they should be kept consistent in writing.

      All mEPSC frequencies have been changed to sec<sup>-1</sup>, except we have left “Hz” for repetitive stimulation and filtering.

      (2) Paragraph starting from line 163 (as well as other places where multiple groups are compared, such as the occlusion discussion), the authors assessed whether there was a change in baseline between WT and mutant group by doing pairwise tests, this is not the right test. A two-way ANOVA, or at least a multivariant test would be more appropriate.

      We have performed a two-way ANOVA, with genotype as one factor, and treatment as the other factor. The p values in Figures 1 and 2 have been revised to reflect p values from the post-hoc Tukey test on the specific interactions (for each particular genotype, TTX vs CON effects). The difference in the two WT strains, untreated, was not significant in the Post-Hoc Tukey test, and we have revised the text. The difference between the untreated WT from the Rab3A+/Ebd colony and the untreated Rab3AEbd/Ebd mutant was still significant in the Post-Hoc Tukey test, and this has replaced the Kruskal-Wallis test. The two-way ANOVA was also applied to the neuron-glia experiments and p values in Figure 6 adjusted accordingly.

      (3) Relevant to the second point under minor concerns, I suggest this sentence be removed, as reducing variability and avoiding inhibitory projects are reasons good enough to restrict the analysis to the apical dendrites.

      We have revised the description of the Turrigiano et al., 1998 finding from their Figure 3 and feel it still strengthens the justification for choosing to analyze only synapses on the apical dendrite.

      Reviewer #3 (Recommendations for the authors):

      Minor points:

      The comments on lines 256-7 could seem misleading - the NASPM results wouldn't rule out contribution of those other subunits, only non-GluA2 containing combinations of those subunits. I would suggest revising this statement. Also, NASPM does likely have an effect, just not one that changes much with TTX treatment.

      At new line 213 (markup) we have added the modifier “homomeric” to clarify our point that the lack of NASPM effect on the increase in mEPSC amplitude after TTX indicates that the increase is not due to more homomeric Ca<sup>2+</sup>-permeable receptors. We have always stated that NASPM reduces mEPSC amplitude, but it is in both control and treated cultures.

      Strong conclusions based on a single culture (lines 314-5) seem unwarranted.

      We have softened this statement with a “suggesting that” substituted for the previous “Therefore,” but stand by our point that the mEPSC amplitude data support a homeostatic effect of TTX in Culture #3, so the lack of increase in GluA2 cluster size needs an explanation other than variability in the homeostatic effect itself.

      Saying (line 554) something is 'the only remaining possibility' also seems unwarranted.

      We have softened this statement to read, “A remaining possibility…”.

      Beattie EC, Stellwagen D, Morishita W, Bresnahan JC, Ha BK, Von Zastrow M, Beattie MS, Malenka RC (2002) Control of synaptic strength by glial TNFalpha. Science 295:2282-2285.

      Mansour M, Nagarajan N, Nehring RB, Clements JD, Rosenmund C (2001) Heteromeric AMPA receptors assemble with a preferred subunit stoichiometry and spatial arrangement. Neuron 32:841-853. Stellwagen D, Malenka RC (2006) Synaptic scaling mediated by glial TNF-alpha. Nature 440:1054-1059.

      Stellwagen D, Beattie EC, Seo JY, Malenka RC (2005) Differential regulation of AMPA receptor and GABA receptor trafficking by tumor necrosis factor-alpha. J Neurosci 25:3219-3228.

      Swanson GT, Kamboj SK, Cull-Candy SG (1997) Single-channel properties of recombinant AMPA receptors depend on RNA editing, splice variation, and subunit composition. J Neurosci 17:5869.

      Turrigiano GG, Leslie KR, Desai NS, Rutherford LC, Nelson SB (1998) Activity-dependent scaling of quantal amplitude in neocortical neurons. Nature 391:892-896.

      Wang X, Wang Q, Yang S, Bucan M, Rich MM, Engisch KL (2011) Impaired activity-dependent plasticity of quantal amplitude at the neuromuscular junction of Rab3A deletion and Rab3A earlybird mutant mice. J Neurosci 31:3580-3588.

      Wang X, Li Y, Engisch KL, Nakanishi ST, Dodson SE, Miller GW, Cope TC, Pinter MJ, Rich MM (2005) Activity-dependent presynaptic regulation of quantal size at the mammalian neuromuscular junction in vivo. J Neurosci 25:343-351.

    1. Author Response:

      Reviewer #1 (Public review):

      The authors of this study use electron microscopy and 3D reconstruction techniques to study the morphology of distinct classes of Drosophila sensory neurons *across many neurons of the same class.* This is a comprehensive study attempting to look at nearly all the sensory neurons across multiple sensilla to determine a) how much morphological variability exists between and within neurons of different and similar sensory classes, and 2) identify dendritic features that may have evolved to support particular sensory functions. This study builds upon the authors' previous work, which allowed them to identify and distinguish sensory neuron subtypes in the EM volumes without additional staining so that reconstructed neurons could reliably be placed in the appropriate class. This work is unique in looking at a large number of individual neurons of the same class to determine what is consistent and what is variable about their class-specific morphologies.

      This means that in addition to providing specific structural information about these particular cells, the authors explore broader questions of how much morphological diversity exists between sensory neurons of the same class and how different dendritic morphologies might affect sensory and physiological properties of neurons.

      The authors found that CO2-sensing neurons have an unusual, sheet-like morphology in contrast to the thin branches of odor-sensing neurons. They show that this morphology greatly increases the surface area to volume ratio above what could be achieved by modest branching of thin dendrites, and posit that this might be important for their sensory function, though this was not directly tested in their study. The study is mainly descriptive in nature, but thorough, and provides a nice jumping-off point for future functional studies. One interesting future analysis could be to examine all four cell types within a single sensilla together to see if there are any general correlations that could reveal insights about how morphology is determined and the relative contributions of intrinsic mechanisms vs interactions with neighboring cells. For example, if higher than average branching in one cell type correlated with higher than average branching in another type, if in the same sensilla. This might suggest higher extracellular growth or branching cues within a sensilla. Conversely, if higher branching in one cell type consistently leads to reduced length or branching in another, this might point to dendrite-dendrite interactions between cells undergoing competitive or repulsive interactions to define territories within each sensilla as a major determinant of the variability.

      We thank the reviewer for the insightful comments and appreciation for our study.

      Reviewer #2 (Public review):

      Summary:

      The manuscript employs serial block‐face electron microscopy (SBEM) and cryofixation to obtain high‐resolution, three‐dimensional reconstructions of Drosophila antennal sensilla containing olfactory receptor neurons (ORNs) that detect CO2. This method has been used previously by the same lab in Gonzales et. al, 2021. (https://elifesciences.org/articles/69896), which had provided an exemplary model by integrating high-resolution EM with electrophysiology and cell-type-specific labeling.

      We thank the reviewer for expressing appreciation for our published study.

      The previous study ended up correlating morphology with activity for multiple olfactory sensillar types. Compared to the 2021 study, this current manuscript appears somewhat incomplete and lacks integration with activity.

      We thank the reviewer for their feedback. However, we would like to clarify that our previous study did not correlate morphology with activity to a greater extent than the current study. Both employed the same cryofixation, SBEM-based approach without recording odor-induced activity, but the focus of the current work is fundamentally different. While the previous study examined multiple sensillum types, the current study concentrates on a single sensillum type to address a distinct biological question regarding morphological heterogeneity. We appreciate the opportunity to clarify this distinction, and we hope that the revised manuscript more clearly conveys the unique scope and contributions of this study.

      In fact older studies have also reported two-dimensional TEM images of the putative CO2 neuron in Drosophila (Shanbhag et al., 1999) and in mosquitoes (McIver and Siemicki, 1975; Lu et al, 2007), and in these instances reported that the dendritic architecture of the CO2 neuron was somewhat different (circular and flattened, lamellated) from other olfactory neurons.

      We thank the reviewer for pointing this out. As noted in both the Introduction and Discussion sections, previous studies—including those cited by the reviewer—suggested that CO2-sensing neurons may have a distinct dendritic morphology. However, those earlier studies lacked the means to definitively link the observed morphology to CO2 neuron identity.

      In contrast, our study assigns neuronal identity based on quantitative morphometric measurements, allowing us to confidently associate the unique dendritic architecture with CO2 neurons. Furthermore, we extend previous observations by providing full 3D reconstructions and nanoscale morphometric analyses, offering a much more comprehensive and definitive characterization of these neurons. We believe this represents a significant advancement over earlier work.

      The authors claim that this approach offers an artifact‐minimized ultrastructural dataset compared to earlier. In this study, not only do they confirm this different morphology but also classify it into distinct subtypes (loosely curled, fully curled, split, and mixed). This detailed morphological categorization was not provided in prior studies (e.g., Shanbhag et al., 1999 ).

      We thank the reviewer for acknowledging the significance of our study.

      The authors would benefit from providing quantitative thresholds or objective metrics to improve reproducibility and to clarify whether these structural distinctions correlate with distinct functional roles.

      We thank the reviewer for raising this point. However, we would like to clarify that assigning neurons to strict morphological subtypes was not the primary aim of our study. In practice, dendritic architectures can be highly complex, with individual neurons often displaying features characteristic of multiple subtypes. This is precisely why we included a “mixed” subtype category—to acknowledge and capture this morphological heterogeneity rather than impose rigid classification boundaries.

      Our intent in defining subtypes was not to imply discrete functional classes, but rather to highlight the range of morphological variation observed across ab1C neurons. While we agree that exploring potential correlations between structure and function is an important future direction, the current study focuses on characterizing this diversity using 3D reconstruction and morphometric analysis. We hope this clarifies the purpose and scope of our morphological categorization.

      Strengths:

      The study makes a convincing case that ab1C neurons exhibit a unique, flattened dendritic morphology unlike the cylindrical dendrites found in ab1D neurons. This observation extends previous qualitative TEM findings by not only confirming the presence of flattened lamellae in CO₂ neurons but also quantifying key morphometrics such as dendritic length, surface area, and volume, and calculating surface area-to-volume ratios. The enhanced ratios observed in the flattened segments are speculated to be linked to potential advantages in receptor distribution (e.g., Gr21a/Gr63a) and efficient signal propagation.

      We thank the reviewer for appreciating the significance our current study.

      Weaknesses:

      While the manuscript offers valuable ultrastructural insights and reveals previously unappreciated heterogeneity among CO₂-sensing neurons, several issues warrant further investigation in addition to the points made above.

      (1) Although this quantitative approach is robust compared to earlier descriptive reports, its impact is somewhat limited by the absence of direct electrophysiological data to confirm that ultrastructural differences translate into altered neuronal function. A direct comparison or discussion of how the present findings align with the functional data obtained from electrophysiology would strengthen the overall argument.

      We thank the reviewer for this comment. We would like to clarify, however, that our study does not claim that the observed morphological heterogeneity necessarily leads to functional diversity. Rather, we consider this as a possible implication and discuss it as a potential question for future research. This idea is raised only in the Discussion section, and we are carefully not to present functional diversity as a conclusion of our study. Nonetheless, we have reviewed the relevant paragraph to ensure the language remains cautious and does not overstate our interpretation.

      We also acknowledge the significance of directly linking ultrastructural features to neuronal function through electrophysiological recordings. However, at present, it is technically challenging to correlate the nanoscale morphology of individual ORNs with their functional activity, as this would require volume EM imaging of the very same neurons that were recorded via electrophysiology. Currently, there is no dye-labeling method compatible with single-sensillum recording and SBEM sample preparation that allows for unambiguous identification and segmentation of recorded ORNs at the necessary ultrastructural resolution.

      To acknowledge this important limitation, we have added a paragraph in the Discussion section, as suggested, to clarify the current technical barriers and to highlight this as a promising direction for future methodological advances.

      (2) Clarifying the criteria for dendritic subtype classification with quantitative parameters would enhance reproducibility and interpretability. Moreover, incorporating electrophysiological recordings from ab1C neurons would provide compelling evidence linking structure and function, and mapping key receptor proteins through immunolabeling could directly correlate receptor distribution with the observed morphological diversity.

      Please see our response to the comment regarding the technical limitations of directly correlating ultrastructure with electrophysiological data.

      In addition, we would like to address the suggestion of using immunolabeling to map receptor distribution in relation to the 3D EM models. Currently, antibodies against Gr21a or Gr63a (the receptors expressed in ab1C neurons) are not available. Even if such antibodies were available, immunogold labeling for electron microscopy requires harsh detergent treatment to increase antibody permeability, damaging morphological integrity. These treatments would compromise the very morphological detail that our study aims to capture and quantify.

      (3) Even though Cryofixation is claimed to be superior to chemical fixation for generating fewer artifacts, authors need to confirm independently the variation observed in the CO2 neuron morphologies across populations. All types of fixation in TEMs cause some artifacts, as does serial sectioning. Without understanding the error rates or without independent validation with another method, it is hard to have confidence in the conclusions drawn by the authors of the paper.

      We thank the reviewer for raising concerns regarding potential artifacts in morphological analyses. However, we would like to clarify that cryofixation is widely regarded as a gold standard for ultrastructural preservation and minimizing fixation-induced artifacts, as supported by extensive literature. This is why we adopted high-pressure freezing and freeze substitution in our study.

      We have also published a separate methods paper (Tsang et al., eLife, 2018) directly comparing our cryofixation-based protocol with conventional chemical fixation, demonstrating substantial improvements in morphological preservation (see the image below, adapted from Figure 2 of our 2018 eLife paper). This provides strong empirical support for the reliability of our approach.

      Author response image 1.

      Regarding the suggestion to validate observed morphological variation across populations: we note that determining the presence of artifacts requires a known ground truth, which is inherently unavailable as we could not measure the morphometrics of fly olfactory receptor neurons in their native state. In the absence of such a benchmark, we have instead prioritized using the best-available preparation methods and high-resolution imaging to ensure structural integrity.

      Addressing these concerns and integrating additional experiments would significantly bolster the manuscript's completeness and advancement.

      We appreciate the reviewer’s feedback. As discussed in our responses to the specific comments above, certain suggested experiments are currently limited by technical constraints, particularly in the context of high-resolution volume EM for insect tissues enclosed in cuticles.

      Nevertheless, we have carefully addressed the reviewer’s concerns to the fullest extent possible within the scope of this study. We have revised the manuscript to clarify methodological limitations, added new explanatory content where appropriate, and ensured that our interpretations remain well grounded in the data. We hope these revisions strengthen the clarity and completeness of the manuscript.

      Reviewer #3 (Public review):

      Summary:

      In the current manuscript entitled "Population-level morphological analysis of paired CO2- and odor-sensing olfactory neurons in D. melanogaster via volume electron microscopy", Choy, Charara et al. use volume electron microscopy and neuron reconstruction to compare the dendritic morphology of ab1C and ab1D neurons of the Drosophila basiconic ab1 sensillum. They aim to investigate the degree of dendritic heterogeneity within a functional class of neurons using ab1C and ab1D, which they can identify due to the unique feature of ab1 sensilla to house four neurons and the stereotypic location on the third antennal segment. This is a great use of volumetric electron imaging and neuron reconstruction to sample a population of neurons of the same type. Their data convincingly shows that there is dendritic heterogeneity in both investigated populations, and their sample size is sufficient to strongly support this observation. This data proposes that the phenomenon of dendritic heterogenity is common in the Drosophila olfactory system and will stimulate future investigations into the developmental origin, functional implications, and potential adaptive advantage of this feature.

      Moreover, the authors discovered that there is a difference between CO2- and odour-sensing neurons of which the first show a characteristic flattened and sheet-like structure not observed in other sensory neurons sampled in this and previous studies. They hypothesize that this unique dendritic organization, which increases the surface area to volume ratio, might allow more efficient Co2 sensing by housing higher numbers of Co2 receptors. This is supported by previous attempts to express Co2 sensors in olfactory sensory neurons, which lack this dendritic morphology, resulting in lower Co2 sensitivity compared to endogenous neurons.

      Overall, this detailed morphological description of olfactory sensory neurons' dendrites convincingly shows heterogeneity in two neuron classes with potential functional impacts for odour sensing.

      Strength:

      The volumetric EM imaging and reconstruction approach offers unprecedented details in single cell morphology and compares dendrite heterogeneity across a great fraction of ab1 sensilla.<br /> The authors identify specific shapes for ab1C sensilla potentially linked to their unique function in CO2 sensing.

      We thank the reviewer for the insightful comments and appreciation for our study.

      Weaknesses:

      While the morphological description is highly detailed, no attempts are made to link this to odour sensitivity or other properties of the neurons. It would have been exciting to see how altered morphology impacts physiology in these olfactory sensory cells.

      We agree that linking morphological variation to physiological properties, such as odor sensitivity, would be a highly valuable direction for future research. However, the aim of the current study is to provide an in-depth nanoscale characterization based on a substantial proportion of ab1 sensilla, highlighting morphological heterogeneity among homotypic ORNs.

      At present, it is technically challenging to correlate the nanoscale morphology of individual ORNs with their physiological responses, as this would require volume EM imaging of the exact neurons recorded via single-sensillum electrophysiology. Currently, no dye-labeling method exists that is compatible with both single-sensillum recording and the stringent requirements of SBEM sample preparation to allow for unambiguous identification and segmentation of recorded ORNs.

      To acknowledge this important limitation, we have added a paragraph in the Discussion section clarifying the current technical barriers and highlighting this as a promising area for future methodological development. Please also see our responses to the reviewer’s 4th comment below, where we present preliminary experiments examining whether odor sensitivity varies among homotypic ORNs.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      In this study, Marocco and colleages perform a deep characterization of the complex molecular mechanism guiding the recognition of a particular CELLmotif previously identified in hepatocytes in another publication. Having miR-155-3p with or without this CELLmotif as initial focus, authors identify 21 proteins differentially binding to these two miRNA versions. From these, they decided to focus on PCBP2. They elegantly demonstrate PCBP2 binding to miR-155-3p WT version but not to CELLmotif-mutated version. miR-155-3p contains a hEXOmotif identified in a different report, whose recognition is largely mediated by another RNA-binding protein called SYNCRIP. Interestingly, mutation of the hEXOmotif contained in miR-155-3p did not only blunt SYNCRIP binding, but also PCBP2 binding despite the maintenance of the CELLmotif. This indicates that somehow SYNCRIP binding is a pre-requisite for PCBP2 binding. EMSA assay confirms that SYNCRIP is necessary for PCBP2 binding to miR-155-3p, while PCBP2 is not needed for SYNCRIP binding. Then authors aim to extend these finding to other miRNAs containing both motifs. For that, they perform a small-RNA-Seq of EVs released from cells knockdown for PCBP2 versus control cells, identifying a subset of miRNAs whose expression either increases or decreases. The assumption is that those miRNAs containing PCBP2-binding CELLmotif should now be less retained in the cell and go more to extracellular vesicles, thus reflecting a higher EV expression. The specific subset of miRNAs having both the CELLmotif and hEXOmotif (9 miRNAs) whose expressions increase in EVs due to PCBP2 reduction is also affected by knocking-down SYNCRIP in the sense that reduction of SYNCRIP leads to lower EV sorting. Further experiments confirm that PCBP2 and SYNCRIP bind to these 9 miRNAs and that knocking down SYNCRIP impairs their EV sorting.

      In the revised manuscript, the authors have addressed most of my concerns and questions. I believe the new experiments provide stronger support for their claims. My only remaining concern is the lack of clarity in the replicates for the EMSA experiment. The one shown in the manuscript is clear; however, the other three replicates hardly show that knocking down SYNCRIP has an effect on PCBP2 binding. Even worse is the fact that these replicates do not support at all that PCBP2 silencing has no effect on SYNCRIP binding, as the bands for those types of samples are, in most of the cases, not visible. I think the authors should work on repeating a couple of times EMSA experiment.

      We thank this Reviewer for having appreciated the novelty and the robustness of our data. In accordance with the Reviewer’s concern, we repeated the EMSA assay, specifically to address the PCBP2-independent SYNCRIP binding. In Author response image 1, we report the new EMSA replicates (top), the quantification of each signal (bottom) and the mean of EMSA signals relative to the three independent experiments (right). We hope that the new evidence will meet the required standards.

      Author response image 1.

      Reviewer #2 (Public review):

      Summary:

      The author of this manuscript aimed to uncover the mechanisms behind miRNA retention within cells. They identified PCBP2 as a crucial factor in this process, revealing a novel role for RNAbinding proteins. Additionally, the study discovered that SYNCRIP is essential for PCBP2's function, demonstrating the cooperative interaction between these two proteins. This research not only sheds light on the intricate dynamics of miRNA retention but also emphasizes the importance of protein interactions in regulating miRNA behavior within cells.

      Strengths:

      This paper makes important progress in understanding how miRNAs are kept inside cells. It identifies PCBP2 as a key player in this process, showing a new role for proteins that bind RNA. The study also finds that SYNCRIP is needed for PCBP2 to work, highlighting how these proteins work together. These discoveries not only improve our knowledge of miRNA behavior but also suggest new ways to develop treatments by controlling miRNA locations to influence cell communication in diseases. The use of liver cell models and thorough experiments ensures the results are reliable and show their potential for RNA-based therapies

      Weaknesses:

      The manuscript is well-structured and presents compelling data, but I noticed a few minor corrections that could further enhance its clarity:

      Figure References: In the response to Reviewer 1, the comment states, "It's not Panel C, it's Panel A of Figure 1"-this should be cross-checked for consistency.

      Supplementary Figure 2 is labeled as "Panel A"-please verify if additional panels (B, C, etc.) are intended.

      Western Blot Quality: The Alix WB shows some background noise. A repeat with optimized conditions (or inclusion of a cleaner replicate) would strengthen the data. Adding statistical analysis for all WBs would also reinforce robustness.

      These are relatively small refinements, and the manuscript is already in excellent shape. With these adjustments, it will be even stronger.

      We deeply thank this Reviewer for having considered this new version of the manuscript and for having described its shape as excellent. In order to address the Reviewer’s concerns, we crosschecked the consistency of the described figures’ panels described in the text accordingly. Regarding the qualitative analysis of EV markers, we repeated the western blot analysis with optimized conditions as suggested and included the new panel (Author response image 2) in the supplementary figure 2, allowing to appreciate the signal relative to ALIX expression.

      Author response image 2.

       

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      Careful reading is required to rectify typo errors.

      We thank the Reviewer for this suggestion. We amended the text to rectify typo errors.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study uncovers a protective role of the ubiquitin-conjugating enzyme variant Uev1A in mitigating cell death caused by over-expressed oncogenic Ras in polyploid Drosophila nurse cells and by RasK12 in diploid human tumor cell lines. The authors previously showed that overexpression of oncogenic Ras induces death in nurse cells, and now they perform a deficiency screen for modifiers. They identified Uev1A as a suppressor of this Ras-induced cell death. Using genetics and biochemistry, the authors found that Uev1A collaborates with the APC/C E3 ubiquitin ligase complex to promote proteasomal degradation of Cyclin A. This function of Uev1A appears to extend to diploid cells, where its human homologs UBE2V1 and UBE2V2 suppress oncogenic Ras-dependent phenotypes in human colorectal cancer cells in vitro and in xenografts in mice.

      Strengths:

      (1) Most of the data is supported by a sufficient sample size and appropriate statistics.

      (2) Good mix of genetics and biochemistry.

      (3) Generation of new transgenes and Drosophila alleles that will be beneficial for the community.

      We greatly appreciate these comments.

      Weaknesses:

      (1) Phenotypes are based on artificial overexpression. It is not clear whether these results are relevant to normal physiology.

      Downregulation of Uev1A, Ben, and Cdc27 together significantly increased the incidence of dying nurse cells in normal ovaries (Figure 2-figure supplement 4), indicating that the mechanism we uncovered also protects nurse cells from death during normal oogenesis.

      (2) The phenotype of "degenerating ovaries" is very broad, and the study is not focused on phenotypes at the cellular level. Furthermore, no information is provided in the Materials and Methods on how degenerating ovaries are scored, despite this being the most important assay in the study.

      Thanks for pointing out this issue. We quantified the phenotype of nurse cell death using “degrading/total egg chambers per ovary”, not “degenerating ovaries” (see all quantification data in our manuscript). Notably, this phenotype ranges from mild to severe. In normal nurse cells, nuclei exhibit a large, round morphology in DAPI staining (see the first panel in Figure 1D). During early death, nurse cell nuclei become disorganized and begin to condense and fragment (see the third panel in Figure 2-figure supplement 2E). In late-stage death, the nuclei are completely fragmented into small, condensed spherical structures (see the second panel in Figure 1D), making cellular-level phenotypic quantification impossible. Since all nurse cells within the same egg chamber are interconnected, their death process is synchronous. Thus, quantifying the phenotype at the egg-chamber level is more practical than at the cellular level. To improve clarity, we will provide a detailed description of the phenotype and integrate this explanation into the main text of the revised manuscript.

      (3) In Figure 5, the authors want to conclude that uev1a is a tumor-suppressor, and so they over-express ubev1/2 in human cancer cell lines that have RasK12 and find reduced proliferation, colony formation, and xenograft size. However, genes that act as tumor suppressors have loss-of-function phenotypes that allow for increased cell division. The Drosophila uev1a mutant is viable and fertile, suggesting that it is not a tumor suppressor in flies. Additionally, they do not deplete human ubev1/2 from human cancer cell lines and assess whether this increases cell division, colony formation, and xenograph growth.

      We apologize for our misleading description. In Figure 5, we aimed to demonstrate that UBE2V1/2, like Uev1A in Drosophilanos>Ras<sup>G12V</sup>+bam-RNAi” germline tumors (Figure 4), suppress oncogenic KRAS-driven overgrowth in diploid human cancer cells. Importantly, this function of Uev1A and UBE2V1/2 is dependent on Ras-driven tumors; there is no evidence that they act as broad tumor suppressors in the absence of oncogenic Ras. Drosophila uev1a mutants were lethal, not viable (see Lines 131-133), and germline-specific knockdown of uev1a (nos>uev1a-RNAi) caused female sterility without inducing tumors. These findings suggest that Uev1A lacks tumor-suppressive activity in the Drosophila female germline in the absence of Ras-driven tumors. We will revise the manuscript to prevent misinterpretation. Furthermore, we will investigate whether depletion of UBE2V1, UBE2V2, or both promotes oncogenic KRAS-driven overgrowth in human cancer cells.

      (4) A critical part of the model does not make sense. CycA is a key part of their model, but they do not show CycA protein expression in WT egg chambers or in their over-expression models (nos.RasV12 or bam>RasV12). Based on Lilly and Spradling 1996, Cyclin A is not expressed in germ cells in region 2-3 of the germarium; whether CycA is expressed in nurse cells in later egg chambers is not shown but is critical to document comprehensively.

      We appreciate this critical comment. CycA is a key cyclin that partners with Cdk1 to promote cell division (Edgar and Lehner, 1996). Notably, nurse cells are post-mitotic endocycling cells (Hammond and Laird, 1985) and typically do not express CycA (Lilly and Spradling, 1996) (see the last sentence, page 2518, paragraph 3). However, their death induced by oncogenic Ras<sup>G12V</sup> is significantly suppressed by monoallelic deletion of either cycA or cdk1 (Zhang et al., 2024). Conversely, ectopic CycA expression in nurse cells triggers their death (Figure 2C, 2D). These findings suggest that polyploid nurse cells exhibit high sensitivity to aberrant division-promoting stress, which may represent a distinct form of cellular stress unique to polyploid cells. To further test our model, we will compare CycA expression levels in normal nurse cells versus those undergoing oncogenic Ras<sup>G12V</sup>-induced cell death.

      (5) The authors should provide more information about the knowledge base of uev1a and its homologs in the introduction.

      Thanks for this suggestion. We will include this information in the introduction of the revised manuscript.

      Reviewer #2 (Public review):

      Summary:

      The authors performed a genetic screen using deficiency lines and identified Uev1a as a factor that protects nurse cells from Ras<sup>G12V</sup>-induced cell death. According to a previous study from the same lab, this cell death is caused by aberrant mitotic stress due to CycA upregulation (Zhang et al.). This paper further reveals that Uev1a forms a complex with APC/C to promote proteasome-mediated degradation of CycA.

      In addition to polyploid nurse cells, the authors also examined the effect of Ras<sup>G12V</sup>-overexpression in diploid germline cells, where Ras<sup>G12V</sup>-overexpression triggers active proliferation, not cell death. Uev1a was found to suppress its overgrowth as well.

      Finally, the authors show that the overexpression of the human homologs, UBE2V1 and UBE2V2, suppresses tumor growth in human colorectal cancer xenografts and cell lines. Notably, the expression of these genes correlates with the survival of colorectal cancer patients carrying the Ras mutation.

      Strength:

      This paper presents a significant finding that UBE2V1/2 may serve as a potential therapy for cancers harboring Ras mutations. The authors propose a fascinating mechanism in which Uev1a forms a complex with APC/C to inhibit aberrant cell cycle progression.

      We greatly appreciate these comments.

      Weakness:

      The quantification of some crucial experiments lacks sufficient clarity.

      Thanks for highlighting this issue. We will provide requested details regarding these quantification data in the revised manuscript.

      References

      Edgar, B.A., and Lehner, C.F. (1996). Developmental control of cell cycle regulators: a fly's perspective. Science 274, 1646-1652.

      Hammond, M.P., and Laird, C.D. (1985). Chromosome structure and DNA replication in nurse and follicle cells of Drosophila melanogaster. Chromosoma 91, 267-278.

      Lilly, M.A., and Spradling, A.C. (1996). The Drosophila endocycle is controlled by Cyclin E and lacks a checkpoint ensuring S-phase completion. Genes Dev 10, 2514-2526.

      Zhang, Q., Wang, Y., Bu, Z., Zhang, Y., Zhang, Q., Li, L., Yan, L., Wang, Y., and Zhao, S. (2024). Ras promotes germline stem cell division in Drosophila ovaries. Stem Cell Reports 19, 1205-1216.

    1. Author response:

      We sincerely thank the reviewers and editors for their thoughtful and constructive evaluation of our manuscript and their recognition of its technical strengths, including advanced spatio-temporal Ca2+ imaging, image processing, and the rational design of selective AVP receptor ligands. We appreciate their acknowledgement that our study contributes to the understanding of glucose-dependent AVP effects in pancreatic islet physiology. Their comments will guide us to refine the scope of our work, which focuses on how α and β cells respond to AVP under varying glucose and hormonal conditions, rather than on linear correlations between the function and transcript levels in individual cells or metabolic profiles in individual cell. Most of the reviewers´ concerns and proposed remedies reflect a reductionist framework, for which we believe cannot not fully account for emergent behavior within the islet collective. As we and others have shown, islet cells do not behave in isolation; their responses often depend on the state of the entire cell population(1, 2). This means that even under identical experimental conditions, responses can differ depending on the islet’s current state. These patterns are not random, but reflect how the islet integrates signals dynamically(3, 4).

      To take advantage of both the systems and molecular side, we do plan to address several of the reviewers' suggestions with new experiments and analyses:

      First, we will add hormone, specifically glucagon, secretion assays to support our conclusions on α cell responses and possible paracrine effects. Second, we will include a targeted transcript analysis of V1bR using RNAscope and extend the pharmacological characterization of downstream signaling using selective agonists and inhibitors. Third, we will clarify the rationale for using forskolin, and added new experiments using GLP-1 analogues to selectively increase cAMP in β cells, allowing us to examine direct AVP effects. And fourth, we will reinforce presence of emergency and that variability in islet responses is not experimental noise, but a hallmark of the collective, non-linear behavior of the islet cell collective, which should later drive a rethinking of experimental designs and the interpretation of pharmacological responses. In conclusion, we believe that our study provides new insights into AVP modulation in pancreatic islets and highlights the importance of context-dependent responses in α and β cells. We are grateful for the opportunity to revise our manuscript and look forward to further strengthening it further through the review process.

      (1) Jin E, Briggs JK, Benninger RKP, Merrins MJ. Glucokinase activity controls peripherally-located subpopulations of β-cells that lead islet Ca2+ oscillations. eLife Sciences Publications, Ltd; 2025.

      (2) Korošak D, Jusup M, Podobnik B, Stožer A, Dolenšek J, Holme P, et al. Autopoietic Influence Hierarchies in Pancreatic β Cells. Phys Rev Lett. 2021;127(16):168101.

      (3) Ball P. How life works : a user's guide to the new biology. Chicago: The University of Chicago Press; 2023. 541 pages p.

      (4) Fancher S, Mugler A. Fundamental Limits to Collective Concentration Sensing in Cell Populations. Phys Rev Lett. 2017;118(7):078101.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      The authors present exciting new experimental data on the antigenic recognition of 78 H3N2 strains (from the beginning of the 2023 Northern Hemisphere season) against a set of 150 serum samples. The authors compare protection profiles of individual sera and find that the antigenic effect of amino acid substitutions at specific sites depends on the immune class of the sera, differentiating between children and adults. Person-to-person heterogeneity in the measured titers is strong, specifically in the group of children's sera. The authors find that the fraction of sera with low titers correlates with the inferred growth rate using maximum likelihood regression (MLR), a correlation that does not hold for pooled sera. The authors then measure the protection profile of the sera against historical vaccine strains and find that it can be explained by birth cohort for children. Finally, the authors present data comparing pre- and post- vaccination protection profiles for 39 (USA) and 8 (Australia) adults. The data shows a cohort-specific vaccination effect as measured by the average titer increase, and also a virus-specific vaccination effect for the historical vaccine strains. The generated data is shared by the authors and they also note that these methods can be applied to inform the bi-annual vaccine composition meetings, which could be highly valuable.

      Thanks for this nice summary of our paper.

      The following points could be addressed in a revision:

      (1) The authors conclude that much of the person-to-person and strain-to-strain variation seems idiosyncratic to individual sera rather than age groups. This point is not yet fully convincing. While the mean titer of an individual may be idiosyncratic to the individual sera, the strain-to-strain variation still reveals some patterns that are consistent across individuals (the authors note the effects of substitutions at sites 145 and 275/276). A more detailed analysis, removing the individual-specific mean titer, could still show shared patterns in groups of individuals that are not necessarily defined by the birth cohort.

      As the reviewer suggests, we normalized the titers for all sera to the geometric mean titer for each individual in the US-based pre-vaccination adults and children. This is only for the 2023-circulating viral strains. We then faceted these normalized titers by the same age groups we used in Figure 6, and the resulting plot is shown below. Although there are differences among virus strains (some are better neutralized than others), there are not obvious age group-specific patterns (eg, the trends in the two facets are similar). To us this suggests that at least for these relatively closely related recent H3N2 strains, the strain-to-strain variation does not obviously segregate by age group. Obviously, it is possible (we think likely) that there would be more obvious age-group specific trends if we looked at a larger swath of viral strains covering a longer time range (eg, over decades of influenza evolution). We plan to add the new plots shown below to a supplemental figure in the revised manuscript.

      Author response image 1.

      Author response image 2.

      (2) The authors show that the fraction of sera with a titer below 138 correlates strongly with the inferred growth rate using MLR. However, the authors also note that there exists a strong correlation between the MLR growth rate and the number of HA1 mutations. This analysis does not yet show that the titers provide substantially more information about the evolutionary success. The actual relation between the measured titers and fitness is certainly more subtle than suggested by the correlation plot in Figure 5. For example, the clades A/Massachusetts and A/Sydney both have a positive fitness at the beginning of 2023, but A/Massachusetts has substantially higher relative fitness than A/Sydney. The growth inference in Figure 5b does not appear to map that difference, and the antigenic data would give the opposite ranking. Similarly, the clades A/Massachusetts and A/Ontario have both positive relative fitness, as correctly identified by the antigenic ranking, but at quite different times (i.e., in different contexts of competing clades). Other clades, like A/St. Petersburg are assigned high growth and high escape but remain at low frequency throughout. Some mention of these effects not mapped by the analysis may be appropriate.

      Thanks for the nice summary of our findings in Figure 5. However, the reviewer is misreading the growth charts when they say that A/Massachusetts/18/2022 has a substantially higher fitness than A/Sydney/332/2023. Figure 5a shows the frequency trajectory of different variants over time. While A/Massachusetts/18/2022 reaches a higher frequency than A/Sydney/332/2023, the trajectory is similar and the reason that A/Massachusetts/18/2022 reached a higher max frequency is that it started at a higher frequency at the beginning of 2023. The MLR growth rate estimates differ from the maximum absolute frequency reached: instead, they reflect how rapidly each strain grows relative to others. In fact, A/Massachusetts/18/2022 and A/Sydney/332/2023 have similar growth rates, as shown in Supplementary Figure 6b. Similarly, A/Saint-Petersburg/RII-166/2023 starts at a low initial frequency but then grows even as A/Massachusetts/18/2022 and A/Sydney/332/2023 are declining, and so has a higher growth rate than both of those. In the revised manuscript, we will clarify how viral growth rates are estimated from frequency trajectories, and how growth rate differs from max frequency.

      (3) For the protection profile against the vaccine strains, the authors find for the adult cohort that the highest titer is always against the oldest vaccine strain tested, which is A/Texas/50/2012. However, the adult sera do not show an increase in titer towards older strains, but only a peak at A/Texas. Therefore, it could be that this is a virus-specific effect, rather than a property of the protection profile. Could the authors test with one older vaccine virus (A/Perth/16/2009?) whether this really can be a general property?

      We are interested in studying immune imprinting more thoroughly using sequencing-based neutralization assays, but we note that the adults in the cohorts we studied would have been imprinted with much older strains than included in this library. As this paper focuses on the relative fitness of contemporary strains with minor secondary points regarding imprinting, these experiments are beyond the scope of this study. We’re excited for future work (from our group or others) to explore these points by making a new virus library with strains from multiple decades of influenza evolution.

      Reviewer #2 (Public review):

      This is an excellent paper. The ability to measure the immune response to multiple viruses in parallel is a major advancement for the field, which will be relevant across pathogens (assuming the assay can be appropriately adapted). I only have a few comments, focused on maximising the information provided by the sera.

      Thanks very much!

      Firstly, one of the major findings is that there is wide heterogeneity in responses across individuals. However, we could expect that individuals' responses should be at least correlated across the viruses considered, especially when individuals are of a similar age. It would be interesting to quantify the correlation in responses as a function of the difference in ages between pairs of individuals. I am also left wondering what the potential drivers of the differences in responses are, with age being presumably key. It would be interesting to explore individual factors associated with responses to specific viruses (beyond simply comparing adults versus children).

      We’re excited by this idea! We plan to include these analyses in our revised pre-print.

      Relatedly, is the phylogenetic distance between pairs of viruses associated with similarity in responses?

      As above, we like this idea and our revised pre-print will include this analysis.

      Figure 5C is also a really interesting result. To be able to predict growth rates based on titers in the sera is fascinating. As touched upon in the discussion, I suspect it is really dependent on the representativeness of the sera of the population (so, e.g., if only elderly individuals provided sera, it would be a different result than if only children provided samples). It may be interesting to compare different hypotheses - so e.g., see if a population-weighted titer is even better correlated with fitness - so the contribution from each individual's titer is linked to a number of individuals of that age in the population. Alternatively, maybe only the titers in younger individuals are most relevant to fitness, etc.

      We’re very interested in these analyses, but suggest they may be better explored in subsequent works that could sample more children, teenagers and adults across age groups. Our sera set, as the reviewer suggests, may be under-powered to perform the proposed analysis on subsetted age groups of our larger age cohorts.

      In Figure 6, the authors lump together individuals within 10-year age categories - however, this is potentially throwing away the nuances of what is happening at individual ages, especially for the children, where the measured viruses cross different groups. I realise the numbers are small and the viruses only come from a small numbers of years, however, it may be preferable to order all the individuals by age (y-axis) and the viral responses in ascending order (x-axis) and plot the response as a heatmap. As currently plotted, it is difficult to compare across panels

      This is a good suggestion, and a revised pre-print will include heatmaps of the different cohorts, ordered by ages of individuals.

      Reviewer #3 (Public review):

      The authors use high-throughput neutralisation data to explore how different summary statistics for population immune responses relate to strain success, as measured by growth rate during the 2023 season. The question of how serological measurements relate to epidemic growth is an important one, and I thought the authors present a thoughtful analysis tackling this question, with some clear figures. In particular, they found that stratifying the population based on the magnitude of their antibody titres correlates more with strain growth than using measurements derived from pooled serum data. However, there are some areas where I thought the work could be more strongly motivated and linked together. In particular, how the vaccine responses in US and Australia in Figures 6-7 relate to the earlier analysis around growth rates, and what we would expect the relationship between growth rate and population immunity to be based on epidemic theory.

      Thank you for this nice summary. This reviewer also notes that the text related to figures 6 and 7 are more secondary to the main story presented in figures 3-5. The main motivation for including figures 6 and 7 were to demonstrate the wide-ranging applications of sequencing-based neutralization data, and this can certainly be clarified in minor text revisions.

    1. Author response:

      The following is the authors’ response to the original reviews

      eLife Assessment

      This valuable study investigates prey capture by archer fish, showing that even though the visuomotor behavior unfolds very rapidly (within 40-70 ms), it is not hardwired; it can adapt to different simulated physics and different prey shapes. Although there was agreement that the model system, experimental design, and main hypothesis are certainly interesting, opinions were divided on whether the evidence supporting the central claims is incomplete. A more rigorous definition and assessment of "reflex speed", more detailed evidence of stimulus control, and a more detailed analysis of individual subjects could potentially increase confidence in the main conclusions.

      Thank you very much. There are several points that we had to absolutely make sure that they are very well understood. (1) Explaining in the best possible way the experiment with a fly sliding on top of a glass plate. Here, the virtual ballistic landing point can be calculated using simple high school physics. It turns out that this is where the fish turn to – even though the fly is not falling at all. Once this is understood it becomes clear that we can precisely measure latency and accuracy of the C-start turns. In the new version we explain this essential aspect in more detail and add an extra Figure (new Figure 2). This may, perhaps, help readers to notice this important background (previously covered in Fig. 1C). (2) The full experimental evidence that the VR method works is presented in more detail and all measurements necessary will be clear after the new Figure 2. They will however not be clear if this Figure is ignored. (3) We have rewritten the manuscript to make it easier to understand what we wanted to show, why we needed VR to proceed and why the archerfish highspeed decision lent itself so readily to tackle the problem. (4) We emphasize the importance of speed-accuracy tradeoffs in standard decision-making and also include data on the absence of such a relation in the archerfish highspeed decisions.

      So, in summary, we have emphasized what we wanted to show and what we did not want to show, we have rewritten the text to make it easier for future readers and we have tried to add more guidance to the figures. We do hope very much that the beauty of the quite unexpected findings is more easily visible to those who take the trouble of actually reading the paper.  

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors test whether the archerfish can modulate the fast response to a falling target. By manipulating the trajectory of the target, they claim that the fish can modulate the fast response. While it is clear from the result that the fish can modulate the fast response, the experimental support for the argument that the fish can do it for a reflex-like behavior is inadequate.

      Please note that we have not simply tested whether archerfish can 'modulate the fast response'. We quantitatively test specific hypotheses on the rules used by the fish. For this the accuracy of the decisions is analyzed with respect to specific points that can be calculated precisely in each of the experiments. These points are shown on the figures and in the movies that were meant to illustrate this important aspect. We had to make sure that the way we calculate the predicted point(s) is made as clear as possible in the text. We added more text and separated the fundamentally important aspects in a separate Figure 2 to make it more difficult to overlook the fundamental aspects that lay the foundation for everything that follows.

      Strengths:

      Overall, the question that the authors raised in the manuscript is interesting.

      Thank you and we do hope very much that, with our revision, you will see the beauty of the findings.

      Weaknesses:

      (1) The argument that the fish can modulate reflex-like behavior relies on the claim that the archerfish makes the decision in 40 ms. There is little support for the 40 ms reaction time. The reaction time for the same behavior in Schlegel 2008, is 6070 ms, and in Tsvilling 2012 about 75 ms, if we take the half height of the maximum as the estimated reaction time in both cases. If we take the peak (or average) of the distribution as an estimation of reaction time, the reaction time is even longer. This number is critical for the analysis the authors perform since if the reaction time is longer, maybe this is not a reflex as claimed. In addition, mentioning the 40 ms in the abstract is overselling the result. The title is also not supported by the results.

      Although the minimum latency is indeed 40 ms (it can be slightly less: e.g., see the evidence in the paper, for instance the plots in the new Fig. 4) the paper's statements are not dependent on a specific number. Even if minimum latency was 100 ms (which it is not) the speed of the response and the absence of a speedaccuracy relation (now shown directly in Fig. 4) is what is of importance. To show this we have completely rewritten large parts of the manuscript.

      (2) A critical technical issue of the stimulus delivery is not clear. The frame rate is 120 FPS and the target horizontal speed can be up to 1.775 m/s. This produces a target jumping on the screen 15 mm in each frame. This is not a continuous motion. Thus, the similarity between the natural system where the target experiences ballistic trajectory and the experiment here is not clear. Ideally, another type of stimulus delivery system is needed for a project of this kind that requires fast-moving targets (e.g. Reiser, J. Neurosci.Meth. 2008). In addition, the screen is rectangular and not circular, so in some directions, the target vanishes earlier than others. It must produce a bias in the fish response but there is no analysis of this type.

      Please note that the new Fig. 3 (former Fig. 2) reports all the evidence that is needed to just show this and in a way that could in no way have been better. We have rewritten the text to explain what needs to be shown experimentally in order to be able to proceed, what critical tests were done and what results were obtained. We also add a short comment on another unsuccessful attempt that we have tried before.

      (3) The results here rely on the ability to measure the error of response in the case of a virtual experiment. It is not clear how this is done since the virtual target does not fall. How do the authors validate that the fish indeed perceives the virtual target as the falling target? Since the deflection is at a later stage of the virtual trajectory, it is not clear what is the actual physics that governs the world of the experiment. Overall, the experimental setup is not well designed.

      Understanding this aspect is essential. If the glass plate experiment is not thoroughly understood (new Fig. 2 with new text to emphasize that this is absolutely essential) nothing that follows makes any sense, including what is meant by the statement that the decision could be hardwired to ballistic motion.

      Reviewer #2 (Public review):

      Summary:

      This manuscript studies prey capture by archer fish, which observe the initial values of motion of aerial prey they made fall by spitting on them, and then rapidly turn to reach the ballistic landing point on the water surface. The question raised by the article is whether this incredibly fast decision-making process is hardwired and thus unmodifiable or can be adjusted by experience to follow a new rule, namely that the landing point is deflected from a certain amount of the expected ballistic landing point. The results show that the fish learn the new rule and use it afterward in a variety of novel situations that include height, side, and speed of the prey, and which preserve the speed of the fish's decision. Moreover, a remarkable finding presented in this work is the fact that fish that have learned to use the new rule can relearn to use the ballistic landing point for an object based on its shape (a triangle) while keeping simultaneously the 'deflected rule' for an object differing in shape (a disc); in other words, fish can master simultaneously two decisionmaking rules based on the different shape of objects.

      Strengths:

      The manuscript relies on a sophisticated and clever experimental design that allows changing the apparent landing point of a virtual prey using a virtual reality system. Several robust controls are provided to demonstrate the reliability and usefulness of the experimental setup.

      Overall, I very much like the idea conveyed by the authors that even stimuli triggering apparently hardwired responses can be relearned in order to be associated with a different response, thus showing the impressive flexibility of circuits that are sometimes considered mediating pure reflexive responses.

      Thank you so much for this precise assessment of what we have shown!

      This is the case - as an additional example - of the main component of the Nasanov pheromone of bees (geraniol), which triggers immediate reflexive attraction and appetitive responses, and which can, nevertheless, be learned by bees in association with an electric shock so that bees end up exhibiting avoidance and the aversive response of sting extension to this odorant (1), which is a fully unnatural situation, and which shows that associative aversive learning is strong enough to override preprogrammed responding, thus reflecting an impressive behavioral flexibility.

      That's very interesting, thanks and we are very happy to mention this important study in the revised version.

      Weaknesses:

      As a general remark, there is some information that I missed and that is mandatory in the analysis of behavioral changes.

      Firstly, the variability in the performances displayed. The authors mentioned that the results reported come from 6 fish (which is a low sample size). How were the individual performances in terms of consistency? Were all fish equally good in adjusting/learning the new rule? How did errors vary according to individual identity? It seems to me that this kind of information should be available as the authors reported that individual fish could be recognized and tracked (see lines 620-635) and is essential for appreciating the flexibility of the system under study.

      Secondly, the speed of the learning process is not properly explained. Admittedly, fish learn in an impressive way the new rule and even two rules simultaneously; yet, how long did they need to achieve this? In the article, Figure 2 mentions that at least 6 training stages (each defined as a block of 60 evaluated turn decisions, which actually shows that the standard term 'Training Block' would be more appropriate) were required for the fish to learn the 'deflected rule'. While this means 360 trials (turning starts), I was left with the question of how long this process lasted. How many hours, days, and weeks were needed for the fish to learn? And as mentioned above, were all fish equally fast in learning? I would appreciate explaining this very important point because learning dynamics is relevant to understanding the flexibility of the system.

      First, it is very important to keep the question in mind that we wanted to clarify: Does the system have the potential to re-tune the decisions to other non-ballistic relations between the input variables and the output? This would have been established if one fish was found capable of doing that. We have rewritten the introduction and discussion to specifically say what our aim was. We feel that the paper is already extremely long and difficult to understand (even after we tried very hard in this revision to explain everything in detail and as good as we could), requires the establishment of a method whose success was really unexpected and finding a degree of plasticity that we did not expect at all. We also have added a section in the discussion stating what we can, and we cannot say given the number of fish examined. For instance, we do not know if there are differences in the speed at which the different individuals mastered the new rules and if social learning could play a role to speed up the acquisition. That is a brilliant idea and we are very interested in checking this - but we wanted to stick with the (quite ambitious) goal of the present study.

      Reference:

      (1) Roussel, E., Padie, S. & Giurfa, M. Aversive learning overcomes appetitive innate responding in honeybees. Anim Cogn 15, 135-141, doi:10.1007/s10071011-0426-1 (2012).

      Thanks for this reference!

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Minor comments:

      (1) What is the difference between Reinel, J. Exp. Bio. 2016 and the current study?

      Clearly in that study all objects were strictly falling ballistically, and latency and accuracy of the turn decisions were determined when the initial motion was not only horizontal but had an additional vertical component of speed. The question of that study was if the need to account to an additional variable (vertical speed) in the decision would affect its latency or accuracy. The study showed that also then archerfish rapidly turn to the later impact point. It also showed that accuracy and latency were not changed by the added degree of freedom.

      (2) How do Figures 2 F and G demonstrate that an accurate start is possible?

      See above.

      (3) Figure 4 is hard to follow, it is not clear what is presented and how it supports the claim that the new rule is represented in a way that allows immediate generalization.

      Yes, this is not at all an easy experiment. Briefly, fish were re-trained at only one height level and then are tested at other levels. The strategy is as in the experiments Schuster et al. 2004 Current Biology, Vol. 14, 1565–1568, Figure 5. We have changed text and Figure (new Figure 5) to show how the predictions were reached.

      Reviewer #2 (Recommendations for the authors):

      Minor remarks

      Lines 88-90: I was surprised to see that in this section, the authors did not mention the speed-accuracy trade-off off which has inspired numerous experiments in animal behavior (1). This could be used to back their point, namely, that speed comes with an apparent cost of a loss in accuracy.

      Yes, that is a crucial aspect that was completely missing even though it demonstrates a key aspect of 'standard' versus some 'highspeed' decisions! We definitely had to include it and also to show, directly under the conditions of our present experiments (in the new Fig. 4) the absence of a significant speedaccuracy relation for the archerfish highspeed decisions! Thank you very much for emphasizing this crucial aspect!

      Lines 182-184: Specify that this situation corresponds to the hatched bar in Figure (this can be specified in the caption of the figure, where the bar is not mentioned).

      Thanks!

      Lines 187-188: here and elsewhere (e.g. lines 224-225, etc), the error made by the fish is presented in cm (see Figure 2 where the inset shows how the error was computed). I wonder if it would not be more appropriate to present it in terms of the angular difference between the trajectory made by the fish and the food delivery location.

      Angles could also be used, but because of the large variation in initial distances (that we wanted to make sure that the fish had to capture a rule, allowing them to respond from various distances) another measure was used that we found somehow more natural: it is simply how close a fish would get to the landing point if it continued in the direction assumed after the turn. Although we describe how we defined accuracy we did not discuss why this measure was used in this (and many previous studies). We are very happy to add this. Please also note that running all tests based on angular errors (which we also have done throughout to ensure that the conclusions are independent on an arbitrary measure of the error) leads to no different conclusion. We have added a brief explanation in the text and in the new Fig. 2.

      Lines 299-323: Is it my impression or did fish have more trouble in generalizing their learned rule to the condition untrained larger height (see for instance red curves in Figures 4 D, E, G)? Could the authors elaborate on this point?

      We changed the code to make this more clear. The red curves (before marked A to highlight impact point option A) correspond to the errors to the ballistic impact point without deflection, so what would have to be compared are the black curves (marked P to highlight the virtual impact point that should be chosen had the fish immediately generated to the untrained conditions). We have rewritten the text and the labels in the Figure (now Figure 5) to illustrate the predictions and to name them in more helpful ways and so that they can't be confused with panel labels. At any rate, what needs to be compared, to check the idea, are the black curves, and these are not statistically different between both heights (p=0.525, Mann-Whitney). Interestingly, none of the black curves from all panels (D-G) differ (p>0.3).

      Line 559: if we are speaking here about luminance contrast, it should read 'Michelson Contrast' rather than 'Michelsen Contrast'.

      Absolutely, thanks!

      References

      (1) Chittka, L., Skorupski, P. & Raine, N. E. Speed-accuracy tradeoffs in animal decision making. Trends Ecol Evol 24, 400-407, doi:10.1016/j.tree.2009.02.010 (2009).

      An excellent paper that helps to stress our main question

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      In this study, the authors aim to understand why decision formation during behavioural tasks is distributed across multiple brain areas. They hypothesize that multiple areas are used in order to implement an information bottleneck (IB). Using neural activity recorded from monkey DLPFC and PMd performing a 2-AFC task, they show that DLPFC represents various task variables (decision, color, target configuration), while downstream PMd primarily represents decision information. Since decision information is the only information needed to make a decision, the authors point out that PMd has a minimal sufficient representation (as expected from an IB). They then train 3-area RNNs on the same task and show that activity in the first and third areas resemble the neural representations of DLPFC and PMd, respectively. In order to propose a mechanism, they analyse the RNN and find that area 3 ends up with primarily decision information because feedforward connections between areas primarily propagate decision information.

      The paper addresses a deep, normative question, namely why task information is distributed across several areas.

      Overall, it reads well and the analysis is well done and mostly correct (see below for some comments). My major problem with the paper is that I do not see that it actually provides an answer to the question posed (why is information distributed across areas?). I find that the core problem is that the information bottleneck method, which is evoked throughout the paper, is simply a generic compression method.

      Being a generic compressor, the IB does not make any statements about how a particular compression should be distributed across brain areas - see major points (1) and (2).

      If I ignore the reference to the information bottleneck and the question of why pieces of information are distributed, I still see a more mechanistic study that proposes a neural mechanism of how decisions are formed, in the tradition of RNN-modelling of neural activity as in Mante et al 2013. Seen through this more limited sense, the present study succeeds at pointing out a good model-data match, and I could support a publication along those lines. I point out some suggestions for improvement below.

      We thank the reviewer for their comments, feedback and suggestions. We are glad to hear you support the good model-data match for this manuscript.  With your helpful comments, we have clarified the connections to the information bottleneck principle and also contrasted it against the information maximization principle (the InfoMax principle), an alternative hypothesis. We elaborate on these issues in response to your points below, particularly major points (1) and (2). We also address all your other comments below.

      Major points

      (1) It seems to me that the author's use of the IB is based on the reasoning that deep neural networks form decisions by passing task information through a series of transformations/layers/areas and that these deep nets have been shown to implement an IB. Furthermore, these transformations are also loosely motivated by the data processing inequality.

      On Major Point 1 and these following subpoints, we first want to make a high-level statement before delving into a detailed response to your points as it relates to the information bottleneck (IB). We hope this high-level statement will provide helpful context for the rest of our point-by-point responses. 

      We want to be clear that we draw on the information bottleneck (IB) principle as a general principle to explain why cortical representations differ by brain area. The IB principle, as applied to cortex, is only stating that a minimal sufficient representation to perform the task is formed in cortex, not how it is formed. The alternative hypothesis to the IB is that brain areas do not form minimal sufficient representations. For example, the InfoMax principle states that each brain area stores information about all inputs (even if they’re not necessary to perform the task). InfoMax isn’t unreasonable: it’s possible that storing as much information about the inputs, even in downstream areas, can support flexible computation and InfoMax also supports redundancy in cortical areas. Indeed, many studies claim that action choice related signals are in many cortical areas, which may reflect evidence of an InfoMax principle in action for areas upstream of PMd.

      While we observe an IB in deep neural networks and cortex in our perceptual decision-making task, we stress that its emergence across multiple areas is an empirical result. At the same time, multiple areas producing an IB makes intuitive sense: due to the data processing inequality, successive transformations typically decrease the information in a representation (especially when, e.g., in neural networks, every activation passes through the Relu function, which is not bijective). Multiple areas are therefore a sufficient and even ‘natural’ way to implement an IB, but multiple areas are not necessary for an IB. That we observe an IB in deep neural networks and cortex emerge through multi-area computation is empirical, and, contrasting InfoMax, we believe it is an important result of this paper. 

      Nevertheless, your incisive comments have helped us to update the manuscript that when we talk about the IB, we should be clear that the alternative hypothesis is non-minimal representations, a prominent example of which is the InfoMax principle. We have now significantly revised our introduction to avoid this confusion. We hope this provides helpful context for our point-by-point replies, below.

      However, assuming as a given that deep neural networks implement an IB does not mean that an IB can only be implemented through a deep neural network. In fact, IBs could be performed with a single transformation just as well. More formally, a task associates stimuli (X) with required responses (Y), and the IB principle states that X should be mapped to a representation Z, such that I(X;Z) is minimal and I(Y,Z) is maximal. Importantly, the form of the map Z=f(X) is not constrained by the IB. In other words, the IB does not impose that there needs to be a series of transformations. I therefore do not see how the IB by itself makes any statement about the distribution of information across various brain areas.

      We agree with you that an IB can be implemented in a single transformation. We wish to be clear that we do not intend to argue necessity: that multiple areas are the only way to form minimal sufficient representations. Rather, multiple areas are sufficient to induce minimal sufficient representations, and moreover, they are a natural and reasonably simple way to do so. By ‘natural,’ we mean that minimal sufficient representations empirically arise in systems with multiple areas (more than 2), including deep neural networks and the cortex at least for our task and simulations. For example, we did not see minimal sufficient representations in 1- or 2-area RNNs, but we did see them emerge in RNNs with 3 areas or more. One potential reason for this result is that sequential transformations through multiple areas can never increase information about the input; it can only maintain or reduce information due to the data processing inequality.

      Our finding that multiple areas facilitate IBs in the brain is therefore an empirical result: like in deep neural networks, we observe the brain has minimal sufficient representations that emerge in output areas (PMd), even as an area upstream (DLPFC) is not minimal. While the IB makes a statement that this minimal sufficient representation emerges, to your point, the fact that it emerges over multiple areas is not a part of the IB – as you have pointed out, the IB doesn’t state where or how the information is discarded, only that it is discarded. Our RNN modeling later proposes one potential mechanism for how it is discarded. We updated the manuscript introduction to make these points:

      “An empirical observation from Machine Learning is that deep neural networks tend to form minimal sufficient representations in the last layers. Although multi-layer computation is not necessary for an IB, they provide a sufficient and even “natural” way to form an IB. A representation z = f(x) cannot contain more information than the input x itself due to the data processing inequality[19]. Thus, adding additional layers typically results in representations that contain less information about the input.”

      And later in the introduction:

      “Consistent with these predictions of the IB principle, we found that DLPFC has information about the color, target configuration, and direction. In contrast, PMd had a minimal sufficient representation of the direction choice. Our recordings therefore identified a cortical IB. However, we emphasize the IB does not tell us where or how the minimal sufficient representation is formed. Instead, only our empirical results implicate DLPFC-PMd in an IB computation. Further, to propose a mechanism for how this IB is formed, we trained a multi-area RNN to perform this task. We found that the RNN faithfully reproduced DLPFC and PMd activity, enabling us to propose a mechanism for how cortex uses multiple areas to compute a minimal sufficient representation.”

      In the context of our work, we want to be clear the IB makes these predictions:

      Prediction 1: There exists a downstream area of cortex that has a minimal and sufficient representation to perform a task (i.e.,. I(X;Z) is minimal while preserving task information so that I(Z;Y) is approximately equal to  I(X;Y)). We identify PMd as an area with a minimal sufficient representation in our perceptual-decision-making task. 

      Prediction 2 (corollary if Prediction 1 is true): There exists an upstream brain area that contains more input information than the minimal sufficient area. We identify DLPFC as an upstream area relative to PMd, which indeed has more input information than downstream PMd in our perceptual decision-making task. 

      Note: as you raise in other points, it could have been possible that the IB is implemented early on, e.g., in either the parietal cortex (dorsal stream) or inferotemporal cortex (ventral stream), so that DLPFC and PMd both contained minimal sufficient representations. The fact that it doesn’t is entirely an empirical result from our data. If DLPFC had minimal sufficient representations for the perceptual decision making task, we would have needed to record in other regions to identify brain areas that are consistent with Prediction 2. But, empirically, we found that DLPFC has more input information relative to PMd, and therefore the DLPFC-PMd connection is implicated in the IB process.

      What is the alternative hypothesis to the IB? We want to emphasize: it isn’t single-area computation. It’s that the cortex does not form minimal sufficient representations. For example, an alternative hypothesis (“InfoMax”) would be for all engaged brain areas to form representations that retain all input information. One reason this could be beneficial is because each brain area could support a variety of downstream tasks. In this scenario, PMd would not be minimal, invalidating Prediction 1. However, this is not supported by our empirical observations of the representations in PMd, which has a minimal sufficient representation of the task. We updated our introduction to make this clear:

      “But cortex may not necessarily implement an IB. The alternative hypothesis to IB is that the cortex does not form minimal sufficient representations. One manifestation of this alternative hypothesis is the “InfoMax” principle, where downstream representations are not minimal but rather contain maximal input information22. This means information about task inputs not required to perform the task are present in downstream output areas. Two potential benefits of an InfoMax principle are (1) to increase redundancy in cortical areas and thereby provide fault tolerance, and (2) for each area to support a wide variety of tasks and thereby improve the ability of brain areas to guide many different behaviors. In contrast to InfoMax, the IB principle makes two testable predictions about cortical representations. Prediction 1: there exists a downstream area of cortex that has a minimal and sufficient representation to perform a task (i.e., I(X; Z) is minimal while preserving task information so that I(Z; Y) ≈ I(X; Y)). Prediction 2 (corollary if Prediction 1 is true): there exists an upstream area of cortex that has more task information than the minimal sufficient area.”

      Your review helped us realize we should have been clearer in explaining that these are the key predictions of the IB principle tested in our paper. We also realized we should be much clearer that these predictions aren’t trivial or expected, and there is an alternative hypothesis. We have re-written the introduction of our paper to highlight that the key prediction of the IB is minimal sufficient representations for the task, in contrast to the alternative hypothesis of InfoMax.

      A related problem is that the authors really only evoke the IB to explain the representation in PMd: Fig 2 shows that PMd is almost only showing decision information, and thus one can call this a minimal sufficient representation of the decision (although ignoring substantial condition independent activity).

      However, there is no IB prediction about what the representation of DLPFC should look like.

      Consequently, there is no IB prediction about how information should be distributed across DLPFC and PMd.

      We agree: the IB doesn’t tell us how information is distributed, only that there is a transformation that eventually makes PMd minimal. The fact that we find input information in DLPFC reflects that this computation occurs across areas, and is an empirical characterization of this IB in that DLPFC has direction, color and context information while PMd has primarily direction information. To be clear: only our empirical recordings verified that the DLPFC-PMd circuit is involved in the IB. As described above, if not, we would have recorded even further upstream to identify an inter-areal connection implicated in the IB.

      We updated the text to clearly state that the IB predicts that an upstream area’s activity should contain more information about the task inputs. We now explicitly describe this in the introduction, copy and pasted again here for convenience.

      “In contrast to InfoMax, the IB principle makes two testable predictions about cortical representations. Prediction 1: there exists a downstream area of cortex that has a minimal and sufficient representation to perform a task (i.e., I(X; Z) is minimal while preserving task information so that I(Z; Y) ≈ I(X; Y)). Prediction 2 (corollary if Prediction 1 is true): there exists an upstream area of cortex that has more task information than the minimal sufficient area.

      Consistent with the predictions of the IB principle, we found that DLPFC has information about the color, target configuration, and direction. In contrast, PMd had a minimal sufficient representation of the direction choice. Our recordings therefore identified a cortical IB. However, we emphasize the IB does not tell us where or how the minimal sufficient representation is formed. Instead, only our empirical results implicate DLPFC-PMd in an IB computation Further, to propose a mechanism for how this IB is formed, we trained a multi-area RNN to perform this task.”  

      The only way we knew DLPFC was not minimal was through our experiments. Please also note that the IB principle does not describe how information could be lost between areas or layers, whereas our RNN simulations show that this may occur through preferential propagation of task-relevant information with respect to the inter-area connections.  

      (2) Now the authors could change their argument and state that what is really needed is an IB with the additional assumption that transformations go through a feedforward network. However, even in this case, I am not sure I understand the need for distributing information in this task. In fact, in both the data and the network model, there is a nice linear readout of the decision information in dPFC (data) or area 1 (network model). Accordingly, the decision readout could occur at this stage already, and there is absolutely no need to tag on another area (PMd, area 2+3).

      Similarly, I noticed that the authors consider 2,3, and 4-area models, but they do not consider a 1-area model. It is not clear why the 1-area model is not considered. Given that e.g. Mante et al, 2013, manage to fit a 1-area model to a task of similar complexity, I would a priori assume that a 1-area RNN would do just as well in solving this task.

      While decision information could indeed be read out in Area 1 in our multi-area model, we were interested in understanding how the network converged to a PMd-like representation (minimal sufficient) for solving this task. Empirically, we only observed a match between our model representations and animal cortical representations during this task when considering multiple areas. Given that we empirically observed that our downstream area had a minimal sufficient representation, our multi-area model allowed how this minimal sufficient representation emerged (through preferential propagation of task-relevant information).

      We also analyzed single-area networks in our initial manuscript, though we could have highlighted these analyses more clearly to be sure they were not overlooked. We are clearer in this revision that we did consider a 1-area network (results in our Fig 5). While a single-area RNN can indeed solve this task, the single area model had all task information present in the representation, and did not match the representations in DLPFC or PMd. It would therefore not allow us to understand how the network converged to a PMd-like representation (minimal sufficient) for solving this task. We updated the schematic in Fig 5 to add in the single-area network (which may have caused the confusion).

      We have added an additional paragraph commenting on this in the discussion. We also added an additional supplementary figure with the PCs of the single area RNN (Fig S15). We highlight that single area RNNs do not resemble PMd activity because they contain strong color and context information. 

      In the discussion:

      “We also found it was possible to solve this task with single area RNNs, although they did not resemble PMd (Figure S15) since it did not form a minimal sufficient representation. Rather, for our RNN simulations, we found that the following components were sufficient to induce minimal sufficient representations: (1) RNNs with at least 3 areas, following Dale’s law (independent of the ratio of feedforward to feedback connections).”

      I think there are two more general problems with the author's approach. First, transformations or hierarchical representations are usually evoked to get information into the right format in a pure feedforward network. An RNN can be seen as an infinitely deep feedforward network, so even a single RNN has, at least in theory, and in contrast to feedforward layers, the power to do arbitrarily complex transformations. Second, the information coming into the network here (color + target) is a classical xor-task. While this task cannot be solved by a perceptron (=single neuron), it also is not that complex either, at least compared to, e.g., the task of distinguishing cats from dogs based on an incoming image in pixel format.

      An RNN can be viewed as an infinitely deep feedforward network in time. However, we wish to clarify two things. First, our task runs for a fixed amount of time, and therefore this RNN in practice is not infinitely deep in time. Second, if it were to perform an IB operation in time, we would expect to see color discriminability decrease as a function of time. Indeed, we considered this as a mechanism (recurrent attenuation, Figure 4a), but as we show in Supplementary Figure S9, we do not observe it to be the case that discriminability decreases through time. This is equivalent to a dynamical mechanism that removes color through successive transformations in time, which our analyses reject (Fig 4). We therefore rule out that an IB is implemented through time via an RNN’s recurrent computation (viewed as feedforward in time). Rather, as we show, the IB comes primarily through inter-areal connections between RNN areas. We clarified that our dynamical hypothesis is equivalent to rejecting the feedforward-in-time filtering hypothesis in the Results: 

      “We first tested the hypothesis that the RNN IB is implemented primarily by recurrent dynamics (left side of Fig. 4a). These recurrent dynamics can be equivalently interpreted as the RNN implementing a feedforward neural network in time.”  

      The reviewer is correct that the task is a classical XOR task and not as complex as e.g., computer vision classification. That said, our related work has looked at IBs for computer vision tasks and found them in deep feedforward networks (Kleinman et al., ICLR 2021). Even though the task is relatively straightforward, we believe it is appropriate for our conclusions because it does not have a trivial minimal sufficient representation: a minimal sufficient representation for XOR must contain only target, but not color or target configuration information. This can only be solved via a nonlinear computation. In this manner, we favor this task because it is relatively simple, and the minimal sufficient representations are interpretable, while at the same time not being so trivially simple (the minimal sufficient representations require nonlinearity to compute).  

      Finally, we want to note that this decision-making task is a logical and straightforward way to add complexity to classical animal decision-making tasks, where stimulus evidence and the behavioral report are frequently correlated. In tasks such as these, it may be challenging to untangle stimulus and behavioral variables, making it impossible to determine if an area like premotor cortex represents only behavior rather than stimulus. However, our task decorrelates both the stimulus and the behaviors. 

      (3) I am convinced of the author's argument that the RNN reproduces key features of the neural data. However, there are some points where the analysis should be improved.

      (a) It seems that dPCA was applied without regularization. Since dPCA can overfit the data, proper regularization is important, so that one can judge, e.g., whether the components of Fig.2g,h are significant, or whether the differences between DLPFC and PMd are significant.

      We note that the dPCA codebase optimizes the regularization hyperparameter through cross-validation and requires single-trial firing rates for all neurons, i.e., data matrices of the form (n_Neurons x Color x Choice x Time x n_Trials), which are unavailable for our data. We recognized that you are fundamentally asking whether differences are significant or not. We therefore believe it is possible to address this through a statistical test, described further below. 

      In order to test whether the differences of variance explained by task variables between DLPFC and PMd are significant, we performed a shuffle test. For this test, we randomly sampled 500 units from the DLPFC dataset and 500 units from the PMd dataset. We then used dPCA to measure the variance explained by target configuration, color choice, and reach direction (e.g., Var<sup>True</sup><sub>DLPFC,Color</sub>, Var<sup>True</sup><sub>PMd,Color</sub>).

      To test if this variance was significant, we performed the following shuffle test. We combined the PMd and DLPFC dataset into a pool of 1000 units and then randomly selected 500 units from this pool to create a surrogate PMd dataset and used the remaining 500 units as a surrogate DLPFC dataset. We then again performed dPCA on these surrogate datasets and estimated the variance for the various task variables (e.g., Var<sub>ShuffledDLPFC,Color</sub>  ,Var<sub>ShuffledPMd,Color</sub>).

      We repeated this process for 100 times and estimated a sampling distribution for the true difference in variance between DLPFC and PMd for various task variables (e.g., Var<sup>True</sup><sub>DLPFC,Color</sub> - Var<sup>True</sup><sub>PMd,Color</sub>). At the same time, we estimated the distribution of the variance difference between surrogate PMd and DLPFC dataset for various task variables (e.g., Var<sub>ShuffleDLPFC,Color</sub> - Var<sub>ShufflePMd,Color</sub>). 

      We defined a p-value as the number of shuffles in which the difference in variance was higher than the median of the true difference and divided it by 100. Note, for resampling and shuffle tests with n shuffles/bootstraps, the lowest theoretical p-value is given as 2/n, even in the case that no shuffle was higher than the median of the true distribution. Thus, the differences were statistically significant (p < 0.02) for color and target configuration but not for direction (p=0.72). These results are reported in Figure S6 and show both the true sampling distribution and the shuffled sampling distributions.

      (b) I would have assumed that the analyses performed on the neural data were identical to the ones performed on the RNN data. However, it looked to me like that was not the case. For instance, dPCA of the neural data is done by restretching randomly timed trials to a median trial. It seemed that this restretching was not performed on the RNN. Maybe that is just an oversight, but it should be clarified. Moreover, the decoding analyses used SVC for the neural data, but a neural-net-based approach for the RNN data. Why the differences?

      Thanks for bringing up these points. We want to clarify that we did include SVM decoding for the multi-area network in the appendix (Fig. S4), and the conclusions are the same. Moreover, in previous work, we also found that training with a linear decoder led to analogous conclusions (Fig. 11 of Kleinman et al, NeurIPS 2021).  As we had a larger amount of trials for the RNN than the monkey, we wanted to allow a more expressive decoder for the RNN, though this choice does not affect our conclusions. We clarified the text to reflect that we did use an SVM decoder.

      “We also found analogous conclusions when using an SVM decoder (Fig. S4).”

      dPCA analysis requires trials of equal length. For the RNN, this is straightforward to generate because we can set the delay lengths to be equal during inference (although the RNN was trained on various length trials and can perform various length trials). Animals must have varying delay periods, or else they will learn the timing of the task and anticipate epoch changes. Because animal trial lengths were therefore different, their trials had to be restretched. We clarified this in the Methods.

      “For analyses of the RNN, we fixed the timing of trials, obviating the need to to restretch trial lengths. Note that while at inference, we generated RNN trials with equal length, the RNN was trained with varying delay periods.” 

      (4) The RNN seems to fit the data quite nicely, so that is interesting. At the same time, the fit seems somewhat serendipitous, or at least, I did not get a good sense of what was needed to make the RNN fit the data. The authors did go to great lengths to fit various network models and turn several knobs on the fit. However, at least to me, there are a few (obvious) knobs that were not tested.

      First, as already mentioned above, why not try to fit a single-area model? I would expect that a single area model could also learn the task - after all, that is what Mante et al did in their 2013 paper and the author's task does not seem any more complex than the task by Mante and colleagues.

      Thank you for bringing up this point. As mentioned in response to your prior point, we did analyze a single-area RNN (Fig. 5d). We updated the schematic to clarify that we analyzed a single area network. Moreover, we also added a supplementary figure to qualitatively visualize the PCs of the single area network (Fig. S15). While a single area network can solve the task, it does not allow us to study how representations change across areas, nor did it empirically resemble our neural recordings. Single-area networks contain significant color, context, and direction information. They therefore do not form minimal representations and do not resemble PMd activity.

      Second, I noticed that the networks fitted are always feedforward-dominated. What happens when feedforward and feedback connections are on an equal footing? Do we still find that only the decision information propagates to the next area? Quite generally, when it comes to attenuating information that is fed into the network (e.g. color), then that is much easier done through feedforward connections (where it can be done in a single pass, through proper alignment or misalignment of the feedforward synapses) than through recurrent connections (where you need to actively cancel the incoming information). So it seems to me that the reason the attenuation occurs in the inter-area connections could simply be because the odds are a priori stacked against recurrent connections. In the real brain, of course, there is no clear evidence that feedforward connections dominate over feedback connections anatomically.

      We want to clarify that we did pick feedforward and feedback connections based on the following macaque atlas, reference 27 in our manuscript: 

      Markov, N. T., Ercsey-Ravasz, M. M., Ribeiro Gomes, A. R., Lamy, C., Magrou, L., Vezoli, J., Misery, P., Falchier, A., Quilodran, R., Gariel, M. A., Sallet, J., Gamanut, R., Huissoud, C., Clavagnier, S., Giroud, P., Sappey-Marinier, D., Barone, P., Dehay, C., Toroczkai, Z., … Kennedy, H. (2014). A weighted and directed interareal connectivity matrix for macaque cerebral cortex. Cerebral Cortex , 24(1), 17–36.

      We therefore believe there is evidence for more feedforward than feedback connections. Nevertheless, as stated in response to your next point below, we ran a simulation where feedback and feedforward connectivity were matched.

      More generally, it would be useful to clarify what exactly is sufficient:

      (a) the information distribution occurs in any RNN, i.e., also in one-area RNNs

      (b) the information distribution occurs when there are several, sparsely connected areas

      (c) the information distribution occurs when there are feedforward-dominated connections between areas

      We better clarify what exactly is sufficient. 

      - We trained single-area RNNs and found that these RNNs contained color information; additionally two area RNNs also contained color information in the last area (Fig 5d). 

      - We indeed found that the minimal sufficient representations emerged when we had several areas, with Dale’s law constraint on the connectivity. When we had even sparser connections, without Dale’s law, there was significantly more color information, even at 1% feedforward connections; Fig 5a.

      - When we matched the percentage of feedforward and feedback connections with Dale’s law constraint on the connectivity (10% feedforward and 10% feedback), we also observed minimal sufficient representations (Fig S9). 

      Together, we found that minimal sufficient representations emerged when we had several areas (3 or greater), with Dale’s law constraint on the connectivity, independent of the ratio of feedforward/feedback connections. We thank the reviewer for raising this point about the space of constraints leading to minimal sufficient representations in the late area. We clarified this in the Discussion.

      “We also found it was possible to solve this task with single area RNNs, although they did not resemble PMd (Figure S15) since it did not form a minimal sufficient representation. Rather, for our RNN simulations, we found that the following components were sufficient to induce minimal sufficient representations: RNNs with at least 3 areas, following Dale’s law (independent of the ratio of feedforward to feedback connections).”

      Thank you for your helpful and constructive comments!

      Reviewer #2 (Public Review):

      Kleinman and colleagues conducted an analysis of two datasets, one recorded from DLPFC in one monkey and the other from PMD in two monkeys. They also performed similar analyses on trained RNNs with various architectures.

      The study revealed four main findings. (1) All task variables (color coherence, target configuration, and choice direction) were found to be encoded in DLPFC. (2) PMD, an area downstream of PFC, only encoded choice direction. (3) These empirical findings align with the celebrated 'information bottleneck principle,' which suggests that FF networks progressively filter out task-irrelevant information. (4) Moreover, similar results were observed in RNNs with three modules.

      We thank the reviewer for their comments, feedback and suggestions, which we address below.

      While the analyses supporting results 1 and 2 were convincing and robust, I have some concerns and recommendations regarding findings 3 and 4, which I will elaborate on below. It is important to note that findings 2 and 4 had already been reported in a previous publication by the same authors (ref. 43).

      Note the NeurIPS paper only had PMd data and did not contain any DLPFC data. That manuscript made predictions about representations and dynamics upstream of PMd, and subsequent experiments reported in this manuscript validated these predictions. Importantly, this manuscript observes an information bottleneck between DLPFC and PMd.

      Major recommendation/comments:

      The interpretation of the empirical findings regarding the communication subspace in relation to the information bottleneck theory is very interesting and novel. However, it may be a stretch to apply this interpretation directly to PFC-PMd, as was done with early vs. late areas of a FF neural network.

      In the RNN simulations, the main finding indicates that a network with three or more modules lacks information about the stimulus in the third or subsequent modules. The authors draw a direct analogy between monkey PFC and PMd and Modules 1 and 3 of the RNNs, respectively. However, considering the model's architecture, it seems more appropriate to map Area 1 to regions upstream of PFC, such as the visual cortex, since Area 1 receives visual stimuli. Moreover, both PFC and PMd are deep within the brain hierarchy, suggesting a more natural mapping to later areas. This contradicts the CCA analysis in Figure 3e. It is recommended to either remap the areas or provide further support for the current mapping choice.

      We updated the Introduction to better clarify the predictions of the information bottleneck (IB) principle. In particular, the IB principle predicts that later areas should have minimal sufficient representations of task information, whereas upstream areas should have more information. In PMd, we observed a minimal sufficient representation of task information during the decision-making task. In DLPFC, we observed more task information, particularly more information about the target colors and the target configuration.

      In terms of the exact map between areas, we do not believe or intend to claim the DLPFC is the first area implicated in the sensorimotor transformation during our perceptual decision-making task. Rather, DLPFC best matches Area 1 of our model. It is important to note that we abstracted our task so that the first area of our model received checkerboard coherence and target configuration as input (and hence did not need to transform task visual inputs). Indeed, in Figure 1d we hypothesize that the early visual areas should contain additional information, which we do not model directly in this work. Future work could model RNNs to take in an image or video input of the task stimulus. In this case, it would be interesting to assess if earlier areas resemble visual cortical areas. We updated the results, where we first present the RNN, to state the inputs explicitly and be clear the inputs are not images or videos of the checkerboard task.

      “The RNN input was 4D representing the target configuration and checkerboard signed coherence, while the RNN output was 2D, representing decision variables for a left and right reach (see Methods).”

      Another reason that we mapped Area 1 to DLPFC is because anatomical, physiological and lesion studies suggest that DLPFC receives inputs from both the dorsal and ventral stream (Romanski, et, al, 2007; Hoshi, et al, 2006; Wilson, at al, 1993). The dorsal stream originates from the occipital lobe, passes through the posterior parietal cortex, to DLPFC, which carries visuospatial information of the object. The ventral stream originates from the occipital lobe, passes through the inferior temporal cortex, ventrolateral prefrontal cortex to DLPFC, which encodes the identity of the object, including color and texture. In our RNN simulation, Area 1 receives processed inputs of the task: target configuration and the evidence for each color in the checkerboard. Target configuration contains information of the spatial location of the targets, which represents the inputs from the dorsal stream, while evidence for each color by analogy is the input from the ventral stream. Purely visual areas would not fit this dual input from both the dorsal and ventral stream. A potential alternative candidate would be the parietal cortex which is largely part of the dorsal stream and is thought to have modest color inputs (although there is some shape and color selectivity in areas such as LIP, e.g., work from Sereno et al.). On balance given the strong inputs from both the dorsal and ventral stream, we believe Area 1 maps better on to DLPFC than earlier visual areas.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) Line 35/36: Please specify the type of nuisance that the representation is robust to. I guess this refers to small changes in the inputs, not to changes in the representation itself.

      Indeed it refers to input variability unrelated to the task. We clarified the text.

      (2) For reference, it would be nice to have a tick for the event "Targets on" in Fig.2c.

      In this plot, the PSTHs are aligned to the checkerboard onset. Because there is a variable time between target and checkerboard onset, there is a trial-by-trial difference of when the target was turned on, so there is no single place on the x-axis where we could place a “Targets on” tick. In response to this point, we generated a plot with both targets on and check on alignment, with a break in the middle, shown in Supplementary Figure S5. 

      (3) It would strengthen the comparison between neural data and RNN if the DPCA components of the RNN areas were shown, as they are shown in Fig.2g,h for the neural data.

      We include the PSTHs plotted onto the dPCA components here for Area 1 of the exemplar network. Dashed lines indicate a left reach, while solid lines indicate a right reach, and the color corresponds to the color of the selected target. As expected, we find that the dPCA components capture the separation between components. We emphasize that the trajectory paths along the decoder axes are not particularly meaningful to interpret, except to demonstrate whether variables can be decoded or not (as in Fig 2g,h, comparing DLPFC and PMd). The decoder axes of dPCA are not constrained in any way, in contrast to the readout (encoder) axis (see Methods). This is why our manuscript focuses on analyzing the readout axes. However, if the reviewer strongly prefers these plots to be put in the manuscript, we will add them.   

      Author response image 1.

      (4) The session-by-session decode analysis presented in Fig.2i suggests that DLPFC has mostly direction information while in Area 1 target information is on top, as suggested by Fig.3g. An additional decoding analysis on trial averaged neural data, i.e. a figure for neural data analogous to Fig.3g,h, would allow for a more straightforward and direct comparison between RNN and neural data. 

      We first clarify that we did not decode trial-averaged neural data for either recorded neural data or RNNs. In Fig 3g, h (for the RNN) all decoding was performed on single trial data and then averaged. We have revised the main manuscript to make this clear. Because of this, the mean accuracies we reported for DLPFC and PMd in the text are therefore computed in the same way as the mean accuracies presented in Fig 3g, h. We believe this likely addresses your concern: i.e., the mean decode accuracies presented for both neural data and the RNN were computed the same way. 

      If the above paragraph did not address your concern, we also wish to be clear that we presented the neural data as histograms, rather than a mean with standard error, because we found that accuracies were highly variable depending on electrode insertion location. For example, some insertions in DLPFC achieved chance-levels of decoding performance for color and target configuration. For this reason, we prefer to keep the histogram as it shows more information than reporting the mean, which we report in the main text. However, if the reviewer strongly prefers us to make a bar plot of these means, we will add them.

      (5) Line 129 mentions an analysis of single trials. But in Fig.2i,j sessions are analyzed. Please clarify.

      For each session, we decode from single trials and then average these decoding accuracies, leading to a per-session average decoding accuracy. Note that for each session, we record from different neurons. In the text, we also report the average over the sessions. We clarified this in the text and Methods.

      (6) Fig.4c,f show how color and direction axes align with the potent subspaces. We assume that the target axis was omitted here because it highly aligns with the color axis, yet we note that this was not pointed out explicitly.

      You are correct, and we revised the text to point this out explicitly.

      “We quantified how the color and direction axis were aligned with these potent and null spaces of the intra-areal recurrent dynamics matrix of Area 1 ($\W^1_{rec}$). We did not include the target configuration axis for simplicity, since it highly aligns with the color axis for this network.”

      (7) The caption of Fig.4c reads: "Projections onto the potent space of the intra-areal dynamics for each area." Yet, they only show area 1 in Fig.4c, and the rest in a supplement figure. Please refer properly.

      Thank you for pointing this out. We updated the text to reference the supplementary figure.

      (8) Line 300: "We found the direction axis was more aligned with the potent space and the color axis was more aligned with the null space." They rather show that the color axis is as aligned to the potent space as a random vector, but nothing about the alignments with the null space. Contrarily, on line 379 they write "...with the important difference that color information isn't preferentially projected to a nullspace...". Please clarify.

      Thank you for pointing this out. We clarified the text to read: “We found the direction axis was more aligned with the potent space”. The text then describes that the color axis is aligned like a random vector: “In contrast, the color axis was aligned to a random vector.”

      (9) Line 313: 'unconstrained' networks are mentioned. What constraints are implied there, Dale's law? Please define and clarify.

      Indeed, the constraint refers to Dale’s law constraints. We clarified the text: “Further, we found that W<sub>21</sub> in unconstrained 3 area networks (i.e., without Dale's law constraints) had significantly reduced…”

      (10) Line 355 mentions a 'feedforward bottleneck'. What does this exactly mean? No E-I feedforward connections, or...? Please define and clarify.

      This refers to sparser connections between areas than within an area, as well as a smaller fraction of E-I connections. We clarified the text to read:

      “Together, these results suggest  that a connection bottleneck in the form of neurophysiological architecture constraints (i.e., sparser connections between areas than within an area, as well as a smaller fraction of E-I connections) was the key design choice leading to RNNs with minimal color representations and consistent with the information bottleneck principle.”

      (11) Fig.5c is supposedly without feedforward connections, but it looks like the plot depicts these connections (i.e. identical to Fig.5b).

      In Figure 5, we are varying the E to I connectivity in panel B, and the E-E connectivity in panel C. We vary the feedback connections in Supp Fig. S12. We updated the caption accordingly. 

      (12) For reference, it would be nice to have the parameters of the exemplar network indicated in the panels of Fig.5.

      We updated the caption to reference the parameter configuration in Table 1 of the Appendix.

      (13) Line 659: incomplete sentence

      Thank you for pointing this out. We removed this incomplete sentence.

      (14) In the methods section "Decoding and Mutual information for RNNs" a linear neural net decoder as well as a nonlinear neural net decoder are described, yet it was unclear which one was used in the end.

      We used the nonlinear network, and clarified the text accordingly. We obtained consistent conclusions using a linear network, but did not include these results in the text. (These are reported in Fig. 11 of Kleinman et al, 2021). Moreover, we also obtain consistent results by using an SVM decoder in Fig. S4 for our exemplar parameter configuration.

      (15) In the discussion, the paragraph starting from line 410 introduces a new set of results along with the benefits of minimal representations. This should go to the results section.

      We prefer to leave this as a discussion, since the task was potentially too simplistic to generate a clear conclusion on this matter. We believe this remains a discussion point for further investigation.

      (16) Fig S5: hard to parse. Show some arrows for trajectories (a) (d) is pretty mysterious: where do I see the slow dynamics?

      Slow points are denoted by crosses, which forms an approximate line attractor. We clarified this in the caption.

      Reviewer #2 (Recommendations For The Authors):

      Minor recommendations (not ordered by importance)

      (1) Be more explicit that the recordings come from different monkeys and are not simultaneously recorded. For instance, say 'recordings from PFC or PMD'. Say early on that PMD recordings come from two monkeys and that PFC recordings come from 1 of those monkeys. Furthermore, I would highlight which datasets are novel and which are not. For instance, I believe the PFC dataset is a previously unpublished dataset and should be highlighted as such.

      We added: “The PMd data was previously described in a study by Chandrasekaran and colleagues” to the main text which clarifies that the PMd data was previously recorded and has been analyzed in other studies.

      (2) I personally feel that talking about 'optimal', as is done in the abstract, is a bit of a stretch for this simple task.

      In using the terminology “optimal,” we are following the convention of IB literature that optimal representations are sufficient and minimal. The term “optimal” therefore is task-specific; every task will have its own optimal representation. We clarify in the text that this definition comes from Machine Learning and Information Theory, stating:

      “The IB principle defines an optimal representation as a representation that is minimal and sufficient for a task or set of tasks.”

      In this way, we take an information-theoretic view for describing multi-area representations. This view was satisfactory for explaining and reconciling the multi-area recordings and simulations for this task, and we think it is helpful to provide a normative perspective for explaining the differences in cortical representations by brain area. Even though the task is simple, it still allows us to study how sensory/perceptual information is represented, and well as how choice-related information is being represented.

      (3) It is mentioned (and even highlighted) in the abstract that we don't know why the brain distributes computations. I agree with that statement, but I don't think this manuscript answers that question. Relatedly, the introduction mentions robustness as one reason why the brain would distribute computations, but then raises the question of whether there is 'also a computational benefit for distributing computations across multiple areas'. Isn't the latter (robustness) a clear 'computational benefit'?

      We decided to keep the word “why” in the abstract, because this is a generally true statement (it is unclear why the brain distributes computation) that we wish to convey succinctly, pointing to the importance of studying this relatively grand question (which could only be fully answered by many studies over decades). We consider this the setting of our work. However, to avoid confusion that we are trying to give a full answer to this question, we are now more precise in the first paragraph of our introduction as to the particular questions we ask that will take a step towards this question. In particular, the first paragraph now asks these questions, which we answer in our study.

      “For example, is all stimuli and decision-related information present in all brain areas, or do the cortical representations differ depending on their processing stage? If the representations differ, are there general principles that can explain why the cortical representations differ by brain area?”

      We also removed the language on robustness, as we agree it was confusing. Thank you for these suggestions. 

      (4) Figure 2e and Fig. 3d, left, do not look very similar. I suggest zooming in or rotating Figure 2 to highlight the similarities. Consider generating a baseline CCA correlation using some sort of data shuffle to highlight the differences.

      The main point of the trajectories is to demonstrate that both Area 1 and DLPFC represent both color and direction. We now clarify this in the manuscript. However, we do not intend for these two plots to be a rigorous comparison of similarity. Rather, we quantify similarity using CCA and our decoding analysis. We also better emphasize the relative values of the CCA, rather than the absolute values.

      (5) Line 152: 'For this analysis, we restricted it to sessions with significant decode accuracy with a session considered to have a significant decodability for a variable if the true accuracy was above the 99th percentile of the shuffled accuracy for a session.' Why? Sounds fishy, especially if one is building a case on 'non-decodability'. I would either not do it or better justify it.

      The reason to choose only sessions with significant decoding accuracy is that we consider those sessions to be the sessions containing information of task variables. In response to this comment, we also now generate a plot with all recording sessions in Supplementary Figure S7. We modified the manuscript accordingly.

      “For this analysis, we restricted it to sessions with significant decode accuracy with a session considered to have a significant decodability for a variable if the true accuracy was above the 99th percentile of the shuffled accuracy for a session. This is because these sessions contain information about task variables. However, we also present the same analyses using all sessions in Fig. S7.”

      (6) Line 232: 'The RNN therefore models many aspects of our physiological data and is therefore'. Many seems a stretch?

      We changed “many” to “key.”

      (7) The illustration in Fig. 4B is very hard to understand, I recommend removing it.

      We are unsure what this refers to, as Figure 4B represents data of axis overlaps and is not an illustration. 

      (8) At some point the authors use IB instead of information bottleneck (eg line 288), I would not do it.

      We now clearly write that IB is an abbreviation of Information Bottleneck the first time it is introduced.  

      (9) Fig. 5 caption is insufficient to understand it. Text in the main document does not help. I would move most part of this figure, or at least F, to supplementary. Instead, I would move the results in S11 and S10 to the main document.

      We clarified the caption to summarize the key points. It now reads: 

      “Overall, neurophysiological architecture constraints in the form of multiple areas, sparser connections between areas than within an area, as well as a smaller fraction of E-I connections lead to a minimal color representation in the last area.”

      (10) Line 355: 'Together, these results suggest that a connection bottleneck in the form of neurophysiological architecture constraints was the key design choice leading to RNNs with minimal color representations and consistent with the information bottleneck principle.' The authors show convincingly that increased sparsity leads to the removal of irrelevant information. There is an alternative model of the communication subspace hypothesis that uses low-rank matrices, instead of sparse, to implement said bottlenecks (https://www.biorxiv.org/content/10.1101/2022.07.21.500962v2)

      We thank the reviewer for pointing us to this very nice paper. Indeed, a low-rank connectivity matrix is another mechanism to limit the amount of information that is passed to subsequent areas. In fact, the low-rank matrix forms a hard-version of our observations as we found that task-relevant information was preferentially propagated along the top singular mode of the inter-areal connectivity matrix. In our paper we observed this tendency naturally emerges through training with neurophysiological architecture constraints. In the paper, for the multi-area RNN, they hand-engineered the multi-area network, whereas our network is trained. We added this reference to our discussion. 

      Thank you for your helpful and constructive comments.

    1. Author response:

      The following is the authors’ response to the current reviews.

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Pakula et al. explore the impact of reactive oxygen species (ROS) on neonatal cerebellar regeneration, providing evidence that ROS activates regeneration through Nestin-expressing progenitors (NEPs). Using scRNA-seq analysis of FACS-isolated NEPs, the authors characterize injury-induced changes, including an enrichment in ROS metabolic processes within the cerebellar microenvironment. Biochemical analyses confirm a rapid increase in ROS levels following irradiation and forced catalase expression, which reduces ROS levels, and impairs external granule layer (EGL) replenishment post-injury.

      Strengths:

      Overall, the study robustly supports its main conclusion and provides valuable insights into ROS as a regenerative signal in the neonatal cerebellum.

      Comments on revisions:

      The authors have addressed most of the previous comments. However, they should clarify the following response:

      *"For reasons we have not explored, the phenotype is most prominent in these lobules, that is why they were originally chosen. We edited the following sentence (lines 578-579):

      First, we analyzed the replenishment of the EGL by BgL-NEPs in vermis lobules 3-5, since our previous work showed that these lobules have a prominent defect."*

      It has been reported that the anterior part of the cerebellum may have a lower regenerative capacity compared to the posterior lobe. To avoid potential ambiguity, the authors should clarify that "the phenotype" and "prominent defect" refer to more severe EGL depletion at an earlier stage after IR rather than a poorer regenerative outcome. Additionally, they should provide a reference to support their statement or indicate if it is based on unpublished observations.

      Our comment does not refer to a more severe EGL depletion at an earlier stage. There is instead poorer regeneration of the anterior region. The irradiation approach used provides consistent cell killing of GCPs across the cerebellum. This can be seen in Fig. 1c, e, g, i in our previous publication: Wojcinski, et al. (2017) Cerebellar granule cell replenishment post-injury by adaptive reprogramming of Nestin+ progenitors. Nature Neuroscience, 20:1361-1370). Also, Fig 2e, g, k, m in the paper shows that by P5 and P8, posterior lobule 8 recovers better than anterior lobules 1-5.

      Reviewer #2 (Public review):

      Summary:

      The authors have previously shown that the mouse neonatal cerebellum can regenerate damage to granule cell progenitors in the external granular layer, through reprogramming of gliogenic nestin-expressing progenitors (NEPs). The mechanisms of this reprogramming remain largely unknown. Here the authors used scRNAseq and ATACseq of purified neonatal NEPs from P1-P5 and showed that ROS signatures were transiently upregulated in gliogenic NEPs ve neurogenic NEPs 24 hours post injury (P2). To assess the role of ROS, mice transgenic for global catalase activity were assessed to reduce ROS. Inhibition of ROS significantly decreased gliogenic NEP reprogramming and diminished cerebellar growth post-injury. Further, inhibition of microglia across this same time period prevented one of the first steps of repair - the migration of NEPs into the external granule layer. This work is the first demonstration that the tissue microenvironment of the damaged neonatal cerebellum is a major regulator of neonatal cerebellar regeneration. Increased ROS is seen in other CNS damage models, including adults, thus there may be some shared mechanisms across age and regions, although interestingly neonatal cerebellar astrocytes do not upregulate GFAP as seen in adult CNS damage models. Another intriguing finding is that global inhibition of ROS did not alter normal cerebellar development.

      Strengths:

      This paper presents a beautiful example of using single cell data to generate biologically relevant, testable hypotheses of mechanisms driving important biological processes. The scRNAseq and ATACseq analyses are rigorously conducted and conclusive. Data is very clearly presented and easily interpreted supporting the hypothesis next tested by reduce ROS in irradiated brains.

      Analysis of whole tissue and FAC sorted NEPS in transgenic mice where human catalase was globally expressed in mitochondria were rigorously controlled and conclusively show that ROS upregulation was indeed decreased post injury and very clearly the regenerative response was inhibited. The authors are to be commended on the very careful analyses which are very well presented and again, easy to follow with all appropriate data shown to support their conclusions.

      Weaknesses:

      The authors also present data to show that microglia are required for an early step of mobilizing gliogenic NEPs into the damaged EGL. While the data that PLX5622 administration from P0-P5 or even P0-P8 clearly shows that there is an immediate reduction of NEPs mobilized to the damaged EGL, there is no subsequent reduction of cerebellar growth such that by P30, the treated and untreated irradiated cerebella are equivalent in size. There is speculation in the discussion about why this might be the case. Additional experiments and tools are required to assess mechanisms. Regardless, the data still implicate microglia in the neonatal regenerative response, and this finding remains an important advance.

      As stated previously, the suggested follow up experiments while relevant are extensive and considered beyond the scope of the current paper.


      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Pakula et al. explore the impact of reactive oxygen species (ROS) on neonatal cerebellar regeneration, providing evidence that ROS activates regeneration through Nestin-expressing progenitors (NEPs). Using scRNA-seq analysis of FACS-isolated NEPs, the authors characterize injury-induced changes, including an enrichment in ROS metabolic processes within the cerebellar microenvironment. Biochemical analyses confirm a rapid increase in ROS levels following irradiation, and forced catalase expression, which reduces ROS levels, and impairs external granule layer (EGL) replenishment post-injury.

      Strengths:

      Overall, the study robustly supports its main conclusion and provides valuable insights into ROS as a regenerative signal in the neonatal cerebellum.

      Weaknesses:

      (1) The diversity of cell types recovered from scRNA-seq libraries of sorted Nes-CFP cells is unexpected, especially the inclusion of minor types such as microglia, meninges, and ependymal cells. The authors should validate whether Nes and CFP mRNAs are enriched in the sorted cells; if not, they should discuss the potential pitfalls in sampling bias or artifacts that may have affected the dataset, impacting interpretation.

      In our previous work, we thoroughly assessed the transgene using RNA in situ hybridization for Cfp, immunofluorescent analysis for CFP and scRNA-seq analysis for Cfp transcripts (Bayin et al., Science Adv. 2021, Fig. S1-2)(1), and characterized the diversity within the NEP populations of the cerebellum. Our present scRNA-seq data also confirms that Nes transcripts are expressed in all the NEP subtypes. A feature plot for Nes expression has been added to the revised manuscript (Fig 1E), as well as a sentence explaining the results. Of note, since this data was generated from FACS-isolated CFP+ cells, the perdurance of the protein allows for the detection of immediate progeny of Nes-expressing cells, even in cells where Nes is not expressed once cells are differentiated. Finally, oligodendrocyte progenitors, perivascular cells, some rare microglia and ependymal cells have been demonstrated to express Nes in the central nervous system; therefore, detecting small groups of these cells is expected (2-4). We have added the following sentence (lines 391-394):

      “Detection of Nes mRNA confirmed that the transgene reflects endogenous Nes expression in progenitors of many lineages, and also that the perdurance of CFP protein in immediate progeny of Nes-expressing cells allowed the isolation of these cells by FACS (Figure 1E)”.

      (2) The authors should de-emphasize that ROS signaling and related gene upregulation exclusively in gliogenic NEPs. Genes such as Cdkn1a, Phlda3, Ass1, and Bax are identified as differentially expressed in neurogenic NEPs and granule cell progenitors (GCPs), with Ass1 absent in GCPs. According to Table S4, gene ontology (GO) terms related to ROS metabolic processes are also enriched in gliogenic NEPs, neurogenic NEPs, and GCPs.

      As the reviewer requested, we have de-emphasized that ROS signaling is preferentially upregulated in gliogenic NEPs, since we agree with the reviewer that there is some evidence for similar transcriptional signatures in neurogenic NEPs and GCPs. We added the following (lines 429-531):

      “Some of the DNA damage and apoptosis related genes that were upregulated in IR gliogenic-NEPs (Cdkn1a, Phlda3, Bax) were also upregulated in the IR neurogenic-NEPs and GCPs at P2 (Supplementary Figure 2B-E).”

      And we edited the last few sentences of the section to state (lines 453-459):

      “Interestingly, we did not observe significant enrichment for GO terms associated with cellular stress response in the GCPs that survived the irradiation compared to controls, despite significant enrichment for ROS signaling related GO-terms (Table S4). Collectively, these results indicate that injury induces significant and overlapping transcriptional changes in NEPs and GCPs. The gliogenic- and neurogenic-NEP subtypes transiently upregulate stress response genes upon GCP death, and an overall increase in ROS signaling is observed in the injured cerebella.”

      (3) The authors need to justify the selection of only the anterior lobe for EGL replenishment and microglia quantification.

      We thank the reviewers for asking for this clarification. Our previous publications on regeneration of the EGL by NEPs have all involved quantification of these lobules, thus we think it is important to stay with the same lobules. For reasons we have not explored, the phenotype is most prominent in these lobules, that is why they were originally chosen. We edited the following sentence (lines 578-579):

      “First, we analyzed the replenishment of the EGL by BgL-NEPs in vermis lobules 3-5, since our previous work showed that these lobules have a prominent defect.”

      (4) Figure 1K: The figure presents linkages between genes and GO terms as a network but does not depict a gene network. The terminology should be corrected accordingly.

      We have corrected the terminology and added the following (lines 487-489):

      “Finally, linkages between the genes in differentially open regions identified by ATAC-seq and the associated GO-terms revealed an active transcriptional network involved in regulating cell death and apoptosis (Figure 1K).”

      (5) Figure 1H and S2: The x-axis appears to display raw p-values rather than log10(p.value) as indicated. The x-axis should ideally show -log10(p.adjust), beginning at zero. The current format may misleadingly suggest that the ROS GO term has the lowest p-values.

      Apologies for the mistake. The data represents raw p-values and the x-axis has been corrected.

      (6) Genes such as Ppara, Egln3, Foxo3, Jun, and Nos1ap were identified by bulk ATAC-seq based on proximity to peaks, not by scRNA-seq. Without additional expression data, caution is needed when presenting these genes as direct evidence of ROS involvement in NEPs.

      We modified the text to discuss the discrepancies between the analyses. While some of this could be due to the lower detection limits in the scRNA-seq, it also highlights that chromatin accessibility is not a direct readout for expression levels and further analysis is needed. Nevertheless, both scRNA-seq and ATAC-seq have identified similar mechanisms, and our mutant analysis confirmed our hypothesis that an increase in ROS levels underlies repair, further increasing the confidence in our analyses. Further investigation is needed to understand the downstream mechanisms. We added the following sentence (lines 478-481):

      “However, not all genes in the accessible areas were differentially expressed in the scRNA-seq data. While some of this could be due to the detection limits of scRNA-seq, further analysis is required to assess the mechanisms of how the differentially accessible chromatin affects transcription.”

      (7) The authors should annotate cell identities for the different clusters in Table S2.

      All cell types have been annotated in Table S2.

      (8) Reiterative clustering analysis reveals distinct subpopulations among gliogenic and neurogenic NEPs. Could the authors clarify the identities of these subclusters? Can we distinguish the gliogenic NEPs in the Bergmann glia layer from those in the white matter?

      Thank you for this clarification. As shown in our previous studies, we can not distinguish between the gliogenic NEPs in the Bergmann glia layer and the white matter based on scRNA-seq, but expression of the Bergmann glia marker Gdf10 suggests that a large proportion of the cells in the Hopx+ clusters are in the Bergmann glia layer. The distinction within the major subpopulations that we characterized (Hopx-, Ascl1-expressing NEPs and GCPs) are driven by their proliferative/maturation status as we previously observed. We have included a detailed annotation of all the clusters in Table S2, as requested and a UMAP for mKi57 expression in Fig 1E. We have clarified this in the following sentence (lines 383-385):

      “These groups of cells were further subdivided into molecularly distinct clusters based on marker genes and their cell cycle profiles or developmental stages (Figure 1D, Table S2).”

      (9) In the Methods section, the authors mention filtering out genes with fewer than 10 counts. They should specify if these genes were used as background for enrichment analysis. Background gene selection is critical, as it influences the functional enrichment of gene sets in the list.

      As requested, the approach used has been added to the Methods section of the revised paper. Briefly, the background genes used by the goseq function are the same genes used for the probability weight function (nullp). The mm8 genome annotation was used in the nullp function, and all annotated genes were used as background genes to compute GO term enrichment. The following was added (lines 307-308):

      “The background genes used to compute the GO term enrichment includes all genes with gene symbol annotations within mm8.”

      (10) Figure S1C: The authors could consider using bar plots to better illustrate cell composition differences across conditions and replicates.

      As suggested, we have included bar plots in Fig. S1D-F.

      (11) Figures 4-6: It remains unclear how the white matter microglia contribute to the recruitment of BgL-NEPs to the EGL, as the mCAT-mediated microglia loss data are all confined to the white matter.

      We have thought about the question and had initially quantified the microglia in the white matter and the rest of the lobules (excluding the EGL) separately. However, there are very few microglia outside the white matter in each section, thus it is not possible to obtain reliable statistical data on such a small population. We therefore did not include the cells in the analysis. We have added this point in the main text (line 548).

      “As a possible explanation for how white matter microglia could influence NEP behaviors, given the small size of the lobules and how the cytoarchitecture is disrupted after injury, we think it is possible that secreted factors from the white matter microglia could reach the BgL NEPs. Alternatively, there could be a relay system through an intermediate cell type closer to the microglia.” We have added these ideas to the Discussion of the revised paper (lines 735-738).

      Reviewer #2 (Public review):

      Summary:

      The authors have previously shown that the mouse neonatal cerebellum can regenerate damage to granule cell progenitors in the external granular layer, through reprogramming of gliogenic nestin-expressing progenitors (NEPs). The mechanisms of this reprogramming remain largely unknown. Here the authors used scRNAseq and ATACseq of purified neonatal NEPs from P1-P5 and showed that ROS signatures were transiently upregulated in gliogenic NEPs ve neurogenic NEPs 24 hours post injury (P2). To assess the role of ROS, mice transgenic for global catalase activity were assessed to reduce ROS. Inhibition of ROS significantly decreased gliogenic NEP reprogramming and diminished cerebellar growth post-injury. Further, inhibition of microglia across this same time period prevented one of the first steps of repair - the migration of NEPs into the external granule layer. This work is the first demonstration that the tissue microenvironment of the damaged neonatal cerebellum is a major regulator of neonatal cerebellar regeneration. Increased ROS is seen in other CNS damage models including adults, thus there may be some shared mechanisms across age and regions, although interestingly neonatal cerebellar astrocytes do not upregulate GFAP as seen in adult CNS damage models. Another intriguing finding is that global inhibition of ROS did not alter normal cerebellar development.

      Strengths:

      This paper presents a beautiful example of using single cell data to generate biologically relevant, testable hypotheses of mechanisms driving important biological processes. The scRNAseq and ATACseq analyses are rigorously conducted and conclusive. Data is very clearly presented and easily interpreted supporting the hypothesis next tested by reduce ROS in irradiated brains.

      Analysis of whole tissue and FAC sorted NEPS in transgenic mice where human catalase was globally expressed in mitochondria were rigorously controlled and conclusively show that ROS upregulation was indeed decreased post injury and very clearly the regenerative response was inhibited. The authors are to be commended on the very careful analyses which are very well presented and again, easy to follow with all appropriate data shown to support their conclusions.

      Weaknesses:

      The authors also present data to show that microglia are required for an early step of mobilizing gliogenic NEPs into the damaged EGL. While the data that PLX5622 administration from P0-P5 or even P0-P8 clearly shows that there is an immediate reduction of NEPs mobilized to the damaged EGL, there is no subsequent reduction of cerebellar growth such that by P30, the treated and untreated irradiated cerebella are equivalent in size. There is speculation in the discussion about why this might be the case, but there is no explanation for why further, longer treatment was not attempted nor was there any additional analyses of other regenerative steps in the treated animals. The data still implicate microglia in the neonatal regenerative response, but how remains uncertain.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      This is an exemplary manuscript.

      The methods and data are very well described and presented.

      I actually have very little to ask the authors except for an explanation of why PLX treatment was discontinued after P5 or P8 and what other steps of NEP reprogramming were assessed in these animals? Was NEP expansion still decreased at P8 even in the presence of PLX at this stage? Also - was there any analysis attempted combining mCAT and PLX?

      We agree with the reviewer that a follow up study that goes into a deeper analysis of the role of microglia in GCP regeneration and any interaction with ROS signaling would interesting. However, it would require a set of tools that we do not currently have. We did not have enough PLX5622 to perform addition experiments or extend the length of treatment. Plexxikon informed us in 2021 that they were no longer manufacturing PLX5622 because they were focusing on new analogs for in vivo use, and thus we had to use what we had left over from a completed preclinical cancer study. We nevertheless think it is important to publish our preliminary results to spark further experiments by other groups.

      References

      (1) Bayin N. S. Mizrak D., Stephen N. D., Lao Z., Sims P. A., Joyner A. L. Injury induced ASCL1 expression orchestrates a transitory cell state required for repair of the neonatal cerebellum. Sci Adv. 2021;7(50):eabj1598.

      (2) Cawsey T, Duflou J, Weickert CS, Gorrie CA. Nestin-Positive Ependymal Cells Are Increased in the Human Spinal Cord after Traumatic Central Nervous System Injury. J Neurotrauma. 2015;32(18):1393-402.

      (3) Gallo V, Armstrong RC. Developmental and growth factor-induced regulation of nestin in oligodendrocyte lineage cells. The Journal of neuroscience : the official journal of the Society for Neuroscience. 1995;15(1 Pt 1):394-406.

      (4) Huang Y, Xu Z, Xiong S, Sun F, Qin G, Hu G, et al. Repopulated microglia are solely derived from the proliferation of residual microglia after acute depletion. Nat Neurosci. 2018;21(4):530-40.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1 (Public review):

      Jin et al. investigated how the bacterial DNA damage (SOS) response and its regulator protein RecA affects the development of drug resistance under short-term exposure to beta-lactam antibiotics. Canonically, the SOS response is triggered by DNA damage, which results in the induction of error-prone DNA repair mechanisms. These error-prone repair pathways can increase mutagenesis in the cell, leading to the evolution of drug resistance. Thus, inhibiting the SOS regulator RecA has been proposed as means to delay the rise of resistance.

      In this paper, the authors deleted the RecA protein from E. coli and exposed this ∆recA strain to selective levels of the beta-lactam antibiotic, ampicillin. After an 8h treatment, they washed the antibiotic away and allowed the surviving cells to recover in regular media. They then measured the minimum inhibitory concentration (MIC) of ampicillin against these treated strains. They note that after just 8 h treatment with ampicillin, the ∆recA had developed higher MICs towards ampicillin, while by contrast, wild-type cells exhibited unchanged MICs. This MIC increase was also observed subsequent generations of bacteria, suggesting that the phenotype is driven by a genetic change.

      The authors then used whole genome sequencing (WGS) to identify mutations that accounted for the resistance phenotype. Within resistant populations, they discovered key mutations in the promoter region of the beta-lactamase gene, ampC; in the penicillin-binding protein PBP3 which is the target of ampicillin; and in the AcrB subunit of the AcrAB-TolC efflux machinery. Importantly, mutations in the efflux machinery can impact the resistances towards other antibiotics, not just beta-lactams. To test this, they repeated the MIC experiments with other classes of antibiotics, including kanamycin, chloramphenicol, and rifampicin. Interestingly, they observed that the ∆recA strains pre-treated with ampicillin showed higher MICs towards all other antibiotic tested. This suggests that the mutations conferring resistance to ampicillin are also increasing resistance to other antibiotics.

      The authors then performed an impressive series of genetic, microscopy, and transcriptomic experiments to show that this increase in resistance is not driven by the SOS response, but by independent DNA repair and stress response pathways. Specifically, they show that deletion of the recA reduces the bacterium's ability to process reactive oxygen species (ROS) and repair its DNA. These factors drive accumulation of mutations that can confer resistance towards different classes of antibiotics. The conclusions are reasonably well-supported by the data, but some aspects of the data and the model need to be clarified and extended.

      Strengths:

      A major strength of the paper is the detailed bacterial genetics and transcriptomics that the authors performed to elucidate the molecular pathways responsible for this increased resistance. They systemically deleted or inactivated genes involved in the SOS response in E. coli. They then subjected these mutants the same MIC assays as described previously. Surprisingly, none of the other SOS gene deletions resulted an increase in drug resistance, suggesting that the SOS response is not involved in this phenotype. This led the authors to focus on the localization of DNA PolI, which also participates in DNA damage repair. Using microscopy, they discovered that in the RecA deletion background, PolI co-localizes with the bacterial chromosome at much lower rates than wild-type. This led the authors to conclude that deletion of RecA hinders PolI and DNA repair. Although the authors do not provide a mechanism, this observation is nonetheless valuable for the field and can stimulate further investigations in the future.

      In order to understand how RecA deletion affects cellular physiology, the authors performed RNA-seq on ampicillin-treated strains. Crucially, they discovered that in the RecA deletion strain, genes associated with antioxidative activity (cysJ, cysI, cysH, soda, sufD) and Base Excision Repair repair (mutH, mutY, mutM), which repairs oxidized forms of guanine, were all downregulated. The authors conclude that down-regulation of these genes might result in elevated levels of reactive oxygen species in the cells, which in turn, might drive the rise of resistance. Experimentally, they further demonstrated that treating the ∆recA strain with an antioxidant GSH prevents the rise of MICs. These observations will be useful for more detailed mechanistic follow-ups in the future.

      Weaknesses:

      Throughout the paper, the authors use language suggesting that ampicillin treatment of the ∆recA strain induces higher levels of mutagenesis inside the cells, leading to the rapid rise of resistance mutations. However, as the authors note, the mutants enriched by ampicillin selection can play a role in efflux and can thus change a bacterium's sensitivity to a wide range of antibiotics, in what is known as cross-resistance. The current data is not clear on whether the elevated "mutagenesis" is driven ampicillin selection or by a bona fide increase in mutation rate.

      Furthermore, on a technical level, the authors employed WGS to identify resistance mutations in the treated ampicillin-treated wild-type and ∆recA strains. However, the WGS methodology described in the paper is inconsistent. Notably, wild-type WGS samples were picked from non-selective plates, while ΔrecA WGS isolates were picked from selective plates with 50 μg/mL ampicillin. Such an approach biases the frequency and identity of the mutations seen in the WGS and cannot be used to support the idea that ampicillin treatment induces higher levels of mutagenesis.

      Finally, it is important to establish what the basal mutation rates of both the WT and ∆recA strains are. Currently, only the ampicillin-treated populations were reported. It is possible that the ∆recA strain has inherently higher mutagenesis than WT, with a larger subpopulation of resistant clones. Thus, ampicillin treatment might not in fact induce higher mutagenesis in ∆recA.

      Comments on revisions:

      Thank you for responding to the concerns raised previously. The manuscript overall has improved.

      We sincerely thank the reviewer for raising this important point. In our initial submission, we acknowledge that our mutation analysis was based on a limited number of replicates (n=6), which may not have been sufficient to robustly distinguish between mutation induction and selection. In response to this concern, we have substantially expanded our experimental dataset. Specifically, we redesigned the mutation rate validation experiment by increasing the number of biological replicates in each condition to 96 independent parallel cultures. This enabled us to systematically assess mutation frequency distributions under four conditions (WT, WT+ampicillin, ΔrecA, ΔrecA+ampicillin), using both maximum likelihood estimation (MLE) and distribution-based fluctuation analysis (new Figure 1F, 1G, and Figure S5).

      These expanded datasets revealed that:

      (1) While the estimated mutation rate was significantly elevated in ΔrecA+ampicillin compared to ΔrecA alone (Fig. 1G),

      (2) The distribution of mutation frequencies in ΔrecA+ampicillin was highly skewed with evident jackpot cultures (Fig. 1F), and

      (3) The observed pattern significantly deviated from Poisson expectations, which is inconsistent with uniform mutagenesis and instead supports clonal selection from an early-arising mutational pool (Fig. S5).

      Importantly, these new results do not contradict our original conclusions but rather extend and refine them. The previous evidence for ROS-mediated mutagenesis remains valid and is supported by our GSH experiments, transcriptomic analysis of oxidative stress genes, and DNA repair pathway repression. However, the additional data now indicate that ROS-induced variants are not uniformly induced after antibiotic exposure but are instead generated stochastically under the stress-prone ΔrecA background and then selectively enriched upon ampicillin treatment.

      Taken together, we now propose a two-step model of resistance evolution in ΔrecA cells (new Figure 5):

      Step i: RecA deficiency creates a hypermutable state through impaired repair and elevated ROS, increasing the probability of resistance-conferring mutations.

      Step ii: β-lactam exposure acts as a selective bottleneck, enriching early-arising mutants that confer resistance.

      We have revised both the Results and Discussion sections to clearly articulate this complementary relationship between mutational supply and selection, and we believe this integrated model better explains the observed phenotypes and mechanistic outcomes.

      Reviewer #2 (Public review):

      This study aims to demonstrate that E. coli can acquire rapid antibiotic resistance mutations in the absence of a DNA damage response. The authors employed a modified Adaptive Laboratory Evolution (ALE) workflow to investigate this, initiating the process by diluting an overnight culture 50-fold into an ampicillin selection medium. They present evidence that a recA- strain develops ampicillin resistance mutations more rapidly than the wild-type, as indicated by the Minimum Inhibitory Concentration (MIC) and mutation frequency. Whole-genome sequencing of recA- colonies resistant to ampicillin showed predominant inactivation of genes involved in the multi-drug efflux pump system, contrasting with wild-type mutations that seem to activate the chromosomal ampC cryptic promoter. Further analysis of mutants, including a lexA3 mutant incapable of inducing the SOS response, led the authors to conclude that the rapid evolution of antibiotic resistance occurs via an SOS-independent mechanism in the absence of recA. RNA sequencing suggests that antioxidative response genes drive the rapid evolution of antibiotic resistance in the recA- strain. They assert that rapid evolution is facilitated by compromised DNA repair, transcriptional repression of antioxidative stress genes, and excessive ROS accumulation.

      Strengths:

      The experiments are well-executed and the data appear reliable. It is evident that the inactivation of recA promotes faster evolutionary responses, although the exact mechanisms driving this acceleration remain elusive and deserve further investigation.

      Weaknesses:

      Some conclusions are overstated. For instance, the conclusion regarding the LexA3 allele, indicating that rapid evolution occurs in an SOS-independent manner (line 217), contradicts the introductory statement that attributes evolution to compromised DNA repair.

      We thank the reviewer for this insightful observation, which highlights a central conceptual advance of our study. Our data indeed indicate that resistance evolution in ΔrecA occurs independently of canonical SOS induction (as shown by the lack of resistance in lexA3, dpiBA, and translesion polymerase mutants), yet is clearly associated with impaired DNA repair capacity (e.g., downregulation of polA, mutH, mutY).

      This apparent “contradiction” reflects the dual role of RecA: it functions both as the master activator of the SOS response and as a key factor in SOS-independent repair processes. Thus, the rapid resistance evolution in ΔrecA is not due to loss of SOS, but rather due to the broader suppression of DNA repair pathways that RecA coordinates, which elevates mutational load under stress (This point is discussed in further detail in our response to Reviewer 1).

      The claim made in the discussion of Figure 3 that the hindrance of DNA repair in recA- is crucial for rapid evolution is at best suggestive, not demonstrative. Additionally, the interpretation of the PolI data implies its role, yet it remains speculative.

      We appreciate this comment and would like to respectfully clarify that our conclusion regarding the role of DNA repair impairment is supported by several independent lines of mechanistic evidence.

      First, our RNA-seq analysis revealed transcriptional suppression of multiple DNA repair genes in ΔrecA cells following ampicillin treatment, including polA (DNA Pol I) and the base excision repair genes mutH, mutY, and mutM (Fig. 4K). This indicates that multiple repair pathways, including those responsible for correcting oxidative DNA lesions, are downregulated under these conditions.

      Second, we observed a significant reduction in DNA Pol I protein expression as well as reduced colocalization with chromosomal DNA in ΔrecA cells, suggesting impaired engagement of repair machinery (Fig. 3C-E). These phenotypes are not limited to transcriptional signatures but extend to functional protein localization.

      Third, and most importantly, resistance evolution was fully suppressed in ΔrecA cells upon co-treatment with glutathione (GSH), which reduces ROS levels. As GSH did not affect ampicillin killing (Fig. 4J), these findings suggest that mutagenesis and thus the emergence of resistance requires both ROS accumulation and the absence of efficient repair.

      Therefore, we believe these data go beyond correlation and demonstrate a mechanistic role for DNA repair impairment in driving stress-associated resistance evolution in ΔrecA. We have revised the Discussion to emphasize the strength of this evidence while avoiding overstatement.

      In Figure 2A table, mutations in amp promoters are leading to amino acid changes.

      We thank the reviewer for spotting this inconsistency. Indeed, the ampC promoter mutations we identified reside in non-coding regulatory regions and do not result in amino acid substitutions. We have corrected the annotation in Fig. 2A and clarified in the main text that these mutations likely affect gene expression through transcriptional regulation, rather than protein sequence alteration.

      The authors' assertion that ampicillin significantly influences persistence pathways in the wild-type strain, affecting quorum sensing, flagellar assembly, biofilm formation, and bacterial chemotaxis, lacks empirical validation.

      We thank the reviewer for pointing this out. In the original version, we acknowledged transcriptional enrichment of genes related to quorum sensing, flagellar assembly, and chemotaxis in the wild-type strain upon ampicillin treatment. However, as we did not directly assess persistence phenotypes (e.g., biofilm formation or persister levels), we agree that such functional inferences were not fully supported. We have revised the relevant statements to focus solely on transcriptomic changes and have removed language suggesting direct effects on persistence pathways.

      Figure 1G suggests that recA cells treated with ampicillin exhibit a strong mutator phenotype; however, it remains unclear if this can be linked to the mutations identified in Figure 2's sequencing analysis.

      We appreciate the reviewer’s comment. This point is discussed in further detail in our response to Reviewer 1.

      Reviewer #3 (Public review):

      In the present work, Zhang et al investigate involvement of the bacterial DNA damage repair SOS response in the evolution of beta-lactam drug resistance evolution in Escherichia coli. Using a combination of microbiological, bacterial genetics, laboratory evolution, next-generation, and live-cell imaging approaches, the authors propose short-term (transient) drug resistance evolution can take place in RecA-deficient cells in an SOS response-independent manner. They propose the evolvability of drug resistance is alternatively driven by the oxidative stress imposed by accumulation of reactive oxygen species and compromised DNA repair. Overall, this is a nice study that addresses a growing and fundamental global health challenge (antimicrobial resistance).

      Strengths:

      The authors introduce new concepts to antimicrobial resistance evolution mechanisms. They show short-term exposure to beta-lactams can induce durably fixed antimicrobial resistance mutations. They propose this is due to comprised DNA repair and oxidative stress. Antibiotic resistance evolution under transient stress is poorly studied, so the authors' work is a nice mechanistic contribution to this field.

      Weaknesses:

      The authors do not show any direct evidence of altered mutation rate or accumulated DNA damage in their model.

      We appreciate the reviewer’s comment. This point is discussed in further detail in our response to Reviewer 1.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      I would like to suggest two minor changes to the text.

      (1) Re. WGS data.

      The authors write in their response "We appreciate your concern regarding potential inconsistencies in the WGS methodology. However, we would like to clarify that the primary aim of the WGS experiment was to identify the types of mutations present in the wild type and ΔrecA strains after treatment of ampicillin, rather than to quantify or compare mutation frequencies. This purpose was explicitly stated in the manuscript.

      I think the source of my confusion stemmed from this part in the text:

      "In bacteria, resistance to most antibiotics requires the accumulation of drug resistance associated DNA mutations developed over time to provide high levels of resistance (29). To verify whether drug resistance associated DNA mutations have led to the rapid development of antibiotic resistance in recA mutant strain, we..."

      I would change the phrase "verify whether drug resistance associated DNA mutations have led to the rapid development of antibiotic resistance in recA mutant strain" to "identify the types of mutations present in the wild type and ΔrecA strains after treatment of ampicillin." This would explicitly state what the sequencing was for (ie. ID-ing mutations). The current phrase can give the impression that WGS was used to validate rapid or high mutagenesis.

      Thanks for this suggestion. We have revised this description to “In bacteria, resistance to most antibiotics requires the accumulation of drug resistance associated DNA mutations that can arise stochastically and, under stress conditions, become enriched through selection over time to confer high levels of resistance (33). Having observed a non-random and right-skewed distribution of mutation frequencies in ΔrecA isolates following ampicillin exposure, we next sought to determine whether specific resistance-conferring mutations were enriched in ΔrecA isolates following antibiotic exposure.”

      (2) Re. whether the mutations are "induced" or "pre-existing."

      The authors write:

      "We appreciate your detailed feedback on the language used to describe our data. We understand the concern regarding the use of the term "induced" in relation to beta-lactam exposure. To clarify, we employed not only beta-lactam antibiotics but also other antibiotics, such as ciprofloxacin and chloramphenicol, in our experiments (data not shown). However, we observed that beta-lactam antibiotics specifically induced the emergence of resistance or altered the MIC in our bacterial populations. If resistance had pre-existed before antibiotic exposure, we would expect other antibiotics to exhibit a similar selective effect, particularly given the potential for cross-resistance to multiple antibiotics."

      I think it is important to discuss the negative data for the other antibiotics (along with the other points made in your Reviewer response) in the main text.

      This point is discussed in further detail in our response to Reviewer 1 (Public Review).

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public reviews):

      (1) A cartoon paradigm of the HFD treatment window would be a helpful addition to Figure 1. Relatedly, the authors might consider qualifying MHFD as 'lactational MHFD.' Readers might miss the fact that the exposure window starts at birth.

      This is a good suggestion. The MHFD-L model has been used previously (e.g. Vogt et al. 2014). We have included a cartoon of the MHFD-L model and the PLX treatments to Figure 4, which we feel helps the readers and thank the reviewer for the suggestion.

      (2) More details on the modeling pipeline are needed either in Figure 1 or text. Of the ~50 microglia that were counted (based on Figure 1J), were all 50 quantified for the morphological assessments? Were equal numbers used for the control and MHFD groups? Were the 3D models adjusted manually for accuracy? How much background was detected by IMARIS that was discarded? Was the user blind to the treatment group while using the pipeline? Were the microglia clustered or equally spread across the PVN?

      In response to this suggestion, we have expanded the description of the image analysis routine in the methods. The analysis focused on detailed changes in microglial morphology as opposed to overall changes in microglia throughout the PVH as a whole. Accordingly, we applied anatomically matched ROIs to the PVH for the measurements. As described in the methods, the Imaris Filaments tool was used to visualize microglia fully contained within a tissue section and a mask derived from the 3D model for these cells was used to isolate them for further analysis, thereby separating these cells from interstitial labeling corresponding to parts of cell processes or other labeling not associated with selected cells. There was no formal “background subtraction.” This was an error in the previous version of the manuscript and we have revised the methods to reflect the process actually used. The images were segmented (to enhance signal to noise for 3D rendering), and then a Gaussian filter was applied to improve edge detection, which facilitates the morphological measurements.

      (3) Suggest toning back some of the language. For example: "...consistent with enhanced activity and surveillance of their immediate microenvironment" (Line 195) could be "...perhaps consistent with...". Likewise, "profound" (Lines 194, 377) might be an overstatement.

      Revisions have been made to both the Introduction and Discussion to modulate our representation of this controversial issue.

      (4) Representative images for AgRP+ cells (quantified in Figure 2J) are missing. Why not a co-label of Iba1+/AgRP+ as per Figure 1, 3? Also, what was quantified in Figure 2J - soma? Total immunoreactivity?

      Because the density of AgRP labeling does not change in the ARH we omitted the red channel image (AgRP labeling) to highlight the similarity of the microglial morphology. To address the reviewer’s concerns, in the revised figure we have reconstituted the figure with both the green (microglial) and red (AgRP) channels depicted.

      Figure 2J displays the numbers of AgRP neurons counted in the ARH in selected R01s through the ARH. The Methods section has been revised to include the visualization procedure used for the cell counts.

      (5) For the PLX experiment:

      a) "...we depleted microglia during the lactation period" (Line 234). This statement suggests microglia decreased from the first injection at P4 and throughout lactation, which is inaccurate. PLX5622 effects take time, upwards of a week. Thus, if PLX5622 injections started at P4, it could be P11 before the decrease in microglia numbers is stable. Moreover, by the time microglia are entirely knocked down, the pups might be supplementing some chow for milk, making it unclear how much PLX5622 they were receiving from the dam, which could also impact the rate at which microglia repopulation commences in the fetal brain. Quantifying microglia across the P4-P21 treatment window would be helpful, especially at P16, since the PVN AgRP microglia phenotypes were demonstrated and roughly when pups might start eating some chow. b) I am surprised that ~70% of the microglia are present at P21. Does this number reflect that microglia are returning as the pups no longer receive PLX5622 from milk from the dam? Does it reflect the poor elimination of microglia in the first place?

      This is an important point and have revised the first sentence in section 2.3 to clarify the PLX treatment logic and added a cartoon to Fig. 4 to show the treatment timeline. The PLX5622 was not administered to the dams but daily to the pups. We also agree with the interpretation that PLX5622 depleted numbers of microglia, as supported by the microglial cell counts, rather than effected a complete elimination and have made revisions to clarify this distinction. Although mice were weighed at weaning, cellular measurements were only made in mice perfused at P55.

      (6) Was microglia morphology examined for all microglia across the PVN? It is possible that a focus on PVNmpd microglia would reveal a stronger phenotype? In Figure 4H, J, AgRP+ terminals are counted in PVN subregions - PVNmpd and PVNpml, with PVNmpd showing a decrease of ~300 AgRP+ terminals in MHFD/Veh (rescued in MHFD/PLX5622). In Figure 1K, AgRP+ terminals across what appears to be the entire PVN decrease by ~300, suggesting that PVNmpd is driving this phenotype. If true, then do microglia within the PVNmpd display this morphology phenotype?

      We have revised the description of the analysis procedures to clarify these points. All measurements were made in user defined, matched regions of interest according to morphological features of the PVH. No measurements were made that included the entire PVH and we revised the Methods section to improve clarity.

      (7) What chow did the pups receive as they started to consume solid food? Is this only a MHFD challenge, or could the pups be consuming HFD chow that fell into the cage?

      The pups were weaned onto the same normal chow diet that the dams received prior to MHFD-L treatment. The cages were inspected daily and minimal HFD spillage was observed, although we cannot rule out with certainty any contribution of the pups directly consuming the HFD. We have edited Methods section 5.2 for clarity.

      (8) Figure 5: Does internalized AgRP+ co-localize with CD68+ lysosomes? How was 'internalized' determined?

      This important point has been clarified by revisions to the Methods section.

      (9) Different sample sizes are used across experiments (e.g., Figure 4 NCD n=5, MHFD n=4). Does this impact statistical significance?

      Sample size does impact power of ANOVA with larger samples reducing the chance of errors. ANOVA is generally robust in the face of moderate departures from the assumption of equal sample sizes and equal variance such as we experienced in the PLX5622 experiment. Here we used t-tests to detect differences in a single variable between two groups and two-way ANOVA to compare treatment by diet and treatment changes in the PLX5622 studies. Additional detail has been added to the Methods section to clarify this point.

      Reviewer #2 (Public reviews):

      (1) Under chow-fed conditions, there is a decrease in the number of microglia in the PVH and ARH between P16 and P30, accompanied by an increase in complexity/volume. With the exception of PVH microglia at P16, this maturation process is not affected by MHFD. This "transient" increase in microglial complexity could also reflect premature maturation of the circuit.

      This is an interesting possibility that requires future investigation (see response to Recommended Suggestions, above).

      (2) The key experiment in this paper, the ablation of microglia, was presumably designed to prevent microglial expansion/activation in the PVH of MHFD pups. However, it also likely accelerates and exaggerates the decrease in cell number during normal development regardless of maternal diet. Efforts to interpret these findings are further complicated because microglial and AgRP neuronal phenotypes were not assessed at earlier time points when the circuit is most sensitive to maternal influences.

      We agree that evaluations of microglia and hypothalamic circuits at many more time points would indeed be informative (see comments above).

      (3) Microglial loss was induced broadly in the forebrain. Enhanced AgRP outgrowth to the PVH could be caused by actions elsewhere, such as direct effects on AgRP neurons in the ARH or secondary effects of changes in growth rates.

      A local effect of microglia in the ARH that affects growth of AgRP axons remains a distinct possibility that deserves a targeted examination (see response to Recommended Suggestions, above).

      (4) Prior publications from the authors and other groups support the idea that the density of AgRP projections to the PVH is primarily driven by factors regulating outgrowth and not pruning. The failure to observe increased engulfment of AgRP fibers by PVH microglia is therefore not surprising. The possibility that synaptic connectivity is modulated by microglia was not explored.

      Synaptic pruning and regulation of axon targeting are not mutually exclusive processes and microglia may participate in both. Here we evaluated innervation of the PVH, which is sensitive to MHFD-L exposure, and engulfment of AgRP terminals by microglia, which does appear to be altered by MHFD-L. Given previous observations of terminal engulfment by microglia in other brain regions in response to environmental changes (e.g. prolonged stress) it is not unreasonable to expect this outcome in the offspring of MHFD-L dams.  In future work it will be important to profile multiple cell types in the PVH for microglial dependent and MHFDL-sensitive changes in targeting of AgRP axons. Equally important is a full characterization of postsynaptic changes in PVH neurons.

      Reviewer #3 (Public reviews):

      There was no attempt to interrogate microglia in different parts of the hypothalamus functionally. Morphology alone does not reflect a potential for significant signaling alterations that may occur within and between these and other cell types.

      The authors should discuss the limitations of their approach and findings and propose future directions to address them.

      We agree that evaluations of microglia and hypothalamic circuits at many more time points that include analyses of multiple regions would indeed be informative. We have added statements to the manuscript that address the limitations of our experimental approach and suggest future studies that will extend understanding of underlying mechanisms beyond those investigated here.

      Recommendations for the authors:

      Reviewing Editors Comments:

      (1) The Abstract is 405 words and should be shortened to less than 200 words.  

      The abstract has been edited to 200 words.

      (2) The authors might consider raising the question in the Introduction of whether reduced AgRP innervation of the PVN in MHFD-treated mice is due to decreased axonal growth, enhanced microglial-mediated pruning, or a combination of both. The potential effects on axonal growth should be given more consideration.

      This is an important point that we agree deserves additional consideration in the manuscript. Our past work has focused on leptin’s ability to influence axonal targeting of PVH neurons by AgRP and PPG neurons through a cell-autonomous mechanism and our conclusion is that leptin primarily induces axon growth. Because in this study our design did not focus on changes in axon growth over time but on regional changes in microglia and their interactions with AgRP terminals we did not want to divert attention from our logic in the introduction by highlighting multiple mechanisms. However, we have added a brief mention in the Introduction and have expanded consideration of axonal growth effects to the Discussion. Distinguishing between microglia’s role in synaptic density or axon targeting in this pathway is an important goal of future work.

      (3) Line 37, a high-fat diet should be defined here as HFD and used consistently thereafter. Note that "high-fat-diet exposure" requires two hyphens.

      The suggested revisions have been made throughout the manuscript.

      (4) Line 38 and elsewhere, MHFD does not adequately describe the treatment being limited to the lactation period, perhaps MLHFD would be better or just LHFD (because the pups can't lactate).

      The suggested revisions have been made throughout the manuscript, and we have used MHFD-L to describe maternal consumption of a high-fat diet that is restricted to the lactation period.

      (5) Line 110, leptin-deficient mice (add hyphen).

      (6) Line 183, NCD should be defined.

      The suggested revisions have been made throughout the manuscript.

      (7) Lines 237- 238, it is not clear what is widespread in the rostral forebrain. Is it the loss of microglia? What is the dividing point between the rostral and caudal forebrain? Were microglia depleted in the caudal forebrain too?

      We have revised this section of the manuscript to focus the description on the hypothalamus alone and specify that the reduction in microglial density is not restricted to the PVH.  

      (8) Line 245, microglial-mediated effects (add hyphen).

      (9) Line 247, vehicle-treated mice (add hyphen).

      The suggested revisions have been made throughout the manuscript.

      (10) Line 457, when referring to genes, the approved gene name should be used in italics, AgRP should be Agrp (italics).

      The suggested revision has been made throughout the manuscript.

      (11) Line 459, the name of the Syn-Tom mice in the Key Resource table, Methods, and Text should be consistent. It would be best to use the formal name of the Ai34 line of mice on the JAX website.

      The suggested revisions have been made throughout the manuscript.

      (12) Figure 1G H, and I um should have Greek micro; Fig. 1J and K, Replace # with Number. The same suggestions apply to all the other figures.

      Both the manuscript and figures have been revised in accordance with this recommendation.

      (13) Figures 4 G, H, I and J. and Figures 5 M and O. The font size is too small to see well.

      Fonts have been changed in the figures to improve visibility.

      Reviewer #1 (Recommendations for the authors):

      (1) Figures are out of order in the text. For example, Figure 1A is followed next by the results for Figure 1J instead of Figure 1B.

      We regret that the organization of figure panels makes for awkward matching for the reader as they proceed through the text. We designed the figures to facilitate comparisons between cellular responses and differences in labeling. After evaluating a reorganization, we decided to maintain the original panel configurations, but have revised the text to more closely follow the presentation of cellular features in the figures.

      (2) Figure 1B.: All images lack scale bars.

      (3) Line 433 - 'underlie' is spelled wrong.

      (4) Rosin et al should be 2019 and not 2018.

      These corrections have been implemented in the revised text and figures.

      (5) The statement that "the effects of MHFD on microglial morphology in the PVH of offspring display both temporal and regional specificity, which correspond to a decrease in the density of AgRP inputs to the PVH" (Line 196) needs clarification, as the phrase "regional specificity" has not been substantiated in this section even though it is discussed later.

      We agree with this comment and have revised section 2.1 to more closely match the data presented to this point in the manuscript.

      Reviewer #2 (Recommendations for the authors):

      (1) The claim of "spatial specificity" in the effects of MHFD on microglia is based on an increase in the complexity/volume of microglia at P16 in the PVH that was not seen in the ARH or BNST. The transient nature of the effect raises several questions: Does the effect on the PVH represent premature maturation?

      This is an interesting suggestion. However, given how little is known about microglial maturation in the hypothalamus it is difficult to address. It is indeed possible that microglia mature at different rates in each AgRP target, and that MHFD-L exposure alters the rate of maturation in some regions but not others. This will require a great deal more analysis of both microglia and ARH projections to understand fully (see below).

      (2) To support their central claim that microglia in the PVH "sculpt the density of AgRP inputs to the PVH" the authors report effects on Iba1+ cells in the PVH of chow-fed dams at P55, body weight at P21, and AgRP projections in the PVH at an unspecified age. It is hard to understand what is happening across "normal" development in chow-fed dams since the number of Iba1+ cells decreases from ~50 to ~25 between P16 and P30 (Figure 1), but then increases to >60 cells at P55 (Figure 4). Given the large fluctuations in microglial population across time, analyzing the same parameters (i.e. microglial number/morphology in the ARH and PVH, AgRP neuronal number in the ARH, and fiber density in the PVH, and body weight) across time points before, during and after the critical period in chow and MHFD conditions would be very helpful.

      The time points we evaluated were chosen to be during and after the previously determined critical period for development of AgRP projections to the PVH, which were then compared with adults (which were all P55) to assess longevity of the effects. We have incorporated revisions to improve the clarity of when measurements were assessed, and treatments implemented. Defining the cellular dynamics of microglia across time remains a major challenge for the field and will certainly be informed by future studies with additional time points, as well as by in vivo imaging studies focused on regions identified here. Although such studies are beyond the scope of the present work, their completion would advance our current understanding of how microglia respond to nutritional changes during development of feeding circuits.

      (3) As microglia are also ablated in the ARH, direct effects on AgRP neurons or indirect effects via changes in growth rates could also contribute to increased AgRP fiber density in the PVH. In support of the first possibility, postnatal microglial depletion increases the number of AgRP neurons (Sun, et al. 2023).

      We agree with the suggestion, also raised by the Reviewing Editor, which has been addressed briefly in the Introduction, and in more detail by revisions to the Discussion section.

      (4) The failure to assess alpha-MSH fibers in the same animals was a missed opportunity. They are also affected by MHFD but likely involve a distinct mechanism (Vogt, et al 2014).

      Given the paired interest in POMC neurons and AgRP neurons I understand the reviewer’s comment. We chose to focus solely on AgRP neurons because we do not currently have a way to genetically target axonal labeling exclusively to POMC neurons due to the shared precursor origin of POMC neurons and a percentage of NPY neurons in the ARH, as shown by Lori Zeltser’s laboratory. Moreover, the elegant work by Vogt et al. focused on responses of POMC neurons in the MHFD-L model. However, it certainly remains possible that microglia in the PVH interact with terminals derived from POMC neurons, as well as with terminals derived from other afferent populations of neurons.

      (5) All statistical analyses involved unpaired t-tests. Two-way ANOVAs should be used to assess the effects of age and HFD and interactions between these factors.

      We used t-tests to detect differences in a single variable between two groups and two-way ANOVA to compare treatment by diet and treatment changes in the PLX5622 studies.  Additional detail has been added to the Methods section and information added to the figure legend for Fig. 4 to clarify this point.

      Reviewer #3 (Recommendations for the authors):

      I suggest exploring the deeper characterization of the microglia in various parts of the hypothalamus in different conditions. This could include cytokine assessment or spatial transcriptomic.

      We agree that a great deal more work is needed to improve our understanding of how microglia impact hypothalamic development more broadly and to identify underlying molecular mechanisms. We are hopeful that the data presented here will motivate additional study of microglial dynamics in multiple hypothalamic regions, as well as detailed studies of cellular signaling events for factors derived from MHFD-L dams that impact neural development in the hypothalamus.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      n this manuscript, the authors used a leucine/pantothenate auxotrophic strain of Mtb to screen a library of FDA-approved compounds for their antimycobacterial activity and found significant antibacterial activity of the inhibitor semapimod. In addition to alterations in pathways, including amino acid and lipid metabolism and transcriptional machinery, the authors demonstrate that semapimod treatment targets leucine uptake in Mtb. The work presents an interesting connection between nutrient uptake and cell wall composition in mycobacteria.

      Strengths:

      The link between the leucine uptake pathway and PDIM is interesting but has not been characterized mechanistically. The authors discuss that PDIM presents a barrier to the uptake of nutrients and shows binding of the drug with PpsB. However it is unclear why only the leucine uptake pathway was affected.

      We observe interference of L-leucine, but not of pantothenate, uptake in mc2 6206 strain upon semapimod treatment. At present, we do not have any clue whether PDIM presents a barrier exclusively to the uptake of L-leucine. Further studies may shed a light on underlying mechanism(s) by which L-leucine uptake is modulated by this small molecule.

      We still do not know what PpsB actually does for amino acid uptake - is it a transporter?

      By BLI-Octet we do not find any interaction between L-leucine and PpsB. Therefore, we doubt that PpsB is a transporter of L-leucine.

      Does semapimod binding affect its activity?

      Our study suggests that semapimod treatment alters PDIM architecture which becomes restrictive to L-leucine. However, at present the exact mechanism is not clear. Further studies are required to thoroughly examine the effect of semapimod on Mtb PpsB activity and alterations in PDIM by mass spectrometry.

      Does the auxotrophic Mtb have lower PDIM levels compared to wild-type Mtb?

      As per the published report by Mulholland et al, and by vancomycin susceptibility phenotype in our study, both the strains appear to have comparable PDIM levels.

      The authors show an interesting result where they observed antibacterial activity of semapimod against H37Rv only in vivo and not in vitro. Why do the authors think this is the basis of this observation? It is possible semapimod has an immunomodulatory effect on the host since leucine is an essential amino acid in mice. The authors could check pro-inflammatory cytokine levels in infected mouse lungs with and without drug treatment.

      Semapimod inhibits production of proinflammatory cytokines such as TNF-α, IL-1β, and IL-6, which would indeed help pathogen establish chronic infection. However, a significant reduction in bacterial loads in lungs and spleen upon semapimod treatment despite inhibition of proinflammatory cytokines clearly indicates bacterial dependence on host-derived exogenous leucine during intracellular growth.

      The authors show that the semapimod-resistant auxotroph lacks PDIM. The conclusions would be further strengthened by including validations using PDIM mutants, including del-ppsB Mtb and other genes of the PDIM locus, whether in vivo this mutant would be more susceptible (or resistant) to semapimod treatment.

      PDIM is a virulence factor, and plays an important role in the intracellular survival of the TB pathogen. Mtb strains lacking PDIM are expected to show attenuated growth during infection, even without semapimod treatment. In such a case, it might be difficult to draw any conclusions about the effect of semapimod against PDIM(-) strains in vivo.

      Prolonged subculturing can introduce mutations in PDIM, which can be overcome by supplementing with propionate (Mullholland et al, Nat Microbiol, 2024). Did the authors also supplement their cultures with propionate? It would be interesting to see what mutations would result in Semr strains with propionate supplementation along with prolonged semapimod treatment.

      Considering the fact that extensive subculturing may result in loss of PDIM, we avoided prolonged subculturing of bacteria. As presented in Fig. 6b, the WT bacteria retain PDIM. While performing the initial screening of drugs, we did not anticipate such phenotype, and hence bacteria were cultured in regular 7H9-OADS medium without propionate supplementation.

      A comprehensive future study would help examining the effect of propionate on generation of semapimod resistant mutants in Mtb mc2 6206.

      Weaknesses:

      I have summarized the limitations above in my comments. Overall, it would be helpful to provide more mechanistic details to study the connection between leucine uptake and PDIM.

      Reviewer #2 (Public review):

      Summary

      This important study uncovers a novel mechanism for L-leucine uptake by M. tuberculosis and shows that targeting this pathway with 'Semapimod' interferes with bacterial metabolism and virulence. These results identify the leucine uptake pathway as a potential target to design new anti-tubercular therapy.

      Strengths

      The authors took numerous approaches to prove that L-leucine uptake of M. tuberculosis is an important physiological phenomenon and may be effectively targeted by 'Semapimod'. This study utilizes a series of experiments using a broad set of tools to justify how the leucine uptake pathway of M. tuberculosis may be targeted to design new anti-tubercular therapy.

      Weaknesses

      The study does not explain how L-leucine is taken up by M. tuberculosis, leaving the mechanism unclear. Even though 'Semapimod' binds to the PpsB protein, the relevant connection between changes in PDIM and amino acid transport remains incomplete.

      While Leucine uptake involves specific transporters in other bacteria, such transport system is not known in Mtb. By screening small molecule inhibitors, we came across a molecule, semapimod, which selectively kills the leucine auxotroph (mc2 6206), but not the WT Mtb. To understand the underlying mechanism of differential susceptibility of the WT and auxotrophic strains to this molecule, we evaluated the effect of restoration of leuCD and panCD expression on susceptibility of the auxotrophic strain to semapimod. Interestingly, our results demonstrated that upon endogenous expression of leuCD genes, mc2 6206 strain becomes resistant to killing by semapimod. In contrast, no effect of panCD expression was observed on semapimod susceptibility of mc2 6206. These findings were further substantiated by gene expression analysis of semapimod treated mc2 6206, which exhibits differential regulation of a set of genes that are altered upon leucine depletion in Mtb as well as in other bacteria. Overall results thus provide first evidence of perturbation of L-leucine uptake by semapimod treatment of the leucine auxotroph.

      To further gain mechanistic insights into the effect of semapimod on leucine uptake in Mtb, we generated the semapimod resistant strain which exhibits point mutation in 4 genes including ppsB. Interestingly, overexpression of wild-type ppsB, but not of other genes, restored susceptibility of the resistant bacteria to semapimod. Our observations that semapimod interacts with PpsB, and semapimod resistant strain accumulates mutation in PpsB resulting in loss of PDIM together support the involvement of cell-wall PDIM in regulation of L-leucine transport in Mtb.

      As mentioned above, we anticipate that semapimod treatment brings about certain modifications in PDIM which becomes more restrictive to L-leucine. A comprehensive future study will be helpful to examine the effect of semapimod on Mtb physiology.

      Also, the fact that the drug does not function on WT bacteria makes it a weak candidate to consider its usefulness for a therapeutic option.

      We agree that semapimod is not an appropriate drug candidate against TB owing to its inhibitory effect on production of proinflammatory cytokines such as TNF-α, IL-1β, and IL-6 that help pathogen establish chronic infection. However, a significant reduction in bacterial loads in lungs and spleen upon semapimod treatment despite inhibition of proinflammatory cytokines clearly indicates bacterial dependence on host-derived exogenous leucine during intracellular growth. Therefore targeting L-leucine uptake can be a novel therapeutic strategy against TB.

      Reviewer #3 (Public review):

      Agarwal et al identified the small molecule semapimod from a chemical screen of repurposed drugs with specific antimycobacterial activity against a leucine-dependent strain of M. tuberculosis. To better understand the mechanism of action of this repurposed anti-inflammatory drug, the authors used RNA-seq to reveal a leucine-deficient transcriptomic signature from semapimod challenge. The authors then measured a decreased intracellular concentration of leucine after semapimod challenge, suggesting that semapimod disrupts leucine uptake as the primary mechanism of action. Unexpectedly, however, resistant mutants raised against semapimod had a mutation in the polyketide synthase gene ppsB that resulted in loss of PDIM synthesis. The authors believe growth inhibition is a consequence of decreased accumulation of leucine as a result of an impaired cell wall and a disrupted, unknown leucine transporter. This study highlights the importance of branched-chain amino acids for M. tuberculosis survival, and the chemical genetic interactions between semapimod and ppsB indicate that ppsB is a conditionally essential gene in a medium depleted of leucine.

      The conclusions regarding the leucine and PDIM phenotypes are moderately supported by experimental data. The authors do not provide experimental evidence to support a specific link between leucine uptake and impaired PDIM production. Additional work is needed to support these claims and strengthen this mechanism of action.

      As mentioned above, overall results from this study provide first evidence of perturbation of L-leucine uptake by semapimod treatment of the leucine auxotroph. Our observations that semapimod interacts with PpsB, and semapimod resistant strain accumulates mutation in PpsB resulting in loss of PDIM together support the involvement of cell-wall PDIM in regulation of L-leucine transport in Mtb.

      As hitherto mentioned, it appears that semapimod treatment brings about certain modifications in PDIM which becomes restrictive to L-leucine. Future studies are required to gain detailed mechanistic insights into the effect of semapimod on Mtb physiology.

      Since leucine uptake and PDIM synthesis are important concepts of the manuscript, experiments would benefit from exploring other BCAAs to know if the phenotypes observed are specific to leucine, and adding additional strains to the 2D TLC experiments to provide confidence in the absence of the PDIM band.

      We thank the peer reviewer for this suggestion. We would be happy to analyse the effect of semapimod on the level of other amino acids including BCAA by mass spectrometry.

      The intriguing observation that wild-type H37Rv is resistant to semapimod but the leucine-auxotroph is sensitive should be further explored. If the authors are correct and semapimod does inhibit leucine uptake through a specific transporter or disrupted cell wall (PDIM synthesis), testing semapimod activity against the leucine-auxotroph in various concentrations of BCAAs could highlight the importance of intracellular leucine. H37Rv is still able to synthesize endogenous leucine and is able to circumvent the effect of semapimod.

      We thank the peer reviewer for this suggestion. We would explore the possibility of analysing the effect of increasing concentrations of BCAAs on mc2 6206 susceptibility to semapimod.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript finds a negative relationship between tuberculin skin test-induced type I interferon activity with chest X-ray tuberculosis severity in humans. This evidence is between incomplete and solid. It needs a bioinfomatics/transcriptomics reviewer to make a more insightful judgement. The manuscript demonstrates a convincing role for Stat2 in controlling Mycobacterium marinum infection in zebrafish embryos, incomplete data are presented linking reduced leukocyte recruitment to the infection susceptibility phenotype.

      Strengths:

      (1) An interesting analysis of TST response correlated with chest X-ray pathology.

      (2) Novel data on a protective role for Stat2 in a natural host-mycobacterial species infection pairing.

      We appreciate the reviewer’s positive comments.

      Weaknesses:

      (1) The transcriptional modules are very large sets of genes that do not present a clear picture of what is actually being measured relative to other biological pathways.

      The transcriptional module analysis is a major strength of our approach. These gene signatures are derived from independent experiments, most of which have been previously published/validated [1,2]. To clarify, they represent co-regulated gene sets downstream of signalling pathways. Increased number of genes in these modules increases their combinatorial specificity for a given biological pathway. In the human data, they serve as orthogonal validation for the bioinformatic analysis showing enrichment of the type I IFN pathway among TST transcriptome genes that are negatively correlated with radiographic disease severity in pulmonary TB (see Figure 2). Importantly, our modules confirm the relationship with type I IFN signalling (see Figure 2E) by discriminating from type II IFN signalling, which is not statistically significantly correlated with radiographic TB severity (see Figure S6C-E).

      (2) The link between infection-Stat2-leukocyte recruitment and containment of infection is plausible, but lacks a specific link to the first part of the manuscript.

      For clarification, the first part of the study seeks to identify immune response pathways that relate to severity of human disease, leading to the identification of type I IFN signalling. Since the human data are limited to an observational analysis in which we cannot test causality, the second part of our study uses a genetically tractable experimental model to test the hypothesis that type I IFN signalling is host-protective and explore possible mechanisms for a beneficial effect. This leads to the observation that type I IFN responses contribute to early myeloid cell recruitment to the site of infection, that has previously been shown to be crucial for containment of mycobacterial infection in zebrafish larvae. We will further evaluate the introduction and results sections to ensure a clear link between the human and zebrafish work.

      Major concerns

      (1) Line 158: The two transcriptional modules should be placed in the context of other DEG patterns. The macrophage type I interferon module, in particular, is quite large (361 genes). Can this be made more granular in terms of type I IFN ligands and STAT2-dependent genes?

      We respectfully disagree with this comment. For clarification, the 360 gene module reflects the zebrafish larval response to IFNphi1 protein [3]. Type I IFNs are known to induce hundreds of interferon stimulated genes [4]. As explained above, the size of the modules increases specificity for a given signalling pathway. In this case, we are most interested in discriminating type I and type II IFN signalling pathways that represent very different upstream biological processes. The discrimination we achieve with our modular approach is a major advance over previous reports of gene signatures in TB that do not discriminate between the two pathways. In this study, we did not discriminate between signalling downstream of type I IFN ligands and STAT2, consistent with existing literature showing that type I IFN signalling is STAT2 dependent [5,6].

      (2) The ifnphi1 injection into mxa:mCherry stat2 crispants is a nice experiment to demonstrate loss of type I IFN responsiveness. Further data is required to demonstrate if important mycobacterial control pathways (IFNy, TNF, il6?, etc) are intact in stat2 crispants before being able to conclude that these phenotypes are specific to type I IFN.

      Thank you for the positive comment. We acknowledge this point and will attempt to evaluate whether pro-inflammatory cytokine responses are intact in stat2 CRISPants by qPCR or bulk RNAseq. However, these experiments may prove inconclusive because of the limited sensitivity in this approach.

      Reviewer #2 (Public review):

      Summary:

      This study shows that type I interferon (IFN-I) signaling helps protect against mycobacterial infection. Using human gene expression data and a zebrafish model, the authors find that reduced IFN-I activity is linked to more severe disease. They also show that zebrafish lacking the IFN-I signaling gene stat2 are more vulnerable to infection due to poor macrophage migration. These results suggest a protective role for IFN-I in mycobacterial disease, challenging previous findings from other animal models.

      Strengths:

      Strengths of the manuscript include the use of human clinical samples to support relevance to disease, along with a genetically tractable zebrafish model that enables mechanistic insight.

      We welcome the reviewer’s positive summary of our study.

      Weaknesses:

      (1) The manuscript presents intriguing human data showing an inverse correlation between IFN-I gene signatures and TB disease, but the findings remain correlative and may be cohort-specific. Given that the skin is not a primary site of TB and is relatively immunotolerant, the biological relevance of downregulated IFN-I-related genes in this tissue to systemic or pulmonary TB is unclear.

      We agree with the reviewer that the observational human data are correlative. That is precisely why we extend the study to undertake mechanistic studies in a genetically tractable animal model, using M. marinum infection of zebrafish larvae. In the introduction, we already provide a detailed rationale for the strengths of the TST model to study human immune responses to a standardised mycobacterial challenge. This approach mitigates against the confounding of heterogeneity in bacterial burden and sampling different stages of the natural history of infection in conventional observational human studies. Therefore, the application of the TST is a major strength of this study. We do not understand the context in which the reviewer suggests the skin is immunotolerant. In the present study and previous work we provide molecular level analysis of the TST as a robust cell mediated immune response that reflects molecular perturbation in granuloma from the site of pulmonary TB disease 1.

      (2) The reliance on stat2 CRISPants in zebrafish offers a limited view of IFN-I signaling. Including additional crispant lines targeting other key regulators (e.g., ifnar1, tyk2, irf3, irf7) would strengthen the interpretation and clarify whether the observed effects reflect broader IFN-I pathway disruption.

      We respectfully disagree with this comment. Our objective was to test the role of type I IFN signalling in M. marinum infection of zebrafish. We show that stat2 deletion effectively disrupts type I IFN signalling (Figure S8). Therefore, we do not see a compelling rationale to evaluate other molecules in the signalling pathway.

      (3) The conclusion that IFN-I is protective contrasts with established findings from murine and non-human primate models, where IFN-I is often detrimental. While the authors highlight species differences, the lack of functional human data and reliance on M. marinum in zebrafish limit the translational relevance. A more balanced discussion addressing these discrepancies would improve the manuscript.

      We acknowledge that our findings contrast with the prevailing view in published literature to date. We will further review the discussion to see how we can elaborate on the potential strengths and weaknesses of different experimental approaches, which may underpin these discrepancies.

      (4) Quantification of bacterial burden using fluorescence intensity alone may not accurately reflect bacterial viability. Complementary methods, such as qPCR for bacterial DNA, would provide a more robust assessment of antimicrobial activity.

      We and others have previously validated the use of the quantitative measures of fluorescence, used here as a measure of bacterial load [7,8]. Importantly, our measurements do not rely purely on the total fluorescence signal, but also measures of dissemination of infection, for which we see consistent findings. It is also widely recognised that DNA measurements do not necessarily correlate well with bacterial viability. Therefore, we respectfully disagree that a PCR-based approach will add substantial value to our existing analysis.

      (5) Finally, the authors should clarify whether impaired macrophage recruitment in stat2 crispants results from defects in chemotaxis, differentiation, or survival, and address discrepancies between their human blood findings and prior studies.

      We acknowledge that these are important questions. Our data show that stat2 disruption does not impact total macrophage numbers at baseline (Figure 4A,B) and therefore do not support any effect of Stat2 signalling on steady state macrophage survival or differentiation. The downregulation of macrophage mpeg1 expression in M. marinum infection precludes long-term follow-up of these cells in the context of infection [9]. Therefore, we cannot currently test the hypothesis that Stat2 signalling may influence death of macrophages recruited to the site of infection or make them more susceptible to the cytopathic effects of direct mycobacterial infection. We will attempt to confirm using short-term time-lapse imaging that cellular migration to the site of hindbrain M. marinum infection is reduced in stat2 deficient zebrafish. On the strength of what is possible to test and the established role of type I IFNs in induction of several chemokines [10,11], the most likely effect is that Stat2 signalling increases recruitment through chemokine production. We are exploring the possibility of testing changes to the chemokine profile in stat2 CRISPants by qPCR or bulk RNAseq, but these experiments may prove inconclusive because of the limitations of sensitivity in this approach.

      We recognize that our finding of no relationship between peripheral blood type I IFN activity and severity of human TB contrasts with that of previous studies. As stated in the discussion, the most likely explanation for this is our use of transcriptional modules which reflect exclusive type I IFN responses. The signatures used in other studies include both type I and type II IFN inducible genes and therefore also reflect IFN gamma driven responses.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript, the authors presented an interesting study providing an insight into the role of Type-I interferon responses in tuberculosis (TB) pathogenesis by combining transcriptome analysis of PBMCs and TST from tuberculosis patients. The zebrafish model was used to identify the changes in the innate immune cell population of macrophages and neutrophils. The findings suggested that Type-I interferon signatures inversely correlated with disease severity in the TST transcriptome data. The authors validated the observations by CRISPR-mediated disruption of stat2 (a critical transcription factor for type I interferon signaling) in zebrafish larvae, showing increased susceptibility to M. marinum infection. Traditionally, type-I interferon responses have been viewed as detrimental in mycobacterial infections, with studies suggesting enhanced susceptibility in certain mouse models. The study tried to identify and further characterize the understanding of the role of type-I interferons in TB.

      Strengths:

      Traditionally, type-I interferon responses have been viewed as detrimental in mycobacterial infections, with studies suggesting enhanced susceptibility in certain mouse models. The study tried to further understand the role of type-I interferons in TB pathogenesis.

      We thank the reviewer for their summary.

      Weaknesses:

      Though the study showed an inverse correlation of Type-I interferon with radiological features of TB, the molecular mechanism is largely unexplored in the study, which is making it difficult to understand the basis of the results shown in the manuscript by the authors.

      We respectfully disagree with this comment. The observations in the human data lead to the hypothesis that type I IFN responses may be host-protective, which we then test specifically in the zebrafish model, and explore candidate mechanisms, focussing on myeloid cell recruitment to the site of infection.

      References

      (1) Bell, L.C.K., Pollara, G., Pascoe, M., Tomlinson, G.S., Lehloenya, R.J., Roe, J., Meldau, R., Miller, R.F., Ramsay, A., Chain, B.M., et al. (2016). In Vivo Molecular Dissection of the Effects of HIV-1 in Active Tuberculosis. PLoS Pathog. 12, e1005469. https://doi.org/10.1371/journal.ppat.1005469.

      (2) Pollara, G., Turner, C.T., Rosenheim, J., Chandran, A., Bell, L.C.K., Khan, A., Patel, A., Peralta, L.F., Folino, A., Akarca, A., et al. (2021). Exaggerated IL-17A activity in human in vivo recall responses discriminates active tuberculosis from latent infection and cured disease. Sci. Transl. Med. 13, eabg7673. https://doi.org/10.1126/scitranslmed.abg7673.

      (3) Levraud, J.-P., Jouneau, L., Briolat, V., Laghi, V., and Boudinot, P. (2019). IFN-Stimulated Genes in Zebrafish and Humans Define an Ancient Arsenal of Antiviral Immunity. J. Immunol. Baltim. Md 1950 203, 3361–3373. https://doi.org/10.4049/jimmunol.1900804.

      (4) Schoggins, J.W. (2019). Interferon-Stimulated Genes: What Do They All Do? Annu. Rev. Virol. 6, 567–584. https://doi.org/10.1146/annurev-virology-092818-015756.

      (5) Blaszczyk, K., Nowicka, H., Kostyrko, K., Antonczyk, A., Wesoly, J., and Bluyssen, H.A.R. (2016). The unique role of STAT2 in constitutive and IFN-induced transcription and antiviral responses. Cytokine Growth Factor Rev. 29, 71–81. https://doi.org/10.1016/j.cytogfr.2016.02.010.

      (6) Begitt, A., Droescher, M., Meyer, T., Schmid, C.D., Baker, M., Antunes, F., Knobeloch, K.-P., Owen, M.R., Naumann, R., Decker, T., et al. (2014). STAT1-cooperative DNA binding distinguishes type 1 from type 2 interferon signaling. Nat. Immunol. 15, 168–176. https://doi.org/10.1038/ni.2794.

      (7) Stirling, D.R., Suleyman, O., Gil, E., Elks, P.M., Torraca, V., Noursadeghi, M., and Tomlinson, G.S. (2020). Analysis tools to quantify dissemination of pathology in zebrafish larvae. Sci. Rep. 10, 3149. https://doi.org/10.1038/s41598-020-59932-1.

      (8) Takaki, K., Davis, J.M., Winglee, K., and Ramakrishnan, L. (2013). Evaluation of the pathogenesis and treatment of Mycobacterium marinum infection in zebrafish. Nat. Protoc. 8, 1114–1124. https://doi.org/10.1038/nprot.2013.068.

      (9) Benard, E.L., Racz, P.I., Rougeot, J., Nezhinsky, A.E., Verbeek, F.J., Spaink, H.P., and Meijer, A.H. (2015). Macrophage-expressed perforins mpeg1 and mpeg1.2 have an anti-bacterial function in zebrafish. J. Innate Immun. 7, 136–152. https://doi.org/10.1159/000366103.

      (10) Lehmann, M.H., Torres-Domínguez, L.E., Price, P.J.R., Brandmüller, C., Kirschning, C.J., and Sutter, G. (2016). CCL2 expression is mediated by type I IFN receptor and recruits NK and T cells to the lung during MVA infection. J. Leukoc. Biol. 99, 1057–1064. https://doi.org/10.1189/jlb.4MA0815-376RR.

      (11) Buttmann, M., Merzyn, C., and Rieckmann, P. (2004). Interferon-beta induces transient systemic IP-10/CXCL10 chemokine release in patients with multiple sclerosis. J. Neuroimmunol. 156, 195–203. https://doi.org/10.1016/j.jneuroim.2004.07.016.

    1. Author response:

      Reviewer #1:

      Lipid transfer proteins (LTPs) play a crucial role in the intramembrane lipid exchange within cells. However, the molecular mechanisms that govern this activity remain largely unclear. Specifically, the way in which LTPs surmount the energy barrier to extract a single lipid molecule from a lipid bilayer is not yet fully understood. This manuscript investigates the influence of membrane properties on the binding of Ups1 to the membrane and the transfer of phosphatidic acid (PA) by the LTP. The findings reveal that Ups1 shows a preference for binding to membranes with positive curvature. Moreover, coarse-grained molecular dynamics simulations indicate that positive curvature decreases the energy barrier associated with PA extraction from the membrane. Additionally, lipid transfer assays conducted with purified proteins and liposomes in vitro demonstrate that the size of the donor membrane significantly impacts lipid transfer efficiency by Ups1-Mdm35 complexes, with smaller liposomes (characterized by high positive curvature) promoting rapid lipid transfer.

      This study offers significant new insights into the reaction cycle of phosphatidic acid (PA) transfer by Ups1 in mitochondria. Notably, the authors present compelling evidence that, alongside negatively charged phospholipids, positive membrane curvature enhances lipid transfer - an effect that is particularly relevant at the mitochondrial outer membrane. The experiments are technically robust, and my primary feedback pertains to the interpretation of specific results.

      (1) The authors conclude from the lipid transfer assays (Figure 5) that lipid extraction is the rate-limiting step in the transfer cycle. While this conclusion seems plausible, it should be noted that the authors employed high concentrations of Ups1-Mdm35 along with less negatively charged phospholipids in these reactions. This combination may lead to binding becoming the rate-limiting factor. The authors should take this point into consideration. In this type of assay, it is challenging to clearly distinguish between binding, lipid extraction, and membrane dissociation as separate processes.

      We thank the reviewer for the constructive and positive evaluation of our manuscript. We agree that, while our data support the interpretation that the rate-limiting step occurs at the donor membrane, it is difficult to dissect in our assay which of the individual steps at the donor membrane - such as binding of Ups1, lipid extraction into the binding pocket, or dissociation of Ups1 - is rate-limiting. Nevertheless, although we cannot exclude contributions from membrane binding or dissociation, several observations suggest that lipid extraction is a rate-limiting step under our experimental conditions.

      The acceptor membrane has a similar lipid composition to the donor membrane (in tendency, the donor membrane is even a bit richer in binding-promoting lipids). If binding was ratelimiting, similar constraints would be expected at the acceptor membrane during lipid insertion. However, this is not observed.

      Regarding dissociation, if this step were rate-limiting, one would expect similar constraints to be evident at the acceptor vesicles as well. Nevertheless, membrane dissociation might be mechanistically coupled to lipid extraction and thus difficult to evaluate as an independent step.

      Based on our data and the considerations described above, we suggest that lipid extraction is the dominant rate-limiting step at the donor membrane under our conditions. However, we agree that a clear separation of these individual steps is not possible with the current experimental design. We will revise the corresponding passage to clarify that the rate-limiting step occurs at the donor membrane and, based on our observations, likely involves lipid extraction. Future studies aiming on dissecting these steps, will be important for elucidating the mechanism and regulation of Ups1-mediated lipid transfer both in vitro and in vivo.

      (2) The authors should discuss that variations in the size of liposomes will also affect the distance between them at a constant concentration, which may affect the rate of lipid transfer. Therefore, the authors should determine the average size and size distribution of liposomes after sonication (by DLS or nanoparticle analyzer, etc.)

      We agree that variations in liposome size will influence the average distance between vesicles at a given lipid concentration, which may in turn affect the rate of lipid transfer. As suggested, we will include DLS measurements to characterize the size distribution of our different liposome preparations.

      Our setup was designed to keep the total membrane surface area comparable across conditions. This approach ensures a comparable overall binding capacity for Ups1 and enables the comparison of membrane binding and lipid extraction from different membranes. However, we agree that vesicle spacing, which is affected by liposome size at constant lipid concentration, could potentially influence certain steps in the transfer process, such as the time required for Ups1 to travel between donor and acceptor membranes. Whether this intermembrane travel time contributes to rate limitation is indeed an interesting question, and we will address this point through further discussion in the revised manuscript.

      Investigating such effects in our current experimental system would require altering the vesicle concentration, which would in turn change the total membrane surface area and introduce additional variables. Nevertheless, exploring the influence of vesicle spacing and intermembrane distance on lipid transfer represents a promising direction for future studies aimed at dissecting the rate-limiting steps of the transfer cycle.

      (3) The authors use NBD-PA in the lipid transfer assays. Does the size of the donor liposomes affect the transfer of NBD-PA and DOPA similarly? Since NBD-labeled lipids are somewhat unstable within lipid bilayers (as shown by spontaneous desorption in Figure 5B), monitoring the transfer of unlabeled PA in at least one setting would strengthen the conclusion of the swap experiments.

      Ups1-mediated transfer of PA has been demonstrated both by mass spectrometry analysis of donor and acceptor vesicles (Connerth et al., 2012) and by NBD-fluorescence-based lipid transfer assays (Lu et al., 2020; Miliara et al., 2015; Miliara et al., 2019; Miliara et al., 2023; Potting et al., 2013; Watanabe et al., 2015). The fluorescence-based approach has been the most widely applied across multiple studies and has enabled detailed analysis of various aspects of lipid transfer by Ups1. It has been used to investigate mutants of key structural elements—such as the lipid-binding pocket and the α2–loop region. It has also been used to analyze fusion constructs between Ups1 and Mdm35, the influence of Mdm35 variants, and competition with excess Mdm35. Additionally, by comparing the transfer of NBD-labeled PA and NBD-labeled PS, this assay has provided insights into the determinants of the lipid specificity of Ups1. Hence, our experiments are based on the standard assay used to analyse lipid transfer in the field and thus can be corralated with the majority of published data.

      Nevertheless, we agree that it is important to keep in mind that NBD labeling may alter the biophysical properties of lipids and, consequently, affect their transfer efficiency. Moreover, NBD-labeled lipids are not suitable for comparing the transfer efficiency of different PA species, as the label itself may mask differences in acyl chain composition. Therefore, it will be valuable to establish complementary methods that do not rely on NBD-labeled PA. We aim to develop these non-standard methods for possible inclusion in the present study, but even if not fully implemented at this stage, they will certainly form an important part of future investigations.

      (4) The present study suggests that membrane domains with positive curvature at the outer membrane may serve as starting points for lipid transport by Ups1-Mdm35. Is anything known about the mechanisms that form such structures? This should be discussed in the text.

      The origin of positively curved membrane domains is indeed highly relevant in the context of our findings, and while not the primary focus of this work, we will place more emphasis on discussing how such curvature may arise. Mechanisms include the action of curvature-generating proteins, asymmetric lipid composition and curvature induced at membrane contact sites. We have so far included examples of proteins in the outer mitochondrial membrane that are expected to influence curvature in their vicinity, and we will expand on this aspect and other contributing factors more thoroughly in the revised text.

      Reviewer #2:

      Summary:

      Lipid transfer between membranes is essential for lipid biosynthesis across different organelle membranes. Ups1-Mdm35 is one of the best-characterized lipid transfer proteins, responsible for transferring phosphatidic acid (PA) between the mitochondrial outer membrane (OM) and inner membrane (IM), a process critical for cardiolipin (CL) synthesis in the IM. Upon dissociation from Mdm35, Ups1 binds to the intermembrane space (IMS) surface of the OM, extracts a PA molecule, re-associates with Mdm35, and moves through the aqueous IMS to deliver PA to the IM. Here, the authors analyzed the early steps of this PA transfer - membrane binding and PA extraction - using a combination of in vitro biochemical assays with lipid liposomes and purified Ups1-Mdm35 to measure liposome binding, lipid transfer between liposomes, and lipid extraction from liposomes. The authors found that membrane curvature, a previously overlooked property of the membrane, significantly affects PA extraction but not PA insertion into liposomes. These findings were further supported by MD simulations.

      Strengths:

      The experiments are well-designed, and the data are logically interpreted. The present study provides an important basis for understanding the mechanism of lipid transfer between membranes.  

      Weaknesses:

      The physiological relevance of membrane curvature in lipid extraction and transfer still remains open.

      We thank the reviewer for the constructive feedback on our work. We agree that the physiological relevance of membrane curvature in lipid extraction and transfer remains an open question. Our data show that Ups1 binding to native-like OM membranes under physiological pH conditions is curvature-dependent, supporting the idea that this mechanism may optimize lipid transfer in vivo. While the intricate biophysical basis of this behaviour can only be dissected in vitro, these findings offer valuable insight into how curvature may functionally regulate Ups1 activity in the cellular context. To directly test this, it will be important in future studies to identify Ups1 mutants that lack curvature sensitivity and assess their performance in vivo, which will help clarify the physiological importance of this mechanism.

      Reviewer #3:

      The manuscript by Sadeqi et al. studies the interactions between the mitochondrial protein Ups1 and reconstituted membranes. The authors apply synthetic liposomal vesicles to investigate the role of pH, curvature, and charge on the binding of Ups1 to membranes and its ability to extract PA from them. The manuscript is well wrifen and structured. With minor exceptions, the authors provide all relevant information (see minor points below) and reference the appropriate literature in their introduction. The underlying question of how the energy barrier for lipid extraction from membranes is overcome by Ups1 is interesting, and the data presented by the authors could offer a valuable new perspective on this process. It is also certainly a challenging in vitro reconstitution experiment, as the authors aim to disentangle individual membrane properties (e.g., curvature, charge, and packing density) to study protein adsorption and lipid transfer. I have one major suggestion and a few minor ones that the authors might want to consider to improve their manuscript and data interpretation:

      Major Comments:

      The experiments are performed with reconstituted vesicles, which are incubated with recombinant protein variants and quantitatively assessed in flotation and pelleting assays. According to the Materials and Methods section, the lipid concentration in these assays is kept constant at 5 µM. However, the authors change the size of the vesicles to tune their curvature. Using the same lipid concentration but varying vesicle sizes results in different total vesicle concentrations. Moreover, larger vesicles (produced by freeze-thawing and extrusion) tend to form a higher proportion of multilamellar vesicles, thus also altering the total membrane area available for binding. Could these differences in the experimental system account for the variation in binding? To address this, the authors would need to perform the experiments either under saturation (excess protein) conditions or find an experimental approach to normalize for these differences.

      We thank the reviewer for the constructive and positive comments. We agree that, since the total number of lipids was kept constant, the number of vesicles varied with vesicle size in our experiments. However, the setup was specifically designed to maintain a comparable total membrane surface area across conditions, ensuring a comparable number of available binding sites for Ups1. Because membrane surface area decreases with the square of the vesicle radius, keeping vesicle number constant would have led to a marked reduction in binding surface. Our approach was therefore aimed at preserving comparable binding capacity while varying membrane curvature.

      With respect to multilamellarity, we thank the reviewer for addressing this important point. As described above, we aimed to maintain a constant total membrane surface area across all conditions to ensure an equal number of potential binding sites. We agree that multilamellarity in large liposomes could restrict accessibility to part of the membrane surface. However, we see in our experiments that even when the total membrane surface area of the small liposomes is reduced to one quarter of the standard amount, binding to the small liposomes remained stronger than to the larger liposomes at the higher concentration. This strongly indicates that restricted accessibility cannot account for the curvature-specific effect observed. Nonetheless, we will further address this aspect experimentally and in the discussion of the revised manuscript.

      References

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      Lu, J., Chan, C., Yu, L., Fan, J., Sun, F., & Zhai, Y. (2020). Molecular mechanism of mitochondrial phosphatidate transfer by Ups1. Commun Biol, 3(1), 468. https://doi.org/10.1038/s42003-020-01121-x 

      Miliara, X., Garnef, J. A., Tatsuta, T., Abid Ali, F., Baldie, H., Perez-Dorado, I., Simpson, P., Yague, E., Langer, T., & Mafhews, S. (2015). Structural insight into the TRIAP1/PRELI-like domain family of mitochondrial phospholipid transfer complexes. EMBO Rep, 16(7), 824-835. https://doi.org/10.15252/embr.201540229 

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      Miliara, X., Tatsuta, T., Eiyama, A., Langer, T., Rouse, S. L., & Mafhews, S. (2023). An intermolecular hydrogen bonded network in the PRELID-TRIAP protein family plays a role in lipid sensing. Biochim Biophys Acta Proteins Proteom, 1871(1), 140867. https://doi.org/10.1016/j.bbapap.2022.140867 

      Posng, C., Tatsuta, T., Konig, T., Haag, M., Wai, T., Aaltonen, M. J., & Langer, T. (2013). TRIAP1/PRELI complexes prevent apoptosis by mediating intramitochondrial transport of phosphatidic acid. Cell Metab, 18(2), 287-295. https://doi.org/10.1016/j.cmet.2013.07.008 

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